Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	A	E	L	L	V	N	V	T	P	S	E	T	R	V	A	Y	I	D	G	G	I	L	Q	E	I	H	I	E	R	E	A	R	R	G	I	V	G	N	I	Y	K	G	R	V	S	R	V	L	P	G	M	Q	A	A	F	V	D	I
Secondary structure
SS confidence
Disorder		?	?	?																														?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		G	L	D	K	A	A	F	L	H	A	S	D	I	M	P	H	T	E	C	V	A	G	E	E	Q	K	Q	F	T	V	R	D	I	S	E	L	V	R	Q	G	Q	D	L	M	V	Q	V	V	K	D	P	L	G	T	K	G	A	R	L	T
Secondary structure
SS confidence
Disorder															?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?		?	?																?			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	D	I	T	L	P	S	R	Y	L	V	F	M	P	G	A	S	H	V	G	V	S	Q	R	I	E	S	E	S	E	R	E	R	L	K	K	V	V	A	E	Y	C	D	E	Q	G	G	F	I	I	R	T	A	A	E	G	V	G	E	A
Secondary structure
SS confidence
Disorder																									?	?	?	?																															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	L	A	S	D	A	A	Y	L	K	R	V	W	T	K	V	M	E	R	K	K	R	P	Q	T	R	Y	Q	L	Y	G	E	L	A	L	A	Q	R	V	L	R	D	F	A	D	A	E	L	D	R	I	R	V	D	S	R	L	T	Y	E
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		A	L	L	E	F	T	S	E	Y	I	P	E	M	T	S	K	L	E	H	Y	T	G	R	Q	P	I	F	D	L	F	D	V	E	N	E	I	Q	R	A	L	E	R	K	V	E	L	K	S	G	G	Y	L	I	I	D	Q	T	E	A	M
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		T	T	V	D	I	N	T	G	A	F	V	G	H	R	N	L	D	D	T	I	F	N	T	N	I	E	A	T	Q	A	I	A	R	Q	L	R	L	R	N	L	G	G	I	I	I	I	D	F	I	D	M	N	N	E	D	H	R	R	R	V
Secondary structure
SS confidence
Disorder										?	?	?	?	?	?	?																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		L	H	S	L	E	Q	A	L	S	K	D	R	V	K	T	S	V	N	G	F	S	A	L	G	L	V	E	M	T	R	K	R	T	R	E	S	I	E	H	V	L	C	N	E	C	P	T	C	H	G	R	G	T	V	K	T	V	E	T	V
Secondary structure
SS confidence
Disorder																																												?						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		C	Y	E	I	M	R	E	I	V	R	V	H	H	A	Y	D	S	D	R	F	L	V	Y	A	S	P	A	V	A	E	A	L	K	G	E	E	S	H	S	L	A	E	V	E	I	F	V	G	K	Q	V	K	V	Q	I	E	P	L	Y	N
Secondary structure
SS confidence
Disorder															?	?	?																																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.
Sequence		Q	E	Q	F	D	V	V	M	M
Secondary structure
SS confidence
Disorder				?	?					?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 2c4r chain L Region: 1 - 489 Aligned: 467 Modelled: 489 Confidence: 100.0% Identity: 33% PDB header:hydrolase Chain: L: PDB Molecule:ribonuclease e; PDBTitle: catalytic domain of e. coli rnase e Phyre2 PDB 1smx chain A Region: 40 - 127 Aligned: 85 Modelled: 88 Confidence: 99.9% Identity: 38% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1yz6 chain A Region: 36 - 248 Aligned: 174 Modelled: 188 Confidence: 98.3% Identity: 20% PDB header:translation Chain: A: PDB Molecule:probable translation initiation factor 2 alpha PDBTitle: crystal structure of intact alpha subunit of aif2 from2 pyrococcus abyssi Phyre2 PDB 2ba0 chain A domain 1 Region: 36 - 122 Aligned: 73 Modelled: 87 Confidence: 98.1% Identity: 25% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2z0s chain A domain 1 Region: 36 - 128 Aligned: 82 Modelled: 85 Confidence: 98.0% Identity: 23% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2cqo chain A Region: 30 - 120 Aligned: 77 Modelled: 91 Confidence: 98.0% Identity: 23% PDB header:ribosome Chain: A: PDB Molecule:nucleolar protein of 40 kda; PDBTitle: solution structure of the s1 rna binding domain of human2 hypothetical protein flj11067 Phyre2 PDB 2z0s chain A Region: 36 - 134 Aligned: 88 Modelled: 91 Confidence: 97.9% Identity: 23% PDB header:rna binding protein Chain: A: PDB Molecule:probable exosome complex rna-binding protein 1; PDBTitle: crystal structure of putative exosome complex rna-binding2 protein Phyre2 PDB 2je6 chain I domain 1 Region: 36 - 109 Aligned: 63 Modelled: 74 Confidence: 97.9% Identity: 21% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2je6 chain I Region: 16 - 122 Aligned: 95 Modelled: 107 Confidence: 97.9% Identity: 17% PDB header:hydrolase Chain: I: PDB Molecule:exosome complex rna-binding protein 1; PDBTitle: structure of a 9-subunit archaeal exosome Phyre2 PDB 2k4k chain A Region: 33 - 120 Aligned: 74 Modelled: 88 Confidence: 97.9% Identity: 27% PDB header:rna binding protein Chain: A: PDB Molecule:general stress protein 13; PDBTitle: solution structure of gsp13 from bacillus subtilis Phyre2 PDB 1q46 chain A domain 2 Region: 32 - 122 Aligned: 77 Modelled: 91 Confidence: 97.9% Identity: 18% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1q8k chain A Region: 38 - 160 Aligned: 87 Modelled: 99 Confidence: 97.8% Identity: 23% PDB header:translation Chain: A: PDB Molecule:eukaryotic translation initiation factor 2 PDBTitle: solution structure of alpha subunit of human eif2 Phyre2 PDB 1hh2 chain P domain 1 Region: 35 - 120 Aligned: 65 Modelled: 68 Confidence: 97.8% Identity: 23% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2khi chain A Region: 29 - 122 Aligned: 81 Modelled: 92 Confidence: 97.8% Identity: 21% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1 Phyre2 PDB 2khj chain A Region: 29 - 120 Aligned: 78 Modelled: 80 Confidence: 97.8% Identity: 19% PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1 Phyre2 PDB 2nn6 chain H domain 1 Region: 36 - 128 Aligned: 75 Modelled: 78 Confidence: 97.8% Identity: 19% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1q46 chain A Region: 38 - 160 Aligned: 87 Modelled: 101 Confidence: 97.7% Identity: 20% PDB header:translation Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit; PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia Phyre2 PDB 2ba0 chain A Region: 18 - 122 Aligned: 91 Modelled: 105 Confidence: 97.7% Identity: 19% PDB header:rna binding protein Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4; PDBTitle: archaeal exosome core Phyre2 PDB 1hh2 chain P Region: 35 - 120 Aligned: 65 Modelled: 66 Confidence: 97.7% Identity: 25% PDB header:transcription regulation Chain: P: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima Phyre2 PDB 3bzk chain A domain 4 Region: 34 - 122 Aligned: 75 Modelled: 87 Confidence: 97.7% Identity: 28% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 1 c2c4rL_ 2 d1smxa_ 3 c1yz6A_ 4 d2ba0a1 5 d2z0sa1 6 c2cqoA_ 7 c2z0sA_ 8 d2je6i1 9 c2je6I_ 10 c2k4kA_ 11 d1q46a2 12 c1q8kA_ 13 d1hh2p1 14 c2khiA_ 15 c2khjA_ 16 d2nn6h1 17 c1q46A_ 18 c2ba0A_ 19 c1hh2P_ 20 d3bzka4 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2c4rL_ 100.0 33 PDB header:hydrolase Chain: L: PDB Molecule:ribonuclease e; PDBTitle: catalytic domain of e. coli rnase e 2 d1smxa_ 99.9 38 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 3 c1yz6A_ 98.3 20 PDB header:translation Chain: A: PDB Molecule:probable translation initiation factor 2 alpha PDBTitle: crystal structure of intact alpha subunit of aif2 from2 pyrococcus abyssi 4 d2ba0a1 98.1 25 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 5 d2z0sa1 98.0 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 6 c2cqoA_ 98.0 23 PDB header:ribosome Chain: A: PDB Molecule:nucleolar protein of 40 kda; PDBTitle: solution structure of the s1 rna binding domain of human2 hypothetical protein flj11067 7 c2z0sA_ 97.9 23 PDB header:rna binding protein Chain: A: PDB Molecule:probable exosome complex rna-binding protein 1; PDBTitle: crystal structure of putative exosome complex rna-binding2 protein 8 d2je6i1 97.9 21 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 9 c2je6I_ 97.9 17 PDB header:hydrolase Chain: I: PDB Molecule:exosome complex rna-binding protein 1; PDBTitle: structure of a 9-subunit archaeal exosome 10 c2k4kA_ 97.9 27 PDB header:rna binding protein Chain: A: PDB Molecule:general stress protein 13; PDBTitle: solution structure of gsp13 from bacillus subtilis 11 d1q46a2 97.9 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 12 c1q8kA_ 97.8 23 PDB header:translation Chain: A: PDB Molecule:eukaryotic translation initiation factor 2 PDBTitle: solution structure of alpha subunit of human eif2 13 d1hh2p1 97.8 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 14 c2khiA_ 97.8 21 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 4 of the e. coli ribosomal2 protein s1 15 c2khjA_ 97.8 19 PDB header:ribosomal protein Chain: A: PDB Molecule:30s ribosomal protein s1; PDBTitle: nmr structure of the domain 6 of the e. coli ribosomal2 protein s1 16 d2nn6h1 97.8 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 17 c1q46A_ 97.7 20 PDB header:translation Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit; PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia 18 c2ba0A_ 97.7 19 PDB header:rna binding protein Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4; PDBTitle: archaeal exosome core 19 c1hh2P_ 97.7 25 PDB header:transcription regulation Chain: P: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima 20 d3bzka4 97.7 28 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 21 d1wi5a_ not modelled 97.7 22 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 22 c3go5A_ not modelled 97.6 18 PDB header:gene regulation Chain: A: PDB Molecule:multidomain protein with s1 rna-binding domains; PDBTitle: crystal structure of a multidomain protein with nucleic acid binding2 domains (sp_0946) from streptococcus pneumoniae tigr4 at 1.40 a3 resolution 23 c2eqsA_ not modelled 97.6 25 PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent rna helicase dhx8; PDBTitle: solution structure of the s1 rna binding domain of human2 atp-dependent rna helicase dhx8 24 c1l2fA_ not modelled 97.6 25 PDB header:transcription Chain: A: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima: a2 structure-based role of the n-terminal domain 25 d1sroa_ not modelled 97.5 31 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 26 d1go3e1 not modelled 97.4 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 27 d1kl9a2 not modelled 97.4 22 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 28 c2oceA_ not modelled 97.3 27 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa5201; PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa 29 c2ahoB_ not modelled 97.2 18 PDB header:translation Chain: B: PDB Molecule:translation initiation factor 2 alpha subunit; PDBTitle: structure of the archaeal initiation factor eif2 alpha-2 gamma heterodimer from sulfolobus solfataricus complexed3 with gdpnp 30 c2k52A_ not modelled 97.2 23 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein mj1198; PDBTitle: structure of uncharacterized protein mj1198 from2 methanocaldococcus jannaschii. northeast structural3 genomics target mjr117b 31 c2ba1B_ not modelled 97.1 23 PDB header:rna binding protein Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4; PDBTitle: archaeal exosome core 32 d2nn6i1 not modelled 97.1 21 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 33 c2c35F_ not modelled 97.1 18 PDB header:polymerase Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii 34 d2ahob2 not modelled 97.1 17 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 35 c1kl9A_ not modelled 96.9 25 PDB header:translation Chain: A: PDB Molecule:eukaryotic translation initiation factor 2 subunit 1; PDBTitle: crystal structure of the n-terminal segment of human eukaryotic2 initiation factor 2alpha 36 d1y14b1 not modelled 96.8 12 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 37 c3psiA_ not modelled 96.8 14 PDB header:transcription Chain: A: PDB Molecule:transcription elongation factor spt6; PDBTitle: crystal structure of the spt6 core domain from saccharomyces2 cerevisiae, form spt6(239-1451) 38 c1go3E_ not modelled 96.6 19 PDB header:transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: structure of an archeal homolog of the eukaryotic rna2 polymerase ii rpb4/rpb7 complex 39 c2nn6I_ not modelled 96.5 21 PDB header:hydrolase/transferase Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 40 c2b8kG_ not modelled 96.3 9 PDB header:transferase Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda PDBTitle: 12-subunit rna polymerase ii 41 d2c35b1 not modelled 96.3 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 42 c3h0gS_ not modelled 96.3 17 PDB header:transcription Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 43 d2nn6g1 not modelled 96.0 20 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 44 c2pmzE_ not modelled 95.6 18 PDB header:translation, transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 45 c1nt9G_ not modelled 95.4 9 PDB header:transcription, transferase Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kd polypeptide; PDBTitle: complete 12-subunit rna polymerase ii 46 d2asba1 not modelled 95.0 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 47 c1k0rB_ not modelled 94.9 24 PDB header:transcription Chain: B: PDB Molecule:nusa; PDBTitle: crystal structure of mycobacterium tuberculosis nusa 48 c2asbA_ not modelled 94.5 24 PDB header:transcription/rna Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: structure of a mycobacterium tuberculosis nusa-rna complex 49 c2bh8B_ not modelled 94.4 18 PDB header:transcription Chain: B: PDB Molecule:1b11; PDBTitle: combinatorial protein 1b11 50 c2kcmA_ not modelled 93.9 25 PDB header:nucleic acid binding protein Chain: A: PDB Molecule:cold shock domain family protein; PDBTitle: solution nmr structure of the n-terminal ob-domain of so_1732 from2 shewanella oneidensis. northeast structural genomics consortium3 target sor210a. 51 c2nn6G_ not modelled 92.5 20 PDB header:hydrolase/transferase Chain: G: PDB Molecule:exosome complex exonuclease rrp40; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 52 c3aqqD_ not modelled 92.4 24 PDB header:dna binding protein Chain: D: PDB Molecule:calcium-regulated heat stable protein 1; PDBTitle: crystal structure of human crhsp-24 53 d1c9oa_ not modelled 92.2 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 54 c2ljpA_ not modelled 91.8 14 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease p protein component; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for e.coli2 ribonuclease p protein 55 d2ja9a1 not modelled 91.5 12 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 56 c2ckzB_ not modelled 91.4 10 PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase iii 25 kd PDBTitle: x-ray structure of rna polymerase iii subcomplex c17-c25. 57 c2nn6H_ not modelled 91.2 19 PDB header:hydrolase/transferase Chain: H: PDB Molecule:exosome complex exonuclease rrp4; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 58 d1a6fa_ not modelled 89.9 22 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:RNase P protein 59 d2es2a1 not modelled 89.8 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 60 d1mjca_ not modelled 89.3 21 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 61 d1h95a_ not modelled 88.2 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 62 d1g6pa_ not modelled 88.2 20 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 63 c2ja9A_ not modelled 86.7 12 PDB header:rna-binding protein Chain: A: PDB Molecule:exosome complex exonuclease rrp40; PDBTitle: structure of the n-terminal deletion of yeast exosome2 component rrp40 64 d1nz0a_ not modelled 85.8 19 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:RNase P protein 65 d1d6ta_ not modelled 84.8 15 Fold:Ribosomal protein S5 domain 2-like Superfamily:Ribosomal protein S5 domain 2-like Family:RNase P protein 66 d1k3ra1 not modelled 83.6 26 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Hypothetical protein MTH1 (MT0001), insert domain 67 c2ix1A_ not modelled 83.0 10 PDB header:hydrolase Chain: A: PDB Molecule:exoribonuclease 2; PDBTitle: rnase ii d209n mutant 68 c3a0jB_ not modelled 82.4 23 PDB header:transcription Chain: B: PDB Molecule:cold shock protein; PDBTitle: crystal structure of cold shock protein 1 from thermus2 thermophilus hb8 69 c2bx9J_ not modelled 81.9 38 PDB header:transcription regulation Chain: J: PDB Molecule:tryptophan rna-binding attenuator protein-inhibitory PDBTitle: crystal structure of b.subtilis anti-trap protein, an2 antagonist of trap-rna interactions 70 c3ld0Q_ not modelled 81.1 38 PDB header:gene regulation Chain: Q: PDB Molecule:inhibitor of trap, regulated by t-box (trp) sequence rtpa; PDBTitle: crystal structure of b.licheniformis anti-trap protein, an antagonist2 of trap-rna interactions 71 c3ayhB_ not modelled 80.2 10 PDB header:transcription Chain: B: PDB Molecule:dna-directed rna polymerase iii subunit rpc8; PDBTitle: crystal structure of the c17/25 subcomplex from s. pombe rna2 polymerase iii 72 c2eqjA_ not modelled 80.1 19 PDB header:transcription Chain: A: PDB Molecule:metal-response element-binding transcription PDBTitle: solution structure of the tudor domain of metal-response2 element-binding transcription factor 2 73 c2k5nA_ not modelled 79.9 8 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cold-shock protein; PDBTitle: solution nmr structure of the n-terminal domain of protein2 eca1580 from erwinia carotovora, northeast structural3 genomics consortium target ewr156a 74 c2hl7A_ not modelled 78.0 17 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa 75 c2wp8J_ not modelled 74.4 23 PDB header:hydrolase Chain: J: PDB Molecule:exosome complex exonuclease dis3; PDBTitle: yeast rrp44 nuclease 76 d1nlta3 not modelled 74.0 29 Fold:DnaJ/Hsp40 cysteine-rich domain Superfamily:DnaJ/Hsp40 cysteine-rich domain Family:DnaJ/Hsp40 cysteine-rich domain 77 c3pihA_ not modelled 72.1 21 PDB header:hydrolase/dna Chain: A: PDB Molecule:uvrabc system protein a; PDBTitle: t. maritima uvra in complex with fluorescein-modified dna 78 c2hnkC_ not modelled 68.4 22 PDB header:transferase Chain: C: PDB Molecule:sam-dependent o-methyltransferase; PDBTitle: crystal structure of sam-dependent o-methyltransferase from2 pathogenic bacterium leptospira interrogans 79 c2kw0A_ not modelled 67.2 13 PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli 80 c2e5pA_ not modelled 65.8 24 PDB header:transcription Chain: A: PDB Molecule:phd finger protein 1; PDBTitle: solution structure of the tudor domain of phd finger2 protein 1 (phf1 protein) 81 c3camB_ not modelled 64.9 23 PDB header:gene regulation Chain: B: PDB Molecule:cold-shock domain family protein; PDBTitle: crystal structure of the cold shock domain protein from neisseria2 meningitidis 82 c3trzE_ not modelled 62.4 21 PDB header:rna binding protein/rna Chain: E: PDB Molecule:protein lin-28 homolog a; PDBTitle: mouse lin28a in complex with let-7d microrna pre-element 83 c3d0fA_ not modelled 62.4 14 PDB header:transferase Chain: A: PDB Molecule:penicillin-binding 1 transmembrane protein mrca; PDBTitle: structure of the big_1156.2 domain of putative penicillin-binding2 protein mrca from nitrosomonas europaea atcc 19718 84 c2ytvA_ not modelled 59.6 27 PDB header:rna binding protein Chain: A: PDB Molecule:cold shock domain-containing protein e1; PDBTitle: solution structure of the fifth cold-shock domain of the human2 kiaa0885 protein (unr protein) 85 c1nltA_ not modelled 59.4 24 PDB header:protein transport Chain: A: PDB Molecule:mitochondrial protein import protein mas5; PDBTitle: the crystal structure of hsp40 ydj1 86 d2ix0a2 not modelled 58.7 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 87 c2pe4A_ not modelled 57.1 19 PDB header:hydrolase Chain: A: PDB Molecule:hyaluronidase-1; PDBTitle: structure of human hyaluronidase 1, a hyaluronan hydrolyzing enzyme2 involved in tumor growth and angiogenesis 88 c1x65A_ not modelled 54.7 23 PDB header:rna binding protein Chain: A: PDB Molecule:unr protein; PDBTitle: solution structure of the third cold-shock domain of the human2 kiaa0885 protein (unr protein) 89 c2cttA_ not modelled 54.6 36 PDB header:chaperone Chain: A: PDB Molecule:dnaj homolog subfamily a member 3; PDBTitle: solution structure of zinc finger domain from human dnaj2 subfamily a menber 3 90 c2d9tA_ not modelled 52.0 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:tudor domain-containing protein 3; PDBTitle: solution structure of the tudor domain of tudor domain2 containing protein 3 from mouse 91 c3tr6A_ not modelled 50.4 25 PDB header:transferase Chain: A: PDB Molecule:o-methyltransferase; PDBTitle: structure of a o-methyltransferase from coxiella burnetii 92 c2vy9A_ not modelled 49.5 23 PDB header:gene regulation Chain: A: PDB Molecule:anti-sigma-factor antagonist; PDBTitle: molecular architecture of the stressosome, a signal2 integration and transduction hub 93 d2rdea2 not modelled 48.8 23 Fold:Split barrel-like Superfamily:PilZ domain-like Family:PilZ domain-associated domain 94 c3d3rA_ not modelled 44.6 19 PDB header:chaperone Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf; PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1 95 c2e5qA_ not modelled 44.5 24 PDB header:transcription Chain: A: PDB Molecule:phd finger protein 19; PDBTitle: solution structure of the tudor domain of phd finger2 protein 19, isoform b [homo sapiens] 96 d1we8a_ not modelled 43.5 6 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 97 c2rf4A_ not modelled 43.0 13 PDB header:transferase Chain: A: PDB Molecule:dna-directed rna polymerase i subunit rpa4; PDBTitle: crystal structure of the rna polymerase i subcomplex a14/43 98 d1exka_ not modelled 42.4 46 Fold:DnaJ/Hsp40 cysteine-rich domain Superfamily:DnaJ/Hsp40 cysteine-rich domain Family:DnaJ/Hsp40 cysteine-rich domain 99 c1tt9B_ not modelled 42.2 24 PDB header:transferase, lyase Chain: B: PDB Molecule:formimidoyltransferase-cyclodeaminase PDBTitle: structure of the bifunctional and golgi associated2 formiminotransferase cyclodeaminase octamer 100 d3d3ra1 not modelled 41.8 19 Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like 101 c2hu9B_ not modelled 35.0 30 PDB header:metal transport Chain: B: PDB Molecule:mercuric transport protein periplasmic component; PDBTitle: x-ray structure of the archaeoglobus fulgidus copz n-2 terminal domain 102 d1a62a2 not modelled 34.8 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 103 c3nthA_ not modelled 34.5 29 PDB header:transcription Chain: A: PDB Molecule:maternal protein tudor; PDBTitle: crystal structure of tudor and aubergine [r13(me2s)] complex 104 d1vc1a_ not modelled 34.4 13 Fold:SpoIIaa-like Superfamily:SpoIIaa-like Family:Anti-sigma factor antagonist SpoIIaa 105 d1x4ma1 not modelled 34.3 8 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 106 d1h9ma1 not modelled 32.9 31 Fold:OB-fold Superfamily:MOP-like Family:BiMOP, duplicated molybdate-binding domain 107 c3lz8A_ not modelled 32.0 14 PDB header:chaperone Chain: A: PDB Molecule:putative chaperone dnaj; PDBTitle: structure of a putative chaperone dnaj from klebsiella pneumoniae2 subsp. pneumoniae mgh 78578 at 2.9 a resolution. 108 d1p9ra_ not modelled 31.9 40 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 109 c2vnuD_ not modelled 31.6 19 PDB header:hydrolase/rna Chain: D: PDB Molecule:exosome complex exonuclease rrp44; PDBTitle: crystal structure of sc rrp44 110 c2ygrD_ not modelled 30.9 50 PDB header:hydrolase Chain: D: PDB Molecule:uvrabc system protein a; PDBTitle: mycobacterium tuberculosis uvra 111 c1h9sA_ not modelled 29.9 19 PDB header:transcription regulator Chain: A: PDB Molecule:molybdenum transport protein mode; PDBTitle: molybdate bound complex of dimop domain of mode from e.coli 112 d1h9ra1 not modelled 29.6 15 Fold:OB-fold Superfamily:MOP-like Family:BiMOP, duplicated molybdate-binding domain 113 d1xtda2 not modelled 29.4 21 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 114 c2vkcA_ not modelled 29.1 16 PDB header:hydrolase Chain: A: PDB Molecule:nedd4-binding protein 2; PDBTitle: solution structure of the b3bp smr domain 115 c2dgyA_ not modelled 28.5 32 PDB header:translation Chain: A: PDB Molecule:mgc11102 protein; PDBTitle: solution structure of the eukaryotic initiation factor 1a2 in mgc11102 protein 116 d2ctma1 not modelled 28.1 8 Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I) 117 d2hqxa1 not modelled 27.6 29 Fold:SH3-like barrel Superfamily:Tudor/PWWP/MBT Family:Tudor domain 118 c2hqxB_ not modelled 27.6 29 PDB header:transcription Chain: B: PDB Molecule:p100 co-activator tudor domain; PDBTitle: crystal structure of human p100 tudor domain conserved2 region 119 c2ytxA_ not modelled 27.1 20 PDB header:rna binding protein Chain: A: PDB Molecule:cold shock domain-containing protein e1; PDBTitle: solution structure of the second cold-shock domain of the human2 kiaa0885 protein (unr protein) 120 c2vf7B_ not modelled 26.3 64 PDB header:dna-binding protein Chain: B: PDB Molecule:excinuclease abc, subunit a.; PDBTitle: crystal structure of uvra2 from deinococcus radiodurans

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0