Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	K	L	P	T	G	V	E	I	R	G	R	Y	I	R	I	W	F	M	F	R	G	K	R	C	R	E	T	L	K	G	W	E	I	T	N	S	N	I	K	K	A	G	N	L	R	A	L	I	V	H	E	I	N	S	G	E	F	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																											?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		Y	L	R	R	F	P	Q	S	S	T	G	A	K	M	V	T	T	R	V	I	K	T	F	G	E	L	C	D	I	W	T	K	I	K	E	T	E	L	T	T	N	T	M	K	K	T	K	S	Q	L	K	T	L	R	I	I	I	C	E	S
Secondary structure
SS confidence
Disorder										?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		T	P	I	S	H	I	R	Y	S	D	I	L	N	Y	R	N	E	L	L	H	G	E	T	L	Y	L	D	N	P	R	S	N	K	K	G	R	T	V	R	T	V	D	N	Y	I	A	L	L	C	S	L	L	R	F	A	Y	Q	S	G	F
Secondary structure
SS confidence
Disorder																						?	?	?	?	?	?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	S	T	K	P	F	E	G	V	K	K	L	Q	R	N	R	I	K	P	D	P	L	S	K	T	E	F	N	A	L	M	E	S	E	K	G	Q	S	Q	N	L	W	K	F	A	V	Y	S	G	L	R	H	G	E	L	A	A	L	A	W
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		E	D	V	D	L	E	K	G	I	V	N	V	R	R	N	L	T	I	L	D	M	F	G	P	P	K	T	N	A	G	I	R	T	V	T	L	L	Q	P	A	L	E	A	L	K	E	Q	Y	K	L	T	G	H	H	R	K	S	E	I	T
Secondary structure
SS confidence
Disorder																				?	?	?																														?	?			?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		F	Y	H	R	E	Y	G	R	T	E	K	Q	K	L	H	F	V	F	M	P	R	V	C	N	G	K	Q	K	P	Y	Y	S	V	S	S	L	G	A	R	W	N	A	A	V	K	R	A	G	I	R	R	R	N	P	Y	H	T	R	H	T
Secondary structure
SS confidence
Disorder						?	?	?	?	?													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.
Sequence		F	A	C	W	L	L	T	A	G	A	N	P	A	F	I	A	S	Q	M	G	H	E	T	A	Q	M	V	Y	E	I	Y	G	M	W	I	D	D	M	N	D	E	Q	I	A	M	L	N	A	R	L	S
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 1z1b chain A Region: 2 - 393 Aligned: 328 Modelled: 348 Confidence: 100.0% Identity: 17% PDB header:dna binding protein/dna Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of a lambda integrase dimer bound to a2 coc' core site Phyre2 PDB 2a3v chain A Region: 84 - 394 Aligned: 294 Modelled: 299 Confidence: 100.0% Identity: 16% PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase inti4; PDBTitle: structural basis for broad dna-specificity in integron2 recombination Phyre2 PDB 1ma7 chain A Region: 82 - 407 Aligned: 295 Modelled: 301 Confidence: 100.0% Identity: 14% PDB header:hydrolase, ligase/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: crystal structure of cre site-specific recombinase2 complexed with a mutant dna substrate, loxp-a8/t27 Phyre2 PDB 1crx chain A Region: 84 - 407 Aligned: 298 Modelled: 311 Confidence: 99.9% Identity: 12% PDB header:replication/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: cre recombinase/dna complex reaction intermediate i Phyre2 PDB 1p7d chain A Region: 81 - 397 Aligned: 265 Modelled: 277 Confidence: 99.9% Identity: 17% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 3nkh chain B Region: 219 - 408 Aligned: 175 Modelled: 172 Confidence: 99.9% Identity: 21% PDB header:recombination Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus Phyre2 PDB 1a0p chain A Region: 85 - 403 Aligned: 264 Modelled: 271 Confidence: 99.9% Identity: 16% PDB header:dna recombination Chain: A: PDB Molecule:site-specific recombinase xerd; PDBTitle: site-specific recombinase, xerd Phyre2 PDB 1aih chain A Region: 196 - 405 Aligned: 158 Modelled: 159 Confidence: 99.7% Identity: 18% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1f44 chain A domain 2 Region: 195 - 409 Aligned: 189 Modelled: 215 Confidence: 99.7% Identity: 15% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1a0p chain A domain 2 Region: 200 - 403 Aligned: 171 Modelled: 186 Confidence: 99.5% Identity: 22% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 1ae9 chain A Region: 199 - 394 Aligned: 162 Modelled: 170 Confidence: 99.4% Identity: 18% Fold: DNA breaking-rejoining enzymes Superfamily: DNA breaking-rejoining enzymes Family: Lambda integrase-like, catalytic core Phyre2 PDB 2kj8 chain A Region: 77 - 199 Aligned: 109 Modelled: 109 Confidence: 99.4% Identity: 12% PDB header:dna binding protein Chain: A: PDB Molecule:putative prophage cps-53 integrase; PDBTitle: nmr structure of fragment 87-196 from the putative phage2 integrase ints of e. coli: northeast structural genomics3 consortium target er652a, psi-2 Phyre2 PDB 2kd1 chain A Region: 77 - 203 Aligned: 114 Modelled: 127 Confidence: 99.4% Identity: 18% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dna integration/recombination/invertion protein; PDBTitle: solution nmr structure of the integrase-like domain from2 bacillus cereus ordered locus bc_1272. northeast3 structural genomics consortium target bcr268f Phyre2 PDB 2kj9 chain A Region: 72 - 199 Aligned: 113 Modelled: 114 Confidence: 99.4% Identity: 13% PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: nmr structure of intb phage-integrase-like protein fragment2 90-199 from erwinia carotova subsp. atroseptica: northeast3 structural genomics consortium target ewr217e Phyre2 PDB 2kiw chain A Region: 82 - 201 Aligned: 105 Modelled: 106 Confidence: 99.4% Identity: 20% PDB header:dna binding protein Chain: A: PDB Molecule:int protein; PDBTitle: solution nmr structure of the domain n-terminal to the2 integrase domain of sh1003 from staphylococcus3 haemolyticus. northeast structural genomics consortium4 target shr105f (64-166). Phyre2 PDB 2kkv chain A Region: 76 - 204 Aligned: 114 Modelled: 115 Confidence: 99.4% Identity: 13% PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: solution nmr structure of an integrase domain from protein2 spa4288 from salmonella enterica, northeast structural3 genomics consortium target slr105h Phyre2 PDB 2kkp chain A Region: 77 - 199 Aligned: 110 Modelled: 123 Confidence: 99.4% Identity: 19% PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of the phage integrase sam-like2 domain from moth 1796 from moorella thermoacetica.3 northeast structural genomics consortium target mtr39k4 (residues 64-171). Phyre2 PDB 3lys chain C Region: 78 - 195 Aligned: 103 Modelled: 104 Confidence: 99.3% Identity: 13% PDB header:recombination Chain: C: PDB Molecule:prophage pi2 protein 01, integrase; PDBTitle: crystal structure of the n-terminal domain of the prophage2 pi2 protein 01 (integrase) from lactococcus lactis,3 northeast structural genomics consortium target kr124f Phyre2 PDB 2khq chain A Region: 81 - 199 Aligned: 104 Modelled: 105 Confidence: 99.3% Identity: 13% PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: solution nmr structure of a phage integrase ssp19472 fragment 59-159 from staphylococcus saprophyticus,3 northeast structural genomics consortium target syr103b Phyre2 PDB 2kob chain A Region: 81 - 198 Aligned: 101 Modelled: 102 Confidence: 99.3% Identity: 19% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of clolep_01837 (fragment 61-160)2 from clostridium leptum. northeast structural genomics3 consortium target qlr8a Phyre2 1 c1z1bA_ 2 c2a3vA_ 3 c1ma7A_ 4 c1crxA_ 5 d1p7da_ 6 c3nkhB_ 7 c1a0pA_ 8 d1aiha_ 9 d1f44a2 10 d1a0pa2 11 d1ae9a_ 12 c2kj8A_ 13 c2kd1A_ 14 c2kj9A_ 15 c2kiwA_ 16 c2kkvA_ 17 c2kkpA_ 18 c3lysC_ 19 c2khqA_ 20 c2kobA_ 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

Detailed template information

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

1 c1z1bA_ 100.0 17 PDB header:dna binding protein/dna Chain: A: PDB Molecule:integrase; PDBTitle: crystal structure of a lambda integrase dimer bound to a2 coc' core site 2 c2a3vA_ 100.0 16 PDB header:recombination Chain: A: PDB Molecule:site-specific recombinase inti4; PDBTitle: structural basis for broad dna-specificity in integron2 recombination 3 c1ma7A_ 100.0 14 PDB header:hydrolase, ligase/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: crystal structure of cre site-specific recombinase2 complexed with a mutant dna substrate, loxp-a8/t27 4 c1crxA_ 99.9 12 PDB header:replication/dna Chain: A: PDB Molecule:cre recombinase; PDBTitle: cre recombinase/dna complex reaction intermediate i 5 d1p7da_ 99.9 17 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 6 c3nkhB_ 99.9 21 PDB header:recombination Chain: B: PDB Molecule:integrase; PDBTitle: crystal structure of integrase from mrsa strain staphylococcus aureus 7 c1a0pA_ 99.9 16 PDB header:dna recombination Chain: A: PDB Molecule:site-specific recombinase xerd; PDBTitle: site-specific recombinase, xerd 8 d1aiha_ 99.7 18 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 9 d1f44a2 99.7 15 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 10 d1a0pa2 99.5 22 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 11 d1ae9a_ 99.4 18 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 12 c2kj8A_ 99.4 12 PDB header:dna binding protein Chain: A: PDB Molecule:putative prophage cps-53 integrase; PDBTitle: nmr structure of fragment 87-196 from the putative phage2 integrase ints of e. coli: northeast structural genomics3 consortium target er652a, psi-2 13 c2kd1A_ 99.4 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dna integration/recombination/invertion protein; PDBTitle: solution nmr structure of the integrase-like domain from2 bacillus cereus ordered locus bc_1272. northeast3 structural genomics consortium target bcr268f 14 c2kj9A_ 99.4 13 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: nmr structure of intb phage-integrase-like protein fragment2 90-199 from erwinia carotova subsp. atroseptica: northeast3 structural genomics consortium target ewr217e 15 c2kiwA_ 99.4 20 PDB header:dna binding protein Chain: A: PDB Molecule:int protein; PDBTitle: solution nmr structure of the domain n-terminal to the2 integrase domain of sh1003 from staphylococcus3 haemolyticus. northeast structural genomics consortium4 target shr105f (64-166). 16 c2kkvA_ 99.4 13 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: solution nmr structure of an integrase domain from protein2 spa4288 from salmonella enterica, northeast structural3 genomics consortium target slr105h 17 c2kkpA_ 99.4 19 PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of the phage integrase sam-like2 domain from moth 1796 from moorella thermoacetica.3 northeast structural genomics consortium target mtr39k4 (residues 64-171). 18 c3lysC_ 99.3 13 PDB header:recombination Chain: C: PDB Molecule:prophage pi2 protein 01, integrase; PDBTitle: crystal structure of the n-terminal domain of the prophage2 pi2 protein 01 (integrase) from lactococcus lactis,3 northeast structural genomics consortium target kr124f 19 c2khqA_ 99.3 13 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: solution nmr structure of a phage integrase ssp19472 fragment 59-159 from staphylococcus saprophyticus,3 northeast structural genomics consortium target syr103b 20 c2kobA_ 99.3 19 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of clolep_01837 (fragment 61-160)2 from clostridium leptum. northeast structural genomics3 consortium target qlr8a 21 c2oxoA_ not modelled 99.3 20 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: crystallization and structure determination of the core-2 binding domain of bacteriophage lambda integrase 22 d5crxb2 not modelled 99.2 14 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Lambda integrase-like, catalytic core 23 c2khvA_ not modelled 99.2 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of protein nmul_a0922 from2 nitrosospira multiformis. northeast structural genomics3 consortium target nmr38b. 24 c2kj5A_ not modelled 99.2 10 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:phage integrase; PDBTitle: solution nmr structure of a domain from a putative phage2 integrase protein nmul_a0064 from nitrosospira multiformis,3 northeast structural genomics consortium target nmr46c 25 c2keyA_ not modelled 99.1 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative phage integrase; PDBTitle: solution nmr structure of a domain from a putative phage integrase2 protein bf2284 from bacteroides fragilis, northeast structural3 genomics consortium target bfr257c 26 c3nrwA_ not modelled 99.0 14 PDB header:recombination Chain: A: PDB Molecule:phage integrase/site-specific recombinase; PDBTitle: crystal structure of the n-terminal domain of phage integrase/site-2 specific recombinase (tnp) from haloarcula marismortui, northeast3 structural genomics consortium target hmr208a 27 c3ju0A_ not modelled 98.1 17 PDB header:dna binding protein Chain: A: PDB Molecule:phage integrase; PDBTitle: structure of the arm-type binding domain of hai7 integrase 28 d1a0pa1 not modelled 97.9 12 Fold:SAM domain-like Superfamily:lambda integrase-like, N-terminal domain Family:lambda integrase-like, N-terminal domain 29 c3jtzA_ not modelled 97.6 23 PDB header:dna binding protein Chain: A: PDB Molecule:integrase; PDBTitle: structure of the arm-type binding domain of hpi integrase 30 d1f44a1 not modelled 96.4 14 Fold:SAM domain-like Superfamily:lambda integrase-like, N-terminal domain Family:lambda integrase-like, N-terminal domain 31 c2v6eB_ not modelled 95.7 15 PDB header:hydrolase Chain: B: PDB Molecule:protelemorase; PDBTitle: protelomerase telk complexed with substrate dna 32 c2f4qA_ not modelled 80.5 13 PDB header:isomerase Chain: A: PDB Molecule:type i topoisomerase, putative; PDBTitle: crystal structure of deinococcus radiodurans topoisomerase ib 33 c2h7fX_ not modelled 61.6 12 PDB header:isomerase/dna Chain: X: PDB Molecule:dna topoisomerase 1; PDBTitle: structure of variola topoisomerase covalently bound to dna 34 c3igmA_ not modelled 40.7 18 PDB header:transcription/dna Chain: A: PDB Molecule:pf14_0633 protein; PDBTitle: a 2.2a crystal structure of the ap2 domain of pf14_0633 from p.2 falciparum, bound as a domain-swapped dimer to its cognate dna 35 d1trra_ not modelled 40.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 36 d1jhga_ not modelled 31.6 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Trp repressor, TrpR 37 d1gcca_ not modelled 30.9 17 Fold:DNA-binding domain Superfamily:DNA-binding domain Family:GCC-box binding domain 38 d2iw5b1 not modelled 28.5 11 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 39 d1xc5a1 not modelled 27.5 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 40 d2auwa1 not modelled 23.8 20 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:NE0471 C-terminal domain-like 41 d1hcra_ not modelled 23.7 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 42 d1l8qa1 not modelled 23.7 12 Fold:DNA/RNA-binding 3-helical bundle Superfamily:TrpR-like Family:Chromosomal replication initiation factor DnaA C-terminal domain IV 43 d1ijwc_ not modelled 23.7 25 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Recombinase DNA-binding domain 44 c2eqrA_ not modelled 22.0 18 PDB header:transcription Chain: A: PDB Molecule:nuclear receptor corepressor 1; PDBTitle: solution structure of the first sant domain from human2 nuclear receptor corepressor 1 45 c3lsgD_ not modelled 21.3 16 PDB header:transcription regulator Chain: D: PDB Molecule:two-component response regulator yesn; PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586 46 c2yqkA_ not modelled 19.5 21 PDB header:transcription/apoptosis Chain: A: PDB Molecule:arginine-glutamic acid dipeptide repeats protein; PDBTitle: solution structure of the sant domain in arginine-glutamic2 acid dipeptide (re) repeats 47 d1whna_ not modelled 18.3 17 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 48 c1x3uA_ not modelled 18.0 15 PDB header:transcription Chain: A: PDB Molecule:transcriptional regulatory protein fixj; PDBTitle: solution structure of the c-terminal transcriptional2 activator domain of fixj from sinorhizobium melilot 49 d2crga1 not modelled 17.7 24 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Myb/SANT domain 50 d1fsea_ not modelled 17.4 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 51 d1a41a_ not modelled 17.1 16 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Eukaryotic DNA topoisomerase I, catalytic core 52 c2iw5B_ not modelled 17.1 11 PDB header:oxidoreductase/transcription regulator Chain: B: PDB Molecule:rest corepressor 1; PDBTitle: structural basis for corest-dependent demethylation of2 nucleosomes by the human lsd1 histone demethylase 53 c2x0lB_ not modelled 17.1 11 PDB header:transcription Chain: B: PDB Molecule:rest corepressor 1; PDBTitle: crystal structure of a neuro-specific splicing variant of2 human histone lysine demethylase lsd1. 54 c2xajB_ not modelled 17.1 11 PDB header:transcription Chain: B: PDB Molecule:rest corepressor 1; PDBTitle: crystal structure of lsd1-corest in complex with (-)-trans-2 2-phenylcyclopropyl-1-amine 55 c2v1dB_ not modelled 17.1 11 PDB header:oxidoreductase/repressor Chain: B: PDB Molecule:rest corepressor 1; PDBTitle: structural basis of lsd1-corest selectivity in histone h32 recognition 56 d1a04a1 not modelled 16.6 20 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 57 c2krfB_ not modelled 15.4 14 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein coma; PDBTitle: nmr solution structure of the dna binding domain of competence protein2 a 58 d2aq0a1 not modelled 15.2 18 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like 59 c4a69C_ not modelled 15.2 21 PDB header:transcription Chain: C: PDB Molecule:nuclear receptor corepressor 2; PDBTitle: structure of hdac3 bound to corepressor and inositol tetraphosphate 60 d1k78a1 not modelled 14.6 26 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 61 d1yioa1 not modelled 14.2 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 62 c2rnjA_ not modelled 12.7 26 PDB header:transcription Chain: A: PDB Molecule:response regulator protein vrar; PDBTitle: nmr structure of the s. aureus vrar dna binding domain 63 d1qu6a2 not modelled 11.8 15 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 64 c2jpcA_ not modelled 11.8 18 PDB header:dna binding protein Chain: A: PDB Molecule:ssrb; PDBTitle: ssrb dna binding protein 65 c2auwB_ not modelled 11.4 19 PDB header:unknown function Chain: B: PDB Molecule:hypothetical protein ne0471; PDBTitle: crystal structure of putative dna binding protein ne0471 from2 nitrosomonas europaea atcc 19718 66 d1kwga1 not modelled 10.6 28 Fold:Glycosyl hydrolase domain Superfamily:Glycosyl hydrolase domain Family:alpha-Amylases, C-terminal beta-sheet domain 67 c1u78A_ not modelled 10.3 0 PDB header:dna binding protein/dna Chain: A: PDB Molecule:transposable element tc3 transposase; PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna 68 d1k4ta2 not modelled 10.2 11 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Eukaryotic DNA topoisomerase I, catalytic core 69 d1pdnc_ not modelled 9.4 21 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 70 c1zljE_ not modelled 9.3 19 PDB header:transcription Chain: E: PDB Molecule:dormancy survival regulator; PDBTitle: crystal structure of the mycobacterium tuberculosis hypoxic2 response regulator dosr c-terminal domain 71 d1x48a1 not modelled 9.2 9 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 72 c3sohB_ not modelled 9.1 12 PDB header:motor protein Chain: B: PDB Molecule:flagellar motor switch protein flig; PDBTitle: architecture of the flagellar rotor 73 d2csba1 not modelled 8.8 15 Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Topoisomerase V repeat domain 74 c2ef8A_ not modelled 8.7 19 PDB header:transcription regulator Chain: A: PDB Molecule:putative transcription factor; PDBTitle: crystal structure of c.ecot38is 75 c2x48B_ not modelled 8.3 26 PDB header:viral protein Chain: B: PDB Molecule:cag38821; PDBTitle: orf 55 from sulfolobus islandicus rudivirus 1 76 d1uxca_ not modelled 8.0 10 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:GalR/LacI-like bacterial regulator 77 c3frwF_ not modelled 7.8 11 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:putative trp repressor protein; PDBTitle: crystal structure of putative trpr protein from ruminococcus obeum 78 d1p4wa_ not modelled 7.7 14 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 79 d1bl0a2 not modelled 7.6 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 80 d2b7ta1 not modelled 7.5 19 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 81 d1dwka1 not modelled 7.5 18 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Cyanase N-terminal domain 82 d6paxa1 not modelled 7.4 28 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Paired domain 83 d1l3la1 not modelled 7.4 19 Fold:DNA/RNA-binding 3-helical bundle Superfamily:C-terminal effector domain of the bipartite response regulators Family:GerE-like (LuxR/UhpA family of transcriptional regulators) 84 d1rr8c1 not modelled 7.4 11 Fold:DNA breaking-rejoining enzymes Superfamily:DNA breaking-rejoining enzymes Family:Eukaryotic DNA topoisomerase I, catalytic core 85 c3korD_ not modelled 7.1 14 PDB header:transcription Chain: D: PDB Molecule:possible trp repressor; PDBTitle: crystal structure of a putative trp repressor from staphylococcus2 aureus 86 d1rkta1 not modelled 7.0 15 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:Tetracyclin repressor-like, N-terminal domain 87 c1f8aB_ not modelled 6.8 27 PDB header:isomerase Chain: B: PDB Molecule:peptidyl-prolyl cis-trans isomerase nima- PDBTitle: structural basis for the phosphoserine-proline recognition2 by group iv ww domains 88 c3oouA_ not modelled 6.8 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:lin2118 protein; PDBTitle: the structure of a protein with unkown function from listeria innocua 89 d1d5ya2 not modelled 6.7 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:AraC type transcriptional activator 90 c2khxA_ not modelled 6.6 21 PDB header:gene regulation,nuclear protein Chain: A: PDB Molecule:ribonuclease 3; PDBTitle: drosha double-stranded rna binding motif 91 c3mzyA_ not modelled 6.5 13 PDB header:rna binding protein Chain: A: PDB Molecule:rna polymerase sigma-h factor; PDBTitle: the crystal structure of the rna polymerase sigma-h factor from2 fusobacterium nucleatum to 2.5a 92 d1x47a1 not modelled 6.5 22 Fold:dsRBD-like Superfamily:dsRNA-binding domain-like Family:Double-stranded RNA-binding domain (dsRBD) 93 d2gf5a1 not modelled 6.4 12 Fold:DEATH domain Superfamily:DEATH domain Family:DEATH domain, DD 94 d1rp3a2 not modelled 6.4 5 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Sigma3 and sigma4 domains of RNA polymerase sigma factors Family:Sigma4 domain 95 c3b7hA_ not modelled 6.3 11 PDB header:structural protein Chain: A: PDB Molecule:prophage lp1 protein 11; PDBTitle: crystal structure of the prophage lp1 protein 11 96 d1z91a1 not modelled 6.2 6 Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:MarR-like transcriptional regulators 97 c2l2nA_ not modelled 6.2 17 PDB header:rna binding protein, plant protein Chain: A: PDB Molecule:hyponastic leave 1; PDBTitle: backbone 1h, 13c, and 15n chemical shift assignments for the first2 dsrbd of protein hyl1 98 c3adiC_ not modelled 6.2 17 PDB header:gene regulation/rna Chain: C: PDB Molecule:f21m12.9 protein; PDBTitle: structure of arabidopsis hyl1 and its molecular implications for mirna2 processing 99 c3hugA_ not modelled 6.2 14 PDB header:transcription/membrane protein Chain: A: PDB Molecule:rna polymerase sigma factor; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl

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