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OP068333.1__UVG34062.1__SEA_PAVLO_5__00005

Bact-Vir

OP068333.1__UVG34062.1__SEA_PAVLO_5__00005

Identity

Accession:
OP068333 ↗
Kingdom:
phage

Quality

84.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Microbacterium_phage_Pavlo

TaxID: 2927263

Cluster

Singleton — not in a non-trivial cluster

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 high residues 3-78
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4p4tA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.71 51.0 3.33e-01 100.0% 17.3%
2bbhA01 3.30.460.20 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › CorA soluble domain-like 0.69 40.0 3.21e-01 92.1% 29.1%
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.65 44.0 4.21e-01 73.7% 58.7%
1a0iA01 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.63 45.0 4.37e-01 100.0% 67.5%
4iajA00 3.30.1490.390 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Protein of unknown function DUF4649 0.63 42.0 4.21e-01 77.6% 68.4%
3h20A01 3.30.1490.240 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › RepB DNA-primase, N-terminal domain 0.62 45.0 4.78e-01 100.0% 87.9%
2xf1A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.58 40.0 3.42e-01 88.2% 44.3%
4n0rA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 37.0 3.55e-01 77.6% 56.5%
1r9fA01 3.30.390.180 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › RNA silencing suppressor P19 0.58 45.0 4.06e-01 86.8% 67.9%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.57 40.0 3.71e-01 75.0% 57.9%
4r3aA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.57 39.0 3.07e-01 72.4% 93.8%
2r7kA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.56 39.0 4.28e-01 98.7% 90.2%
2kl5A00 3.50.4.20 Alpha Beta › 3-Layer(bba) Sandwich › Hepatocyte Growth Factor › Uncharacterised protein DUF1027 0.56 50.0 4.43e-01 98.7% 81.8%
4ehoB03 3.30.450.270 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain 0.56 41.0 3.24e-01 81.6% 53.6%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.56 45.0 3.61e-01 89.5% 50.0%
3to8A02 3.30.70.330 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain 0.55 48.0 4.51e-01 100.0% 90.6%
2hg6A00 3.90.1650.10 Alpha Beta › Alpha-Beta Complex › PA1123-like › PA1123-like 0.54 33.0 3.02e-01 88.2% 42.5%
4h32A02 3.90.209.20 Alpha Beta › Alpha-Beta Complex › Hemagglutinin (Ha1 Chain); Chain: A; domain 1 › Haemagglutinin, alpha/beta domain, HA1 chain 0.54 47.0 3.36e-01 96.1% 82.7%
6x5vA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 37.0 3.48e-01 100.0% 57.3%
4jf6A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.51 40.0 2.92e-01 88.2% 62.8%
1txoB00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.51 43.0 3.18e-01 100.0% 97.5%
3na2A00 3.40.1570.20 Alpha Beta › 3-Layer(aba) Sandwich › Heme iron utilization protein-like fold › 0.51 39.0 3.27e-01 97.4% 46.4%
1b04A02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.50 45.0 4.13e-01 100.0% 77.8%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.50 37.0 3.46e-01 100.0% 62.5%
3lsoA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 35.0 3.35e-01 100.0% 60.9%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3414064 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.70 40.0 4.53e-01 76.3% 76.4%
3388590 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.69 38.0 4.26e-01 75.0% 68.3%
3363778 390.1.1.0 ↗ few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.69 41.0 4.75e-01 96.1% 83.6%
4399545 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.65 48.0 4.29e-01 77.6% 99.0%
3859590 386.1.1.248 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_ZNF592 0.64 38.0 4.51e-01 76.3% 90.0%
4228966 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.64 48.0 4.23e-01 78.9% 96.4%
3376944 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.62 46.0 4.13e-01 77.6% 86.7%
3390573 379.1.1.0 ↗ few secondary structure elements › Kazal-type serine protease inhibitors-like › Kazal-type serine protease inhibitors › Kazal-type serine protease inhibitors 0.62 38.0 4.24e-01 76.3% 79.7%
5008812 264.2.1.0 ↗ beta barrels › LigT-like › Prokaryotic type I DNA topoisomerase beta-barrel domain › Prokaryotic type I DNA topoisomerase beta-barrel domain 0.62 47.0 4.25e-01 81.6% 96.2%
3724523 4121.1.1.7 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › PF26616 0.61 44.0 2.90e-01 77.6% 17.5%
5082182 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.60 43.0 4.05e-01 76.3% 98.9%
3701082 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.60 44.0 3.54e-01 77.6% 45.8%
3615055 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.59 44.0 3.56e-01 77.6% 46.8%
3666673 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 42.0 4.31e-01 77.6% 86.7%
3696767 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.59 43.0 2.70e-01 77.6% 15.5%
4935672 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.57 44.0 3.61e-01 82.9% 53.6%
3624909 382.1.1.0 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.57 44.0 3.82e-01 82.9% 81.7%
119217 3085.1.1.1 ↗ a+b complex topology › Uncharacterized protein yutD › Uncharacterized protein yutD › Uncharacterized protein yutD › YutD-like 0.56 50.0 4.43e-01 98.7% 81.8%
3520955 2006.1.3.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › Toprim domain › DNA_gyraseB_C,Toprim 0.56 48.0 3.24e-01 92.1% 55.8%
4954188 2492.1.1.7 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › FdhD-NarQ 0.55 42.0 3.42e-01 82.9% 50.3%
5029977 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.55 41.0 2.75e-01 81.6% 36.3%
3962617 4081.1.1.2 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.55 38.0 2.89e-01 100.0% 27.3%
4970236 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.55 43.0 3.42e-01 86.8% 71.9%
3738582 11.1.1.598 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › RSC4_Ig_like 0.54 35.0 2.85e-01 78.9% 33.3%
3272161 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 37.0 3.59e-01 80.3% 63.5%
3231588 382.1.1.6 ↗ few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › QVR 0.54 41.0 4.19e-01 80.3% 93.2%
3936863 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 40.0 2.89e-01 81.6% 42.0%
4028848 210.2.1.1 ↗ a+b four layers › Ntn/PP2C › Protein serine/threonine phosphatase 2C, catalytic domain › Protein serine/threonine phosphatase 2C, catalytic domain › PP2C 0.53 43.0 2.98e-01 93.4% 48.2%
3333061 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.53 43.0 2.59e-01 90.8% 21.1%
3495764 4081.1.1.2 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.53 38.0 2.97e-01 100.0% 31.9%
3371469 109.4.1.3022 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif, TPR_24 0.53 43.0 2.58e-01 92.1% 25.7%
3696190 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.53 45.0 3.93e-01 98.7% 93.3%
3302114 109.4.1.619 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DYW_deaminase 0.52 40.0 3.29e-01 81.6% 69.6%
3837823 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.52 42.0 2.47e-01 88.2% 56.9%
3437063 109.4.1.3183 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, DYW_deaminase, PPR_long, Eplus_motif, E_motif 0.52 43.0 2.83e-01 94.7% 44.1%
3704468 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 39.0 3.55e-01 98.7% 58.2%
3761694 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.52 44.0 4.16e-01 98.7% 90.5%
3811561 109.4.1.1267 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, E_motif 0.52 43.0 2.52e-01 94.7% 20.7%
3365334 109.4.1.1521 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif, E_motif 0.52 43.0 2.53e-01 92.1% 18.3%
3322777 109.4.1.1738 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.52 43.0 2.80e-01 94.7% 42.7%
3875549 4081.1.1.2 ↗ beta sandwiches › Baculovirus p35 protein-related › Baculovirus p35 protein-related › Baculovirus p35 protein-related › VIT 0.51 36.0 2.83e-01 100.0% 29.7%
3383616 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.51 42.0 2.50e-01 93.4% 20.0%
5027634 10.12.1.39 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_2 0.51 39.0 3.60e-01 100.0% 63.0%
3335541 109.4.1.2173 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, DYW_deaminase, Eplus_motif 0.51 42.0 2.81e-01 94.7% 51.9%
3624465 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.50 42.0 3.93e-01 98.7% 95.0%
1003912 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.50 37.0 3.46e-01 100.0% 62.5%
D2 high residues 85-160
PDB
Domain cluster: rep: MZ605292.1__QYW06422.1__uan_010__00010__D3-93
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3r96B00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 34.0 2.68e-01 100.0% 26.0%