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NC_070888.1__YP_010662546.1__PP939_gp138__00138

Bact-Vir

NC_070888.1__YP_010662546.1__PP939_gp138__00138

Identity

Accession:
NC_070888 ↗
Kingdom:
phage

Quality

78.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Pootjesviridae› Innesvirus› Rhizobium_phage_RL38J1

TaxID: 2663232

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 3-77
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1qysA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.76 64.0 5.99e-01 92.0% 78.3%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.74 61.0 5.68e-01 90.7% 75.5%
4kyzA00 3.30.70.600 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S10 0.69 57.0 4.45e-01 92.0% 43.1%
2hzmG01 3.30.310.180 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › 0.66 45.0 3.91e-01 70.7% 89.6%
3h4rA00 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.65 57.0 4.16e-01 100.0% 57.1%
4ktwA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.64 52.0 4.13e-01 90.7% 55.0%
5hn3A00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.64 51.0 3.35e-01 88.0% 27.4%
2i8eA01 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.61 41.0 4.18e-01 70.7% 95.9%
2kgfA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.61 46.0 3.84e-01 84.0% 92.9%
3nyiB01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 49.0 3.90e-01 92.0% 66.9%
3b8fB00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.59 49.0 3.97e-01 90.7% 52.8%
3ihlB00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 45.0 3.28e-01 85.3% 69.9%
5wm1A02 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.58 45.0 4.11e-01 89.3% 94.5%
2zgyA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 47.0 3.65e-01 94.7% 71.1%
1g6gB00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.57 39.0 3.42e-01 73.3% 100.0%
1yhpA02 2.60.40.1720 Mainly Beta › Sandwich › Immunoglobulin-like › Calcium-dependent cell adhesion molecule-1 0.54 44.0 3.82e-01 90.7% 73.3%
2o3iA01 3.40.1610.10 Alpha Beta › 3-Layer(aba) Sandwich › CV3147-like fold › CV3147-like domain 0.54 47.0 3.33e-01 98.7% 58.9%
3cw3A00 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.52 44.0 4.14e-01 94.7% 94.6%
3tg9A00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 40.0 2.77e-01 89.3% 77.3%
4m0wA03 2.60.120.1680 Mainly Beta › Sandwich › Jelly Rolls › 0.52 40.0 3.32e-01 84.0% 47.4%
6gszA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 40.0 3.65e-01 90.7% 61.8%
2f4pA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.52 45.0 3.80e-01 100.0% 56.0%
2i44B00 3.60.40.10 Alpha Beta › 4-Layer Sandwich › Phosphatase 2c; domain 1 › PPM-type phosphatase domain 0.52 40.0 2.76e-01 88.0% 64.2%
6jptA00 3.30.230.90 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 33.0 2.90e-01 74.7% 41.3%
6z9cA01 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.51 39.0 3.42e-01 85.3% 59.0%
5hdwA00 2.60.40.1470 Mainly Beta › Sandwich › Immunoglobulin-like › ApaG domain 0.51 40.0 3.35e-01 85.3% 55.7%
3k85A00 3.30.230.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.51 41.0 2.83e-01 92.0% 49.3%
3uv0B00 2.60.200.20 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.51 37.0 3.40e-01 86.7% 58.6%
1eerC01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 40.0 3.70e-01 92.0% 68.0%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3440477 2484.1.1.15 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › GDA1_CD39 0.66 45.0 4.21e-01 72.0% 66.3%
1718755 2007.1.2.11 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › Peripla_BP_4 0.63 44.0 4.17e-01 82.7% 60.4%
3320228 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.63 51.0 3.02e-01 90.7% 17.7%
3648991 2492.1.1.39 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › DYW_deaminase 0.61 50.0 4.21e-01 92.0% 78.5%
None — 0.60 50.0 4.15e-01 93.3% 78.3%
3874464 304.48.1.1 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.58 47.0 3.02e-01 88.0% 59.7%
3652038 2484.1.1.67 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › RVT_3 0.57 46.0 4.46e-01 89.3% 90.6%
1323408 3901.1.1.1 ↗ a+b complex topology › Hypothetical protein lpg2422 after-hydrolase domain › Hypothetical protein lpg2422 after-hydrolase domain › Hypothetical protein lpg2422 after-hydrolase domain › DUF5621 0.57 43.0 3.44e-01 81.3% 78.6%
3611587 4342.1.1.0 ↗ alpha complex topology › Tex N-terminal region-like › Tex N-terminal region-like › Tex N-terminal region-like 0.56 47.0 3.52e-01 100.0% 53.2%
3475431 133.1.1.0 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) 0.55 46.0 3.34e-01 97.3% 86.3%
4018289 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.54 45.0 3.70e-01 94.7% 75.9%
10975 4176.1.1.2 ↗ a/b three-layered sandwiches › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › a/b domain in CV3147-like proteins › S-Me-THD_N 0.54 47.0 3.33e-01 98.7% 58.6%
4968356 11.1.1.284 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PKD_4 0.54 39.0 3.37e-01 76.0% 53.0%
4940035 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 38.0 3.39e-01 74.7% 86.4%
4486829 3662.1.1.4 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC_bac 0.53 35.0 3.09e-01 70.7% 92.8%
3778103 386.1.1.281 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › PF27082 0.53 38.0 4.06e-01 100.0% 92.3%
3620045 883.1.1.6 ↗ a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1_N 0.52 37.0 3.00e-01 74.7% 67.7%
4997210 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.52 38.0 3.69e-01 81.3% 97.8%
3676777 212.1.1.12 ↗ a+b two layers › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › Ribosomal protein S5 domain 2-like › UPF0029 0.51 37.0 3.15e-01 81.3% 43.7%
4996589 3662.1.1.4 ↗ a+b two layers › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › Proteasome assembling chaperone 3 (PAC3)-related › PAC_bac 0.51 36.0 3.15e-01 76.0% 91.7%