←Back to structures

MK387337.2__QAU04523.1__Va1_203__00080

Bact-Vir

MK387337.2__QAU04523.1__Va1_203__00080

Identity

Accession:
MK387337 ↗
Kingdom:
phage

Quality

94.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_Va1

TaxID: 2508852

Cluster

View cluster (2 members)

3D Structure

Download PDB Download Scores JSON

Domains

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

D1 medium residues 1-80
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4gouA02 2.30.29.200 Mainly Beta › Roll › PH-domain like › 0.68 55.0 4.35e-01 87.5% 46.8%
5xpyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.64 58.0 5.26e-01 100.0% 82.4%
1vqyB01 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 40.0 3.84e-01 98.8% 63.2%
2hqlA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 40.0 3.87e-01 86.3% 65.9%
3nvnA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.56 40.0 2.63e-01 76.2% 26.1%
4noiA01 3.30.1360.10 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › RNA polymerase, RBP11-like subunit 0.55 40.0 3.75e-01 78.8% 94.2%
3butA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 35.0 2.99e-01 70.0% 93.6%
3abiA02 3.30.360.10 Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › Dihydrodipicolinate Reductase; domain 2 0.51 38.0 3.09e-01 83.7% 49.7%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.51 35.0 2.90e-01 72.5% 53.9%
2bonA02 2.60.200.40 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 44.0 3.68e-01 100.0% 60.4%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.50 38.0 3.22e-01 83.7% 50.3%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3929074 220.1.1.125 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PLEKHM2 0.68 62.0 5.01e-01 100.0% 65.3%
3791785 220.1.1.125 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PLEKHM2 0.66 59.0 4.70e-01 100.0% 62.5%
3494570 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.65 59.0 4.90e-01 100.0% 72.6%
3199454 220.1.1.250 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_25 0.63 55.0 4.81e-01 96.2% 69.2%
3334910 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 53.0 4.64e-01 100.0% 63.2%
3405436 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.61 52.0 4.62e-01 95.0% 99.1%
3937258 220.1.1.159 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_met_RdRP 0.60 53.0 3.99e-01 100.0% 66.3%
3582577 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 50.0 4.31e-01 93.8% 81.5%
3917937 220.1.1.173 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_CERK 0.60 51.0 4.55e-01 96.2% 84.3%
3223396 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 50.0 4.50e-01 95.0% 70.4%
3311131 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.59 50.0 3.90e-01 96.2% 45.9%
4956927 239.1.1.0 ↗ beta barrels › Ribosomal protein L25-like › Ribosomal protein L25-like › Ribosomal protein L25-like 0.59 41.0 3.35e-01 73.8% 54.2%
4943111 327.3.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GMP synthetase C-terminal dimerisation domain › GMP synthetase C-terminal dimerisation domain › GMP_synt_C 0.58 39.0 3.49e-01 70.0% 99.1%
4029464 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 51.0 4.25e-01 100.0% 65.7%
4244646 4263.2.1.1 ↗ a+b two layers › TTHA1528-like › FtsH Periplasmic Domain › FtsH Periplasmic Domain › FtsH_ext 0.57 45.0 4.67e-01 96.2% 93.3%
4938493 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 34.0 3.15e-01 97.5% 47.6%
3590542 235.1.1.10 ↗ a+b complex topology › Lysozyme-like › Lysozyme-like › Lysozyme-like › Glucosaminidase 0.54 39.0 3.15e-01 77.5% 65.6%
5029914 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.53 34.0 3.93e-01 71.2% 94.5%
3507051 327.3.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › GMP synthetase C-terminal dimerisation domain › GMP synthetase C-terminal dimerisation domain › GMP_synt_C 0.53 39.0 3.48e-01 77.5% 99.1%
3678165 304.112.1.1 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain › ArgoL1 0.52 37.0 2.85e-01 73.8% 86.3%
3954736 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.51 39.0 3.08e-01 80.0% 41.2%
3608102 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 35.0 3.75e-01 81.2% 81.4%
3924732 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.51 38.0 2.91e-01 80.0% 84.7%
D2 medium residues 81-151
PDB
Domain cluster: rep: SRR1747046_scaffold_29_prodigal-single.1__X__X__00027__D4-74
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5xpyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.72 67.0 5.70e-01 100.0% 95.4%
4khbC00 2.30.29.210 Mainly Beta › Roll › PH-domain like › FACT complex subunit Spt16p/Cdc68p 0.58 50.0 4.48e-01 100.0% 82.1%
2rrnA01 3.30.70.2040 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 36.0 3.48e-01 100.0% 55.4%
2k3iA01 3.30.70.860 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 40.0 3.83e-01 74.6% 96.5%
3kxyJ00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.57 43.0 3.57e-01 81.7% 63.6%
3natA01 3.40.50.11250 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Protein of unknown function DUF3013 0.56 42.0 3.29e-01 78.9% 95.9%
2wzpR01 2.30.300.20 Mainly Beta › Roll › Phage tail proteins - horseshoe like beta roll fold › Phage tail base-plate attachment protein, domain D1/D2 0.55 41.0 3.00e-01 80.3% 53.6%
3q9oA01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 46.0 3.30e-01 100.0% 51.9%
6f1uK02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.53 41.0 3.23e-01 83.1% 67.6%
2a74A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.52 39.0 3.42e-01 78.9% 93.3%
3anzC00 2.70.240.10 Mainly Beta › Distorted Sandwich › Leukocidin-like › Leukocidin/porin MspA 0.52 42.0 2.80e-01 87.3% 91.2%
1ye9A02 2.40.470.10 Mainly Beta › Beta Barrel › catalase hpii fold › catalase hpii domain 0.52 39.0 3.40e-01 81.7% 67.9%
5odnC00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 40.0 3.59e-01 95.8% 59.8%
3gp6A00 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.51 42.0 3.26e-01 90.1% 83.2%
5cyxA03 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.51 39.0 3.42e-01 83.1% 92.7%
2f7sA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 39.0 2.94e-01 83.1% 93.3%
3aa0B02 3.90.1150.210 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › F-actin capping protein, beta subunit 0.51 39.0 3.07e-01 83.1% 71.0%
1fuiA03 3.20.14.10 Alpha Beta › Alpha-Beta Barrel › L-fucose Isomerase; Chain A, domain 3 › L-fucose/L-arabinose isomerase, C-terminal 0.51 40.0 2.86e-01 90.1% 67.7%
2jxpA01 3.30.160.150 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Lipoprotein like domain 0.50 37.0 3.01e-01 80.3% 70.9%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3494570 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.71 65.0 5.16e-01 100.0% 94.1%
3261701 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.68 60.0 5.29e-01 98.6% 91.4%
3297150 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.67 60.0 5.37e-01 100.0% 95.0%
3254845 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.64 57.0 4.69e-01 100.0% 88.5%
3803797 220.1.1.181 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_ULP 0.64 57.0 4.81e-01 100.0% 88.3%
3423400 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.62 55.0 4.59e-01 100.0% 84.0%
3601670 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.59 42.0 2.75e-01 77.5% 23.5%
5011691 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 44.0 3.69e-01 78.9% 99.1%
1124159 1.1.13.18 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins › Caud_bapl16_1st 0.55 41.0 3.56e-01 80.3% 95.5%
3716709 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.55 46.0 3.86e-01 94.4% 85.4%
3174953 69.1.1.2 ↗ beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hom_end_hint 0.54 42.0 2.96e-01 83.1% 27.9%
5055184 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.54 40.0 3.86e-01 87.3% 67.1%
3222402 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.54 43.0 3.02e-01 84.5% 45.9%
3543052 11.1.1.284 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PKD_4 0.53 40.0 3.42e-01 78.9% 92.7%
3990038 304.136.1.1 ↗ a+b two layers › Alpha-beta plaits › Oligo-peptide binding protein (OPPA) insertion domain › Oligo-peptide binding protein (OPPA) insertion domain › SBP_bac_5 0.53 45.0 3.51e-01 93.0% 86.0%
3774553 223.2.1.22 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Folliculin 0.53 46.0 3.15e-01 97.2% 46.9%
3941659 11.1.1.10 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PapD_N 0.53 39.0 3.23e-01 78.9% 92.3%
4023765 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.53 43.0 3.23e-01 98.6% 90.8%
4643232 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.52 39.0 3.33e-01 87.3% 95.6%
5079051 512.1.1.2 ↗ a+b two layers › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › a+b domain in putative modulator of DNA gyrase, PmbA/TldD (Pfam 01523) › PmbA_TldD_2nd 0.52 40.0 3.36e-01 83.1% 66.7%
3610137 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.52 46.0 2.78e-01 100.0% 50.3%
5025916 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 44.0 3.51e-01 95.8% 58.6%
3909125 11.1.1.640 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ZP-N 0.52 39.0 3.19e-01 80.3% 93.8%
3770448 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.51 42.0 3.20e-01 90.1% 85.3%
None — 0.51 41.0 3.46e-01 97.2% 50.0%
3600840 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.51 42.0 3.81e-01 91.5% 81.0%
1758564 69.1.1.2 ↗ beta complex topology › Hedgehog/intein › Hedgehog/intein › Hint › Hom_end_hint 0.51 41.0 3.07e-01 87.3% 40.2%
3995685 2.1.1.6 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SSB 0.50 42.0 3.76e-01 97.2% 96.3%
4944741 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.50 43.0 3.49e-01 97.2% 78.6%
3928388 633.33.1.1 ↗ alpha bundles › Bromodomain-like › Rogdi › Rogdi › Rogdi_lz 0.50 32.0 2.31e-01 74.6% 20.9%
3215667 2.1.1.6 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SSB 0.50 43.0 3.66e-01 97.2% 89.2%
4944821 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.50 37.0 3.95e-01 84.5% 96.7%
3629780 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.50 41.0 2.58e-01 88.7% 50.8%