Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	T	E	S	F	A	Q	L	F	E	E	S	L	K	E	I	E	T	R	P	G	S	I	V	R	G	V	V	V	A	I	D	K	D	V	V	L	V	D	A	G	L	K	S	E	S	A	I	P	A	E	Q	F	K	N	A	Q	G	E	L
Secondary structure
SS confidence
Disorder		?	?												?	?	?	?	?	?																																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		E	I	Q	V	G	D	E	V	D	V	A	L	D	A	V	E	D	G	F	G	E	T	L	L	S	R	E	K	A	K	R	H	E	A	W	I	T	L	E	K	A	Y	E	D	A	E	T	V	T	G	V	I	N	G	K	V	K	G	G	F
Secondary structure
SS confidence
Disorder		?																											?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	V	E	L	N	G	I	R	A	F	L	P	G	S	L	V	D	V	R	P	V	R	D	T	L	H	L	E	G	K	E	L	E	F	K	V	I	K	L	D	Q	K	R	N	N	V	V	V	S	R	R	A	V	I	E	S	E	N	S	A
Secondary structure
SS confidence
Disorder																	?	?	?	?	?	?			?																																			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	R	D	Q	L	L	E	N	L	Q	E	G	M	E	V	K	G	I	V	K	N	L	T	D	Y	G	A	F	V	D	L	G	G	V	D	G	L	L	H	I	T	D	M	A	W	K	R	V	K	H	P	S	E	I	V	N	V	G	D	E
Secondary structure
SS confidence
Disorder		?																																												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		I	T	V	K	V	L	K	F	D	R	E	R	T	R	V	S	L	G	L	K	Q	L	G	E	D	P	W	V	A	I	A	K	R	Y	P	E	G	T	K	L	T	G	R	V	T	N	L	T	D	Y	G	C	F	V	E	I	E	E	G	V
Secondary structure
SS confidence
Disorder																									?					?	?	?					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		E	G	L	V	H	V	S	E	M	D	W	T	N	K	N	I	H	P	S	K	V	V	N	V	G	D	V	V	E	V	M	V	L	D	I	D	E	E	R	R	R	I	S	L	G	L	K	Q	C	K	A	N	P	W	Q	Q	F	A	E	T
Secondary structure
SS confidence
Disorder																																																				?					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		H	N	K	G	D	R	V	E	G	K	I	K	S	I	T	D	F	G	I	F	I	G	L	D	G	G	I	D	G	L	V	H	L	S	D	I	S	W	N	V	A	G	E	E	A	V	R	E	Y	K	K	G	D	E	I	A	A	V	V	L
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460	.	.	.	.	.	.	.	.	.	470	.	.	.	.	.	.	.	.	.	480
Sequence		Q	V	D	A	E	R	E	R	I	S	L	G	V	K	Q	L	A	E	D	P	F	N	N	W	V	A	L	N	K	K	G	A	I	V	T	G	K	V	T	A	V	D	A	K	G	A	T	V	E	L	A	D	G	V	E	G	Y	L	R	A
Secondary structure
SS confidence
Disorder																	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	490	.	.	.	.	.	.	.	.	.	500	.	.	.	.	.	.	.	.	.	510	.	.	.	.	.	.	.	.	.	520	.	.	.	.	.	.	.	.	.	530	.	.	.	.	.	.	.	.	.	540
Sequence		S	E	A	S	R	D	R	V	E	D	A	T	L	V	L	S	V	G	D	E	V	E	A	K	F	T	G	V	D	R	K	N	R	A	I	S	L	S	V	R	A	K	D	E	A	D	E	K	D	A	I	A	T	V	N	K	Q	E	D	A
Secondary structure
SS confidence
Disorder																																										?	?	?	?	?	?	?						?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	550	.	.	.	.	.	.	.
Sequence		N	F	S	N	N	A	M	A	E	A	F	K	A	A	K	G	E
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 3go5 chain A Region: 273 - 545 Aligned: 235 Modelled: 272 Confidence: 100.0% Identity: 20% 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 Phyre2 PDB 1yz6 chain A Region: 449 - 551 Aligned: 103 Modelled: 103 Confidence: 99.8% Identity: 26% 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 2khj chain A Region: 441 - 528 Aligned: 88 Modelled: 88 Confidence: 99.8% Identity: 100% 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 1q46 chain A Region: 449 - 551 Aligned: 103 Modelled: 103 Confidence: 99.8% Identity: 28% 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 2k4k chain A Region: 446 - 525 Aligned: 80 Modelled: 80 Confidence: 99.8% Identity: 43% PDB header:rna binding protein Chain: A: PDB Molecule:general stress protein 13; PDBTitle: solution structure of gsp13 from bacillus subtilis Phyre2 PDB 1q8k chain A Region: 449 - 552 Aligned: 104 Modelled: 104 Confidence: 99.8% 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 3bzk chain A domain 4 Region: 434 - 523 Aligned: 90 Modelled: 90 Confidence: 99.8% Identity: 29% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2khi chain A Region: 441 - 525 Aligned: 85 Modelled: 85 Confidence: 99.8% Identity: 29% 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 1q46 chain A domain 2 Region: 449 - 521 Aligned: 73 Modelled: 73 Confidence: 99.7% Identity: 33% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1sro chain A Region: 446 - 522 Aligned: 76 Modelled: 77 Confidence: 99.7% Identity: 38% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2k52 chain A Region: 447 - 523 Aligned: 73 Modelled: 77 Confidence: 99.7% Identity: 29% 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 Phyre2 PDB 2cqo chain A Region: 439 - 525 Aligned: 87 Modelled: 87 Confidence: 99.7% 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 2oce chain A Region: 446 - 524 Aligned: 79 Modelled: 79 Confidence: 99.7% Identity: 32% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa5201; PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa Phyre2 PDB 1go3 chain E domain 1 Region: 449 - 538 Aligned: 89 Modelled: 90 Confidence: 99.7% Identity: 24% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2aho chain B Region: 449 - 551 Aligned: 98 Modelled: 103 Confidence: 99.7% Identity: 21% 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 Phyre2 PDB 1wi5 chain A Region: 445 - 526 Aligned: 82 Modelled: 82 Confidence: 99.7% Identity: 24% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 3psi chain A Region: 443 - 525 Aligned: 83 Modelled: 83 Confidence: 99.7% Identity: 18% 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) Phyre2 PDB 2ba0 chain A domain 1 Region: 449 - 524 Aligned: 75 Modelled: 76 Confidence: 99.7% Identity: 24% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 1kl9 chain A Region: 357 - 482 Aligned: 113 Modelled: 113 Confidence: 99.6% Identity: 20% 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 Phyre2 PDB 2eqs chain A Region: 446 - 525 Aligned: 78 Modelled: 80 Confidence: 99.6% Identity: 31% 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 Phyre2 PDB 1l2f chain A Region: 88 - 265 Aligned: 172 Modelled: 171 Confidence: 99.4% Identity: 12% 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 Phyre2 PDB 1hh2 chain P Region: 88 - 265 Aligned: 172 Modelled: 172 Confidence: 99.4% Identity: 13% PDB header:transcription regulation Chain: P: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima Phyre2 PDB 2asb chain A Region: 19 - 115 Aligned: 94 Modelled: 94 Confidence: 98.0% Identity: 20% PDB header:transcription/rna Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: structure of a mycobacterium tuberculosis nusa-rna complex Phyre2 PDB 2nn6 chain H Region: 19 - 87 Aligned: 68 Modelled: 68 Confidence: 97.9% Identity: 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 Phyre2 PDB 2nn6 chain G domain 1 Region: 19 - 86 Aligned: 67 Modelled: 67 Confidence: 97.9% Identity: 24% Fold: OB-fold Superfamily: Nucleic acid-binding proteins Family: Cold shock DNA-binding domain-like Phyre2 PDB 2nn6 chain G Region: 19 - 86 Aligned: 67 Modelled: 67 Confidence: 97.5% Identity: 24% 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 Phyre2 1 c3go5A_ 2 c1yz6A_ 3 c2khjA_ 4 c1q46A_ 5 c2k4kA_ 6 c1q8kA_ 7 d3bzka4 8 c2khiA_ 9 d1q46a2 10 d1sroa_ 11 c2k52A_ 12 c2cqoA_ 13 c2oceA_ 14 d1go3e1 15 c2ahoB_ 16 d1wi5a_ 17 c3psiA_ 18 d2ba0a1 19 c1kl9A_ 20 c2eqsA_ 21 22 23 24 25 26 27 28 c1l2fA_ 29 c1hh2P_ 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 c2asbA_ 51 c2nn6H_ 52 d2nn6g1 53 54 55 56 c2nn6G_ 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

Detailed template information

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

1 c3go5A_ 100.0 20 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 2 c1yz6A_ 99.8 26 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 3 c2khjA_ 99.8 100 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 4 c1q46A_ 99.8 28 PDB header:translation Chain: A: PDB Molecule:translation initiation factor 2 alpha subunit; PDBTitle: crystal structure of the eif2 alpha subunit from2 saccharomyces cerevisia 5 c2k4kA_ 99.8 43 PDB header:rna binding protein Chain: A: PDB Molecule:general stress protein 13; PDBTitle: solution structure of gsp13 from bacillus subtilis 6 c1q8kA_ 99.8 23 PDB header:translation Chain: A: PDB Molecule:eukaryotic translation initiation factor 2 PDBTitle: solution structure of alpha subunit of human eif2 7 d3bzka4 99.8 29 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 8 c2khiA_ 99.8 29 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 9 d1q46a2 99.7 33 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 10 d1sroa_ 99.7 38 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 11 c2k52A_ 99.7 29 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 12 c2cqoA_ 99.7 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 13 c2oceA_ 99.7 32 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pa5201; PDBTitle: crystal structure of tex family protein pa5201 from2 pseudomonas aeruginosa 14 d1go3e1 99.7 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 15 c2ahoB_ 99.7 21 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 16 d1wi5a_ 99.7 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 17 c3psiA_ 99.7 18 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) 18 d2ba0a1 99.7 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 19 c1kl9A_ 99.6 20 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 20 c2eqsA_ 99.6 31 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 21 d1kl9a2 not modelled 99.6 30 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 22 d2z0sa1 not modelled 99.6 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 23 d2je6i1 not modelled 99.6 32 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 24 d2ahob2 not modelled 99.6 29 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 25 d1y14b1 not modelled 99.5 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 26 d2nn6h1 not modelled 99.5 28 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 27 c2z0sA_ not modelled 99.5 17 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 28 c1l2fA_ 99.4 12 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 29 c1hh2P_ 99.4 13 PDB header:transcription regulation Chain: P: PDB Molecule:n utilization substance protein a; PDBTitle: crystal structure of nusa from thermotoga maritima 30 c2ba0A_ not modelled 99.3 26 PDB header:rna binding protein Chain: A: PDB Molecule:archeal exosome rna binding protein rrp4; PDBTitle: archaeal exosome core 31 d1hh2p1 not modelled 99.3 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 32 d2nn6i1 not modelled 99.3 26 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 33 c1go3E_ not modelled 99.3 27 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 34 c2je6I_ not modelled 99.2 29 PDB header:hydrolase Chain: I: PDB Molecule:exosome complex rna-binding protein 1; PDBTitle: structure of a 9-subunit archaeal exosome 35 d2c35b1 not modelled 99.2 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 36 c2pmzE_ not modelled 99.1 30 PDB header:translation, transferase Chain: E: PDB Molecule:dna-directed rna polymerase subunit e; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 37 c2ba1B_ not modelled 99.1 23 PDB header:rna binding protein Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4; PDBTitle: archaeal exosome core 38 c2nn6I_ not modelled 99.1 26 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 39 c2c35F_ not modelled 99.1 21 PDB header:polymerase Chain: F: PDB Molecule:dna-directed rna polymerase ii 19 kda PDBTitle: subunits rpb4 and rpb7 of human rna polymerase ii 40 c2b8kG_ not modelled 98.9 19 PDB header:transferase Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kda PDBTitle: 12-subunit rna polymerase ii 41 c3h0gS_ not modelled 98.8 21 PDB header:transcription Chain: S: PDB Molecule:dna-directed rna polymerase ii subunit rpb7; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 42 d1smxa_ not modelled 98.7 26 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 43 c1nt9G_ not modelled 98.6 18 PDB header:transcription, transferase Chain: G: PDB Molecule:dna-directed rna polymerase ii 19 kd polypeptide; PDBTitle: complete 12-subunit rna polymerase ii 44 c2ix1A_ not modelled 98.5 25 PDB header:hydrolase Chain: A: PDB Molecule:exoribonuclease 2; PDBTitle: rnase ii d209n mutant 45 c2bh8B_ not modelled 98.5 18 PDB header:transcription Chain: B: PDB Molecule:1b11; PDBTitle: combinatorial protein 1b11 46 c2ckzB_ not modelled 98.3 19 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. 47 d2asba1 not modelled 98.1 28 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 48 c3ayhB_ not modelled 98.1 16 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 49 c2wp8J_ not modelled 98.0 28 PDB header:hydrolase Chain: J: PDB Molecule:exosome complex exonuclease dis3; PDBTitle: yeast rrp44 nuclease 50 c2asbA_ 98.0 20 PDB header:transcription/rna Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: structure of a mycobacterium tuberculosis nusa-rna complex 51 c2nn6H_ 97.9 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 52 d2nn6g1 97.9 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 53 c2vnuD_ not modelled 97.8 30 PDB header:hydrolase/rna Chain: D: PDB Molecule:exosome complex exonuclease rrp44; PDBTitle: crystal structure of sc rrp44 54 d2ja9a1 not modelled 97.5 15 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 55 c2rf4A_ not modelled 97.5 11 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 56 c2nn6G_ 97.5 24 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 57 c2ja9A_ not modelled 97.5 17 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 58 c2r7fA_ not modelled 97.3 11 PDB header:hydrolase Chain: A: PDB Molecule:ribonuclease ii family protein; PDBTitle: crystal structure of ribonuclease ii family protein from deinococcus2 radiodurans, hexagonal crystal form. northeast structural genomics3 target drr63 59 c1k0rB_ not modelled 97.2 19 PDB header:transcription Chain: B: PDB Molecule:nusa; PDBTitle: crystal structure of mycobacterium tuberculosis nusa 60 c2c4rL_ not modelled 97.2 29 PDB header:hydrolase Chain: L: PDB Molecule:ribonuclease e; PDBTitle: catalytic domain of e. coli rnase e 61 d2ix0a3 not modelled 96.4 20 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 62 d1jjga_ not modelled 91.0 21 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 63 d1luza_ not modelled 90.5 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 64 c3i4oA_ not modelled 89.6 19 PDB header:translation Chain: A: PDB Molecule:translation initiation factor if-1; PDBTitle: crystal structure of translation initiation factor 1 from2 mycobacterium tuberculosis 65 d1ah9a_ not modelled 89.2 22 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 66 c3d0fA_ not modelled 88.7 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 67 d1k3ra1 not modelled 84.6 15 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Hypothetical protein MTH1 (MT0001), insert domain 68 d1e3pa2 not modelled 82.3 31 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 69 c1h9mB_ not modelled 78.9 19 PDB header:binding protein Chain: B: PDB Molecule:molybdenum-binding-protein; PDBTitle: two crystal structures of the cytoplasmic molybdate-binding2 protein modg suggest a novel cooperative binding mechanism3 and provide insights into ligand-binding specificity.4 peg-grown form with molybdate bound 70 c3dlmA_ not modelled 74.8 19 PDB header:transferase Chain: A: PDB Molecule:histone-lysine n-methyltransferase setdb1; PDBTitle: crystal structure of tudor domain of human histone-lysine n-2 methyltransferase setdb1 71 d1hr0w_ not modelled 66.7 25 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 72 d1wfqa_ not modelled 63.9 11 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 73 c3dm3A_ not modelled 62.8 20 PDB header:replication Chain: A: PDB Molecule:replication factor a; PDBTitle: crystal structure of a domain of a replication factor a2 protein, from methanocaldococcus jannaschii. northeast3 structural genomics target mjr118e 74 d2vnud2 not modelled 62.1 13 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 75 d1krta_ not modelled 60.8 22 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Anticodon-binding domain 76 d1h95a_ not modelled 58.8 14 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 77 d1bbua1 not modelled 47.5 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Anticodon-binding domain 78 c2bkdN_ not modelled 46.8 19 PDB header:nuclear protein Chain: N: PDB Molecule:fragile x mental retardation 1 protein; PDBTitle: structure of the n-terminal domain of fragile x mental2 retardation protein 79 d2ix0a2 not modelled 46.1 18 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 80 d1e1oa1 not modelled 45.8 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Anticodon-binding domain 81 c1ng2A_ not modelled 41.9 16 PDB header:oxidoreductase activator Chain: A: PDB Molecule:neutrophil cytosolic factor 1; PDBTitle: structure of autoinhibited p47phox 82 c2kcmA_ not modelled 41.3 12 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. 83 d1jt8a_ not modelled 39.2 21 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like 84 c2k75A_ not modelled 38.9 16 PDB header:dna binding protein Chain: A: PDB Molecule:uncharacterized protein ta0387; PDBTitle: solution nmr structure of the ob domain of ta0387 from2 thermoplasma acidophilum. northeast structural genomics3 consortium target tar80b. 85 d1fr3a_ not modelled 38.8 18 Fold:OB-fold Superfamily:MOP-like Family:Molybdate/tungstate binding protein MOP 86 c2ytyA_ not modelled 38.1 16 PDB header:rna binding protein Chain: A: PDB Molecule:cold shock domain-containing protein e1; PDBTitle: solution structure of the fourth cold-shock domain of the human2 kiaa0885 protein (unr protein) 87 c2ytvA_ not modelled 33.7 17 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) 88 c2ytxA_ not modelled 33.1 23 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) 89 c1ssfA_ not modelled 32.4 23 PDB header:cell cycle Chain: A: PDB Molecule:transformation related protein 53 binding PDBTitle: solution structure of the mouse 53bp1 fragment (residues2 1463-1617) 90 c1x65A_ not modelled 32.3 16 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) 91 d1nz9a_ not modelled 31.5 20 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:N-utilization substance G protein NusG, C-terminal domain 92 c1ov3A_ not modelled 30.7 12 PDB header:oxidoreductase activator Chain: A: PDB Molecule:neutrophil cytosol factor 1; PDBTitle: structure of the p22phox-p47phox complex 93 d2ot2a1 not modelled 30.0 22 Fold:OB-fold Superfamily:HupF/HypC-like Family:HupF/HypC-like 94 c2h5xA_ not modelled 29.5 19 PDB header:dna binding protein Chain: A: PDB Molecule:holliday junction atp-dependent dna helicase ruva; PDBTitle: ruva from mycobacterium tuberculosis 95 d2do3a1 not modelled 28.0 16 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:SPT5 KOW domain-like 96 c2qqsB_ not modelled 26.9 20 PDB header:oxidoreductase Chain: B: PDB Molecule:jmjc domain-containing histone demethylation PDBTitle: jmjd2a tandem tudor domains in complex with a trimethylated2 histone h4-k20 peptide 97 d1nppa2 not modelled 26.5 24 Fold:SH3-like barrel Superfamily:Translation proteins SH3-like domain Family:N-utilization substance G protein NusG, C-terminal domain 98 c1xniI_ not modelled 26.1 23 PDB header:cell cycle Chain: I: PDB Molecule:tumor suppressor p53-binding protein 1; PDBTitle: tandem tudor domain of 53bp1 99 c2oqkA_ not modelled 25.8 20 PDB header:translation Chain: A: PDB Molecule:putative translation initiation factor eif-1a; PDBTitle: crystal structure of putative cryptosporidium parvum translation2 initiation factor eif-1a 100 c3kygB_ not modelled 24.1 8 PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein vca0042; PDBTitle: crystal structure of vca0042 (l135r) complexed with c-di-gmp 101 d1ixra2 not modelled 24.1 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:DNA helicase RuvA subunit, N-terminal domain 102 d1a8pa1 not modelled 24.1 14 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like 103 d1wjja_ not modelled 23.5 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 104 d1yeza1 not modelled 23.0 22 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:TRAM domain 105 c1e22A_ not modelled 22.7 21 PDB header:ligase Chain: A: PDB Molecule:lysyl-trna synthetase; PDBTitle: lysyl-trna synthetase (lysu) hexagonal form complexed with2 lysine and the non-hydrolysable atp analogue amp-pcp 106 d1fdra1 not modelled 20.8 14 Fold:Reductase/isomerase/elongation factor common domain Superfamily:Riboflavin synthase domain-like Family:Ferredoxin reductase FAD-binding domain-like 107 d1ri9a_ not modelled 20.8 11 Fold:SH3-like barrel Superfamily:SH3-domain Family:SH3-domain 108 c1ri9A_ not modelled 20.8 11 PDB header:signaling protein Chain: A: PDB Molecule:fyn-binding protein; PDBTitle: structure of a helically extended sh3 domain of the t cell2 adapter protein adap

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