Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	Q	G	S	V	T	E	F	L	K	P	R	L	V	D	I	E	Q	V	S	S	T	H	A	K	V	T	L	E	P	L	E	R	G	F	G	H	T	L	G	N	A	L	R	R	I	L	L	S	S	M	P	G	C	A	V	T	E	V	E
Secondary structure
SS confidence
Disorder		?	?	?	?							?	?							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		I	D	G	V	L	H	E	Y	S	T	K	E	G	V	Q	E	D	I	L	E	I	L	L	N	L	K	G	L	A	V	R	V	Q	G	K	D	E	V	I	L	T	L	N	K	S	G	I	G	P	V	T	A	A	D	I	T	H	D	G	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		V	E	I	V	K	P	Q	H	V	I	C	H	L	T	D	E	N	A	S	I	S	M	R	I	K	V	Q	R	G	R	G	Y	V	P	A	S	T	R	I	H	S	E	E	D	E	R	P	I	G	R	L	L	V	D	A	C	Y	S	P	V
Secondary structure
SS confidence
Disorder																																				?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	R	I	A	Y	N	V	E	A	A	R	V	E	Q	R	T	D	L	D	K	L	V	I	E	M	E	T	N	G	T	I	D	P	E	E	A	I	R	R	A	A	T	I	L	A	E	Q	L	E	A	F	V	D	L	R	D	V	R	Q	P
Secondary structure
SS confidence
Disorder											?	?	?	?	?	?	?	?																																						?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	V	K	E	E	K	P	E	F	D	P	I	L	L	R	P	V	D	D	L	E	L	T	V	R	S	A	N	C	L	K	A	E	A	I	H	Y	I	G	D	L	V	Q	R	T	E	V	E	L	L	K	T	P	N	L	G	K	K	S	L
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?					?		?	?		?	?	?																																		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.
Sequence		T	E	I	K	D	V	L	A	S	R	G	L	S	L	G	M	R	L	E	N	W	P	P	A	S	I	A	D	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 1bdf chain C Region: 1 - 235 Aligned: 228 Modelled: 235 Confidence: 100.0% Identity: 99% PDB header:nucleotidyltransferase Chain: C: PDB Molecule:rna polymerase alpha subunit; PDBTitle: structure of escherichia coli rna polymerase alpha subunit2 n-terminal domain Phyre2 PDB 3iyd chain B Region: 1 - 235 Aligned: 235 Modelled: 235 Confidence: 100.0% Identity: 100% PDB header:transcription/dna Chain: B: PDB Molecule:dna-directed rna polymerase subunit alpha; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex Phyre2 PDB 1smy chain B Region: 5 - 235 Aligned: 226 Modelled: 227 Confidence: 100.0% Identity: 46% PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase alpha chain; PDBTitle: structural basis for transcription regulation by alarmone2 ppgpp Phyre2 PDB 1i6h chain C Region: 9 - 232 Aligned: 219 Modelled: 219 Confidence: 100.0% Identity: 18% PDB header:transcription/dna-rna hybrid Chain: C: PDB Molecule:dna-directed rna polymerase ii 45kd polypeptide; PDBTitle: rna polymerase ii elongation complex Phyre2 PDB 3how chain C Region: 9 - 232 Aligned: 219 Modelled: 223 Confidence: 100.0% Identity: 18% PDB header:transcription,transferase/dna/rna hybrid Chain: C: PDB Molecule:dna-directed rna polymerase ii subunit rpb3; PDBTitle: complete rna polymerase ii elongation complex iii with a t-u2 mismatch and a frayed rna 3'-uridine Phyre2 PDB 2pmz chain S Region: 13 - 231 Aligned: 214 Modelled: 219 Confidence: 100.0% Identity: 20% PDB header:translation, transferase Chain: S: PDB Molecule:dna-directed rna polymerase subunit d; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus Phyre2 PDB 3h0g chain O Region: 12 - 233 Aligned: 217 Modelled: 220 Confidence: 100.0% Identity: 24% PDB header:transcription Chain: O: PDB Molecule:dna-directed rna polymerase ii subunit rpb3; PDBTitle: rna polymerase ii from schizosaccharomyces pombe Phyre2 PDB 1bdf chain A domain 2 Region: 53 - 178 Aligned: 121 Modelled: 126 Confidence: 100.0% Identity: 100% Fold: Insert subdomain of RNA polymerase alpha subunit Superfamily: Insert subdomain of RNA polymerase alpha subunit Family: Insert subdomain of RNA polymerase alpha subunit Phyre2 PDB 1smy chain A domain 2 Region: 53 - 178 Aligned: 121 Modelled: 126 Confidence: 100.0% Identity: 45% Fold: Insert subdomain of RNA polymerase alpha subunit Superfamily: Insert subdomain of RNA polymerase alpha subunit Family: Insert subdomain of RNA polymerase alpha subunit Phyre2 PDB 1ynj chain A domain 2 Region: 53 - 178 Aligned: 121 Modelled: 126 Confidence: 100.0% Identity: 46% Fold: Insert subdomain of RNA polymerase alpha subunit Superfamily: Insert subdomain of RNA polymerase alpha subunit Family: Insert subdomain of RNA polymerase alpha subunit Phyre2 PDB 1bdf chain A domain 1 Region: 2 - 232 Aligned: 105 Modelled: 105 Confidence: 100.0% Identity: 99% Fold: DCoH-like Superfamily: RBP11-like subunits of RNA polymerase Family: RNA polymerase alpha subunit dimerisation domain Phyre2 PDB 1ynj chain A domain 1 Region: 8 - 237 Aligned: 103 Modelled: 104 Confidence: 100.0% Identity: 52% Fold: DCoH-like Superfamily: RBP11-like subunits of RNA polymerase Family: RNA polymerase alpha subunit dimerisation domain Phyre2 PDB 1coo chain A Region: 249 - 329 Aligned: 81 Modelled: 81 Confidence: 99.9% Identity: 100% Fold: SAM domain-like Superfamily: C-terminal domain of RNA polymerase alpha subunit Family: C-terminal domain of RNA polymerase alpha subunit Phyre2 PDB 1smy chain A domain 1 Region: 9 - 235 Aligned: 101 Modelled: 101 Confidence: 99.9% Identity: 56% Fold: DCoH-like Superfamily: RBP11-like subunits of RNA polymerase Family: RNA polymerase alpha subunit dimerisation domain Phyre2 PDB 1lb2 chain B Region: 250 - 321 Aligned: 72 Modelled: 72 Confidence: 99.9% Identity: 100% Fold: SAM domain-like Superfamily: C-terminal domain of RNA polymerase alpha subunit Family: C-terminal domain of RNA polymerase alpha subunit Phyre2 PDB 1z3e chain B domain 1 Region: 249 - 314 Aligned: 66 Modelled: 66 Confidence: 99.8% Identity: 41% Fold: SAM domain-like Superfamily: C-terminal domain of RNA polymerase alpha subunit Family: C-terminal domain of RNA polymerase alpha subunit Phyre2 PDB 1doq chain A Region: 248 - 314 Aligned: 67 Modelled: 67 Confidence: 99.8% Identity: 33% Fold: SAM domain-like Superfamily: C-terminal domain of RNA polymerase alpha subunit Family: C-terminal domain of RNA polymerase alpha subunit Phyre2 PDB 1twf chain C domain 2 Region: 52 - 159 Aligned: 107 Modelled: 108 Confidence: 99.7% Identity: 18% Fold: Insert subdomain of RNA polymerase alpha subunit Superfamily: Insert subdomain of RNA polymerase alpha subunit Family: Insert subdomain of RNA polymerase alpha subunit Phyre2 PDB 1twf chain C domain 1 Region: 9 - 232 Aligned: 126 Modelled: 131 Confidence: 99.3% Identity: 17% Fold: DCoH-like Superfamily: RBP11-like subunits of RNA polymerase Family: RNA polymerase alpha subunit dimerisation domain Phyre2 PDB 1szp chain A domain 1 Region: 255 - 310 Aligned: 56 Modelled: 56 Confidence: 97.2% Identity: 14% Fold: SAM domain-like Superfamily: Rad51 N-terminal domain-like Family: DNA repair protein Rad51, N-terminal domain Phyre2 1 c1bdfC_ 2 c3iydB_ 3 c1smyB_ 4 c1i6hC_ 5 c3howC_ 6 c2pmzS_ 7 c3h0gO_ 8 d1bdfa2 9 d1smya2 10 d1ynja2 11 d1bdfa1 12 d1ynja1 13 d1cooa_ 14 d1smya1 15 d1lb2b_ 16 d1z3eb1 17 d1doqa_ 18 d1twfc2 19 d1twfc1 20 d1szpa1 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

Detailed template information

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

1 c1bdfC_ 100.0 99 PDB header:nucleotidyltransferase Chain: C: PDB Molecule:rna polymerase alpha subunit; PDBTitle: structure of escherichia coli rna polymerase alpha subunit2 n-terminal domain 2 c3iydB_ 100.0 100 PDB header:transcription/dna Chain: B: PDB Molecule:dna-directed rna polymerase subunit alpha; PDBTitle: three-dimensional em structure of an intact activator-dependent2 transcription initiation complex 3 c1smyB_ 100.0 46 PDB header:transferase Chain: B: PDB Molecule:dna-directed rna polymerase alpha chain; PDBTitle: structural basis for transcription regulation by alarmone2 ppgpp 4 c1i6hC_ 100.0 18 PDB header:transcription/dna-rna hybrid Chain: C: PDB Molecule:dna-directed rna polymerase ii 45kd polypeptide; PDBTitle: rna polymerase ii elongation complex 5 c3howC_ 100.0 18 PDB header:transcription,transferase/dna/rna hybrid Chain: C: PDB Molecule:dna-directed rna polymerase ii subunit rpb3; PDBTitle: complete rna polymerase ii elongation complex iii with a t-u2 mismatch and a frayed rna 3'-uridine 6 c2pmzS_ 100.0 20 PDB header:translation, transferase Chain: S: PDB Molecule:dna-directed rna polymerase subunit d; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 7 c3h0gO_ 100.0 24 PDB header:transcription Chain: O: PDB Molecule:dna-directed rna polymerase ii subunit rpb3; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 8 d1bdfa2 100.0 100 Fold:Insert subdomain of RNA polymerase alpha subunit Superfamily:Insert subdomain of RNA polymerase alpha subunit Family:Insert subdomain of RNA polymerase alpha subunit 9 d1smya2 100.0 45 Fold:Insert subdomain of RNA polymerase alpha subunit Superfamily:Insert subdomain of RNA polymerase alpha subunit Family:Insert subdomain of RNA polymerase alpha subunit 10 d1ynja2 100.0 46 Fold:Insert subdomain of RNA polymerase alpha subunit Superfamily:Insert subdomain of RNA polymerase alpha subunit Family:Insert subdomain of RNA polymerase alpha subunit 11 d1bdfa1 100.0 99 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 12 d1ynja1 100.0 52 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 13 d1cooa_ 99.9 100 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 14 d1smya1 99.9 56 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 15 d1lb2b_ 99.9 100 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 16 d1z3eb1 99.8 41 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 17 d1doqa_ 99.8 33 Fold:SAM domain-like Superfamily:C-terminal domain of RNA polymerase alpha subunit Family:C-terminal domain of RNA polymerase alpha subunit 18 d1twfc2 99.7 18 Fold:Insert subdomain of RNA polymerase alpha subunit Superfamily:Insert subdomain of RNA polymerase alpha subunit Family:Insert subdomain of RNA polymerase alpha subunit 19 d1twfc1 99.3 17 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RNA polymerase alpha subunit dimerisation domain 20 d1szpa1 97.2 14 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 21 c1b22A_ not modelled 96.9 14 PDB header:dna binding protein Chain: A: PDB Molecule:dna repair protein rad51; PDBTitle: rad51 (n-terminal domain) 22 d1b22a_ not modelled 96.9 14 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 23 d1xppa_ not modelled 95.8 13 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RBP11/RpoL 24 c2pmzL_ not modelled 95.7 23 PDB header:translation, transferase Chain: L: PDB Molecule:dna-directed rna polymerase subunit l; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus 25 d1twfk_ not modelled 95.4 28 Fold:DCoH-like Superfamily:RBP11-like subunits of RNA polymerase Family:RBP11/RpoL 26 d1szpb1 not modelled 95.4 12 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 27 d1pzna1 not modelled 94.9 10 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 28 d2i1qa1 not modelled 94.3 12 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:DNA repair protein Rad51, N-terminal domain 29 c3h0gK_ not modelled 94.3 24 PDB header:transcription Chain: K: PDB Molecule:dna-directed rna polymerase ii subunit rpb11; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 30 c3ldaA_ not modelled 93.5 15 PDB header:dna binding protein Chain: A: PDB Molecule:dna repair protein rad51; PDBTitle: yeast rad51 h352y filament interface mutant 31 d1dgsa1 not modelled 93.2 18 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:NAD+-dependent DNA ligase, domain 3 32 c1t4gA_ not modelled 92.9 15 PDB header:recombination Chain: A: PDB Molecule:dna repair and recombination protein rada; PDBTitle: atpase in complex with amp-pnp 33 c2dflA_ not modelled 92.5 13 PDB header:recombination Chain: A: PDB Molecule:dna repair and recombination protein rada; PDBTitle: crystal structure of left-handed rada filament 34 c2owoA_ not modelled 91.6 20 PDB header:ligase/dna Chain: A: PDB Molecule:dna ligase; PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate 35 c1dgsB_ not modelled 88.7 18 PDB header:ligase Chain: B: PDB Molecule:dna ligase; PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis 36 c1szpC_ not modelled 86.5 12 PDB header:dna binding protein Chain: C: PDB Molecule:dna repair protein rad51; PDBTitle: a crystal structure of the rad51 filament 37 d2q0zx1 not modelled 86.3 8 Fold:Sec63 N-terminal domain-like Superfamily:Sec63 N-terminal domain-like Family:Sec63 N-terminal domain 38 d2bgwa1 not modelled 85.2 20 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 39 c1v9pB_ not modelled 85.2 23 PDB header:ligase Chain: B: PDB Molecule:dna ligase; PDBTitle: crystal structure of nad+-dependent dna ligase 40 d2a1jb1 not modelled 85.2 23 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 41 c1t3nB_ not modelled 85.1 24 PDB header:replication/dna Chain: B: PDB Molecule:polymerase (dna directed) iota; PDBTitle: structure of the catalytic core of dna polymerase iota in2 complex with dna and dttp 42 c1kftA_ not modelled 81.8 21 PDB header:dna binding protein Chain: A: PDB Molecule:excinuclease abc subunit c; PDBTitle: solution structure of the c-terminal domain of uvrc from e-2 coli 43 d1kfta_ not modelled 81.8 21 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Excinuclease UvrC C-terminal domain 44 d1k1sa2 not modelled 80.6 19 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 45 d1zeta2 not modelled 78.3 25 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 46 c1k1qA_ not modelled 76.3 19 PDB header:transcription Chain: A: PDB Molecule:dbh protein; PDBTitle: crystal structure of a dinb family error prone dna2 polymerase from sulfolobus solfataricus 47 c3gqcB_ not modelled 75.7 22 PDB header:transferase/dna Chain: B: PDB Molecule:dna repair protein rev1; PDBTitle: structure of human rev1-dna-dntp ternary complex 48 c2va8A_ not modelled 75.6 21 PDB header:hydrolase Chain: A: PDB Molecule:ski2-type helicase; PDBTitle: dna repair helicase hel308 49 d1jx4a2 not modelled 75.2 17 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 50 c2bhnD_ not modelled 74.6 25 PDB header:hydrolase Chain: D: PDB Molecule:xpf endonuclease; PDBTitle: xpf from aeropyrum pernix 51 d1x2ia1 not modelled 74.2 21 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 52 c2kp7A_ not modelled 74.2 15 PDB header:hydrolase Chain: A: PDB Molecule:crossover junction endonuclease mus81; PDBTitle: solution nmr structure of the mus81 n-terminal hhh.2 northeast structural genomics consortium target mmt1a 53 d1u9la_ not modelled 72.5 17 Fold:SAM domain-like Superfamily:Rad51 N-terminal domain-like Family:NusA extra C-terminal domains 54 c3im2A_ not modelled 71.6 13 PDB header:hydrolase Chain: A: PDB Molecule:pre-mrna-splicing helicase brr2; PDBTitle: structure of the c-terminal sec63 unit of yeast brr2, p41212 form 55 d1cuka2 not modelled 67.9 25 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:DNA helicase RuvA subunit, middle domain 56 c2fllA_ not modelled 65.9 24 PDB header:replication/dna Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: ternary complex of human dna polymerase iota with dna and dttp 57 c1ixrA_ not modelled 64.9 16 PDB header:hydrolase Chain: A: PDB Molecule:holliday junction dna helicase ruva; PDBTitle: ruva-ruvb complex 58 d1gm5a2 not modelled 63.8 19 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:RecG "wedge" domain 59 c1s97D_ not modelled 63.0 20 PDB header:transferase/dna Chain: D: PDB Molecule:dna polymerase iv; PDBTitle: dpo4 with gt mismatch 60 d1ixra1 not modelled 61.8 16 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:DNA helicase RuvA subunit, middle domain 61 c2w9mB_ not modelled 60.5 20 PDB header:dna replication Chain: B: PDB Molecule:polymerase x; PDBTitle: structure of family x dna polymerase from deinococcus2 radiodurans 62 c1d8lA_ not modelled 56.6 25 PDB header:gene regulation Chain: A: PDB Molecule:protein (holliday junction dna helicase ruva); PDBTitle: e. coli holliday junction binding protein ruva nh2 region2 lacking domain iii 63 c1wcnA_ not modelled 53.3 16 PDB header:rna-binding protein Chain: A: PDB Molecule:transcription elongation protein nusa; PDBTitle: nmr structure of the carboxyterminal domains of escherichia2 coli nusa 64 d1kkha2 not modelled 51.4 25 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Mevalonate kinase 65 d1feua_ not modelled 49.3 21 Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Ribosomal protein L25-like 66 d2edua1 not modelled 49.1 16 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:ComEA-like 67 c2kz3A_ not modelled 49.1 28 PDB header:unknown function Chain: A: PDB Molecule:putative uncharacterized protein rad51l3; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for human rad51d2 from 1 to 83 68 d1t94a2 not modelled 47.1 19 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 69 c2rrdA_ not modelled 43.7 16 PDB header:dna binding protein Chain: A: PDB Molecule:hrdc domain from bloom syndrome protein; PDBTitle: structure of hrdc domain from human bloom syndrome protein, blm 70 d1k47a2 not modelled 42.8 14 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Phosphomevalonate kinase (PMK) 71 d2j3wb1 not modelled 42.7 26 Fold:Ligand-binding domain in the NO signalling and Golgi transport Superfamily:Ligand-binding domain in the NO signalling and Golgi transport Family:TRAPP components 72 c1s5lu_ not modelled 41.7 15 PDB header:photosynthesis Chain: U: PDB Molecule:photosystem ii 12 kda extrinsic protein; PDBTitle: architecture of the photosynthetic oxygen evolving center 73 d1im4a_ not modelled 41.3 16 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 74 c3bqsB_ not modelled 40.5 14 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 listeria monocytogenes, trigonal form 75 c1t94B_ not modelled 40.2 19 PDB header:replication Chain: B: PDB Molecule:polymerase (dna directed) kappa; PDBTitle: crystal structure of the catalytic core of human dna2 polymerase kappa 76 d1bvsa2 not modelled 38.2 18 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:DNA helicase RuvA subunit, middle domain 77 d1s4ea2 not modelled 37.2 17 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Galactokinase 78 d2axtu1 not modelled 35.6 15 Fold:SAM domain-like Superfamily:PsbU/PolX domain-like Family:PsbU-like 79 d1piea2 not modelled 35.6 16 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Galactokinase 80 c2q0zX_ not modelled 35.3 8 PDB header:protein transport Chain: X: PDB Molecule:protein pro2281; PDBTitle: crystal structure of q9p172/sec63 from homo sapiens.2 northeast structural genomics target hr1979. 81 c2aq4A_ not modelled 34.3 24 PDB header:transferase Chain: A: PDB Molecule:dna repair protein rev1; PDBTitle: ternary complex of the catalytic core of rev1 with dna and dctp. 82 c3mr2A_ not modelled 33.9 28 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase eta; PDBTitle: human dna polymerase eta in complex with normal dna and incoming2 nucleotide (nrm) 83 c2b0tA_ not modelled 33.7 24 PDB header:oxidoreductase Chain: A: PDB Molecule:nadp isocitrate dehydrogenase; PDBTitle: structure of monomeric nadp isocitrate dehydrogenase 84 d2p6ra2 not modelled 33.4 17 Fold:Sec63 N-terminal domain-like Superfamily:Sec63 N-terminal domain-like Family:Achaeal helicase C-terminal domain 85 c1hjpA_ not modelled 32.8 17 PDB header:dna recombination Chain: A: PDB Molecule:ruva; PDBTitle: holliday junction binding protein ruva from e. coli 86 d1wuua2 not modelled 32.6 16 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Galactokinase 87 d1itwa_ not modelled 32.5 22 Fold:Isocitrate/Isopropylmalate dehydrogenase-like Superfamily:Isocitrate/Isopropylmalate dehydrogenase-like Family:Monomeric isocitrate dehydrogenase 88 d2aq0a1 not modelled 32.2 15 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 89 d1wc9a_ not modelled 30.9 24 Fold:Ligand-binding domain in the NO signalling and Golgi transport Superfamily:Ligand-binding domain in the NO signalling and Golgi transport Family:TRAPP components 90 c1wuuA_ not modelled 30.8 16 PDB header:transferase Chain: A: PDB Molecule:galactokinase; PDBTitle: crystal structure of human galactokinase complexed with2 mgamppnp and galactose 91 d1pyya2 not modelled 29.3 8 Fold:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family:Penicillin-binding protein 2x (pbp-2x), c-terminal domain 92 d1k25a2 not modelled 28.9 8 Fold:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family:Penicillin-binding protein 2x (pbp-2x), c-terminal domain 93 d1wuda1 not modelled 28.9 11 Fold:SAM domain-like Superfamily:HRDC-like Family:HRDC domain from helicases 94 d1jmsa1 not modelled 28.7 19 Fold:SAM domain-like Superfamily:DNA polymerase beta, N-terminal domain-like Family:DNA polymerase beta, N-terminal domain-like 95 c2hfuB_ not modelled 27.8 17 PDB header:transferase Chain: B: PDB Molecule:mevalonate kinase, putative; PDBTitle: crystal structure of l. major mevalonate kinase in complex2 with r-mevalonate 96 c2h5xA_ not modelled 25.1 16 PDB header:dna binding protein Chain: A: PDB Molecule:holliday junction atp-dependent dna helicase ruva; PDBTitle: ruva from mycobacterium tuberculosis 97 c2a2cA_ not modelled 24.8 14 PDB header:transferase Chain: A: PDB Molecule:n-acetylgalactosamine kinase; PDBTitle: x-ray structure of human n-acetyl galactosamine kinase2 complexed with mg-adp and n-acetyl galactosamine 1-3 phosphate 98 d1rp5a2 not modelled 24.4 8 Fold:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Superfamily:Penicillin-binding protein 2x (pbp-2x), c-terminal domain Family:Penicillin-binding protein 2x (pbp-2x), c-terminal domain 99 d2zjrs1 not modelled 23.8 20 Fold:Ribosomal protein L25-like Superfamily:Ribosomal protein L25-like Family:Ribosomal protein L25-like 100 d1s7za_ not modelled 23.7 25 Fold:Another 3-helical bundle Superfamily:B-form DNA mimic Ocr Family:B-form DNA mimic Ocr 101 c1k47F_ not modelled 22.7 12 PDB header:transferase Chain: F: PDB Molecule:phosphomevalonate kinase; PDBTitle: crystal structure of the streptococcus pneumoniae2 phosphomevalonate kinase (pmk) 102 c3c1zA_ not modelled 22.7 18 PDB header:dna binding protein Chain: A: PDB Molecule:dna integrity scanning protein disa; PDBTitle: structure of the ligand-free form of a bacterial dna damage2 sensor protein 103 d2duya1 not modelled 22.3 23 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:ComEA-like 104 d2bcqa1 not modelled 21.8 25 Fold:SAM domain-like Superfamily:DNA polymerase beta, N-terminal domain-like Family:DNA polymerase beta, N-terminal domain-like 105 d1coka_ not modelled 20.3 20 Fold:SAM domain-like Superfamily:SAM/Pointed domain Family:SAM (sterile alpha motif) domain

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