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LacPavin_0818_WC40_scaffold_30711_prodigal-single.1__X__X__00339

Bact-Vir

LacPavin_0818_WC40_scaffold_30711_prodigal-single.1__X__X__00339

Identity

Kingdom:
phage

Quality

86.9 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 105-224
PDB
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1cx8A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.62 48.0 3.59e-01 82.5% 96.1%
2nlkA02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.62 49.0 3.77e-01 84.2% 39.6%
1lyvA00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.60 47.0 3.65e-01 85.8% 45.2%
3dc4A00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.59 46.0 3.48e-01 82.5% 66.0%
1g4wR02 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.59 46.0 3.80e-01 84.2% 52.5%
2r5vB02 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.57 44.0 3.73e-01 80.8% 82.6%
1nhpA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.56 37.0 3.85e-01 94.2% 70.8%
2jysA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.56 33.0 3.67e-01 95.8% 74.7%
1whqA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 34.0 4.08e-01 85.0% 100.0%
1sqiA01 3.10.180.10 Alpha Beta › Roll › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 › 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 0.56 43.0 3.87e-01 81.7% 76.0%
1qs8A01 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.56 42.0 3.68e-01 78.3% 67.4%
1fmbA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.55 34.0 3.63e-01 76.7% 70.2%
3cgbA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.55 38.0 3.94e-01 94.2% 76.4%
6krwA01 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.55 43.0 3.26e-01 84.2% 37.4%
4fx9A03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.55 37.0 3.81e-01 94.2% 72.6%
1lj5A02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.55 41.0 3.76e-01 77.5% 94.2%
2oc3A00 3.90.190.10 Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily 0.54 43.0 3.31e-01 85.0% 39.1%
1yqzA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.54 36.0 3.81e-01 94.2% 75.9%
1srqA01 3.30.1120.160 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.53 31.0 2.96e-01 92.5% 46.4%
2cduA03 3.30.390.30 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › FAD/NAD-linked reductase, C-terminal dimerisation domain 0.53 37.0 3.79e-01 93.3% 74.3%
3icsA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.53 37.0 2.90e-01 70.8% 56.2%
2xswB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.53 44.0 3.27e-01 90.8% 85.9%
4fpvB00 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.53 43.0 3.46e-01 90.8% 94.9%
1y8cA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.53 27.0 3.54e-01 95.0% 95.0%
2bbhA01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.52 42.0 3.91e-01 98.3% 68.2%
2afsA00 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 43.0 3.20e-01 90.8% 87.0%
3s95A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 35.0 3.91e-01 87.5% 92.0%
3bhcA01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.52 39.0 3.95e-01 97.5% 78.0%
4hlnA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.51 46.0 3.48e-01 99.2% 92.2%
4dy0B02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.51 38.0 3.73e-01 77.5% 85.9%
3dmqA04 3.40.50.10810 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Tandem AAA-ATPase domain 0.50 40.0 2.98e-01 84.2% 86.8%
3llcA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.50 41.0 3.25e-01 90.0% 85.4%
1rzuB01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.50 43.0 3.44e-01 98.3% 99.6%
2rs7A01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.50 31.0 3.64e-01 82.5% 97.3%
ECOD (41)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5045089 330.2.1.5 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.60 41.0 4.38e-01 88.3% 82.0%
5011932 330.2.1.5 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.59 40.0 4.21e-01 88.3% 78.1%
4476441 7512.1.1.47 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › DUF3417 0.59 45.0 3.21e-01 80.8% 56.9%
5036579 2011.2.1.7 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › PAC2 0.58 50.0 4.00e-01 95.0% 79.6%
3619212 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.58 46.0 3.43e-01 85.0% 36.1%
4960250 330.2.1.5 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.57 39.0 4.21e-01 89.2% 83.0%
3229426 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.57 45.0 3.41e-01 85.0% 36.5%
4995409 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.56 43.0 3.38e-01 80.0% 43.2%
5040123 330.2.1.5 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.56 38.0 4.09e-01 88.3% 82.0%
3583473 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.56 44.0 3.28e-01 85.0% 33.7%
5067357 2011.2.1.7 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › PAC2 0.56 47.0 3.85e-01 95.0% 82.5%
3234839 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.56 44.0 3.29e-01 84.2% 43.3%
4038135 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.56 44.0 3.49e-01 84.2% 46.0%
3957461 316.1.1.5 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › RsfS 0.56 40.0 4.02e-01 80.8% 72.8%
5013768 330.2.1.5 a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) › PF29181 0.55 36.0 3.94e-01 85.0% 82.1%
3580028 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.55 44.0 3.79e-01 85.0% 55.3%
5066424 2011.2.1.7 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › PAC2 0.55 47.0 3.87e-01 95.0% 83.9%
4012024 4121.1.1.0 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.55 39.0 3.01e-01 74.2% 35.7%
5029968 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.55 41.0 3.18e-01 77.5% 38.0%
3627099 2007.2.3.1 a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.55 43.0 3.27e-01 85.0% 36.6%
4929503 316.1.1.18 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › AbiEii 0.54 40.0 3.38e-01 77.5% 85.7%
3451705 331.4.1.2 a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › NAF 0.54 41.0 3.89e-01 78.3% 90.0%
4977218 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.54 39.0 2.84e-01 74.2% 64.9%
5049844 2011.2.1.7 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › PAC2 0.54 46.0 3.69e-01 94.2% 86.5%
4508878 7512.1.1.24 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_5 0.53 48.0 3.69e-01 99.2% 98.9%
3417532 7512.1.1.24 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_5 0.53 48.0 3.67e-01 99.2% 96.4%
3952888 316.1.1.18 a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › AbiEii 0.53 38.0 3.37e-01 73.3% 69.4%
4031082 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.53 39.0 3.11e-01 75.8% 41.3%
3688219 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.52 39.0 3.01e-01 79.2% 37.2%
3663237 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 33.0 3.83e-01 82.5% 93.8%
3953490 7579.1.1.94 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S9, Peptidase_S15 0.52 43.0 3.15e-01 90.8% 62.9%
3873014 246.3.1.4 a+b four layers › Carbon-nitrogen hydrolase-like › DNase I-like › DNase I-like › Exo_endo_phos2 0.52 43.0 3.11e-01 91.7% 82.5%
4928228 2011.2.1.7 a/b three-layered sandwiches › Phosphorylase/hydrolase-like › Peptidyl-tRNA hydrolase-like › Peptidyl-tRNA hydrolase-like › PAC2 0.52 44.0 3.61e-01 95.8% 86.3%
5036880 330.1.1.35 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › LeuA_dimer 0.51 31.0 3.72e-01 81.7% 100.0%
3950217 7579.1.1.3 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Peptidase_S9 0.51 43.0 3.34e-01 94.2% 86.8%
5075340 211.1.1.7 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase_4 0.51 46.0 4.41e-01 99.2% 92.9%
3281953 211.1.1.7 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase_4 0.51 46.0 4.12e-01 98.3% 96.4%
3734737 7579.1.1.36 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_3 0.51 43.0 3.18e-01 92.5% 86.8%
3262164 4121.1.1.1 a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.51 41.0 3.19e-01 97.5% 39.6%
5052861 211.1.1.7 a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase_4 0.51 45.0 4.29e-01 98.3% 97.9%
4562544 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.50 37.0 3.82e-01 78.3% 93.9%
D2 medium residues 2-103
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4tpuA02 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.73 27.0 4.34e-01 77.5% 94.6%
2xseA00 1.20.120.1440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › JBP1, DNA-binding domain 0.71 35.0 2.95e-01 96.1% 30.8%
2mh3A00 4.10.280.10 Few Secondary Structures › Irregular › MYOD Basic-Helix-Loop-Helix Domain, subunit B › Helix-loop-helix DNA-binding domain 0.70 30.0 3.52e-01 77.5% 55.7%
2cqnA00 1.10.10.440 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › FF domain 0.64 31.0 3.51e-01 86.3% 59.7%
3w0fA02 1.10.8.50 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.53 43.0 3.90e-01 90.2% 65.4%
5al9A01 1.10.520.10 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › 0.52 35.0 3.10e-01 88.2% 47.6%
1t11A02 1.10.3120.10 Mainly Alpha › Orthogonal Bundle › Trigger factor, domain 2 › Trigger factor, C-terminal domain 0.50 43.0 3.68e-01 94.1% 87.3%
ECOD (8)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4281576 7101.1.1.1 extended segments › Prp8-binding region of SLU7 › Prp8-binding region of SLU7 › Prp8-binding region of SLU7 › Slu7 0.63 44.0 4.20e-01 74.5% 63.5%
3782805 109.4.1.1136 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_PRP39_N 0.58 51.0 3.76e-01 95.1% 50.8%
3441839 101.1.2.386 alpha arrays › HTH › HTH › winged helix domain › WH_DRP 0.58 29.0 3.28e-01 84.3% 62.2%
3589056 2003.1.2.56 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › NAD_binding_9 0.55 41.0 2.67e-01 92.2% 16.7%
3250372 130.1.2.1 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › ribosome-binding domain of Mdm38 › LETM1_RBD 0.52 45.0 3.74e-01 93.1% 60.6%
4558763 223.2.1.20 a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.51 33.0 3.00e-01 92.2% 48.9%
4359679 376.1.1.37 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › SLX1_C 0.51 27.0 3.17e-01 84.3% 72.9%
3621625 2484.1.1.0 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.50 43.0 3.51e-01 94.1% 80.8%