←Back to structures

DNA_replication_protein

Euk-Vir

Cricetid_gammaherpesvirus_2

DNA_replication_protein__YP_004207892__Cricetid_gammaherpesvirus_2__1605972

Identity

Accession:
YP_004207892 ↗
Protein ID:
DNA_replication_protein
Kingdom:
euk

Quality

89.1 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Rhadinovirus› Cricetid_gammaherpesvirus_2

TaxID: 1605972

Cluster

View cluster (58 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 high residues 486-674
PDB
Domain cluster: rep: primase__YP_009345453__Noumeavirus__1955558__D12-194
D2 high residues 698-824
PDB
Domain cluster: rep: helicase-primase_primase_subunit__NP_944382__Psittacid_alphaherpesvirus_1__50294__D1138-1286
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03121.21 best Herpes_UL52 64.3 1.00e-17 59.1% 97.3%
D3 medium residues 1-152
PDB
Domain cluster: rep: helicase-primase_primase_subunit__YP_010085930__Wood_mouse_herpesvirus__432370__D12-162
D4 medium residues 153-226
PDB
Domain cluster: rep: helicase-primase_primase_subunit__YP_401662__Human_gammaherpesvirus_4__10376__D153-223
D5 medium residues 227-285
PDB
Domain cluster: rep: E70__YP_007016467__Murid_betaherpesvirus_8__1261657__D218-274
D6 medium residues 340-427
PDB
Domain cluster: rep: ORF56__YP_001129409__Human_gammaherpesvirus_8__37296__D349-421
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1dq3A04 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.71 39.0 3.58e-01 93.2% 41.2%
2lrrA00 3.30.1370.50 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain 0.70 37.0 4.11e-01 89.8% 64.3%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.64 41.0 4.01e-01 93.2% 60.0%
3pxpA02 3.30.450.180 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.60 50.0 3.86e-01 90.9% 77.4%
5axgA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.59 34.0 3.06e-01 92.0% 40.5%
4e1oA03 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.58 40.0 3.91e-01 71.6% 89.8%
4hh2B03 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.56 47.0 4.52e-01 90.9% 96.0%
3wnkA04 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.55 32.0 2.85e-01 94.3% 39.2%
1d06A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.55 46.0 4.07e-01 92.0% 80.8%
1r62A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.55 38.0 3.30e-01 71.6% 96.3%
1s67L00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 45.0 4.11e-01 92.0% 87.4%
2qsrA01 3.90.1150.50 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Transcription-repair-coupling factor, D7 domain 0.54 37.0 3.16e-01 71.6% 90.3%
2anrA02 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.54 33.0 3.50e-01 94.3% 70.7%
4r3aA02 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.53 36.0 3.03e-01 93.2% 43.0%
4za1C00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.53 33.0 3.26e-01 94.3% 58.7%
6dw1A00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.53 40.0 2.99e-01 93.2% 33.3%
3hunA01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.52 37.0 2.62e-01 73.9% 48.6%
2q14A02 1.20.1250.30 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.52 39.0 3.18e-01 98.9% 42.8%
2wdoA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.52 42.0 3.88e-01 94.3% 96.7%
2y8yA01 3.30.70.1200 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Crispr-associated protein; domain 1 0.51 35.0 3.57e-01 93.2% 72.1%
1vs3A02 3.30.70.660 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Pseudouridine synthase I, catalytic domain, C-terminal subdomain 0.51 43.0 3.69e-01 94.3% 58.3%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4993483 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.70 38.0 3.64e-01 93.2% 44.8%
4113237 242.1.1.7 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_3 0.70 39.0 3.79e-01 93.2% 49.5%
4931923 304.5.1.7 ↗ a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 0.69 36.0 3.79e-01 93.2% 53.8%
3972097 304.14.1.0 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) 0.69 36.0 3.92e-01 94.3% 60.0%
3552466 320.1.1.1 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.67 35.0 3.93e-01 89.8% 64.3%
4993850 242.1.1.0 ↗ a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.64 37.0 3.61e-01 94.3% 51.6%
3386674 304.14.1.1 ↗ a+b two layers › Alpha-beta plaits › Sporulation related repeat (SPOR) › Sporulation related repeat (SPOR) › SPOR 0.62 35.0 3.82e-01 97.7% 66.7%
3407270 327.11.2.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.60 36.0 3.88e-01 94.3% 69.3%
3357806 320.1.1.1 ↗ a+b two layers › R3H domain-like › R3H domain › R3H domain › R3H 0.59 32.0 3.61e-01 90.9% 67.7%
4981204 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 42.0 4.24e-01 92.0% 74.2%
5046055 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.57 47.0 4.29e-01 92.0% 87.5%
5007983 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.57 48.0 4.31e-01 92.0% 83.3%
5010582 310.3.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.57 34.0 3.27e-01 93.2% 51.0%
4989318 328.8.1.1 ↗ a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2 0.55 38.0 3.42e-01 95.5% 49.2%
5006311 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.55 45.0 4.07e-01 92.0% 80.0%
4989528 223.1.1.25 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_9 0.54 45.0 4.11e-01 92.0% 76.5%
5004330 328.8.1.1 ↗ a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2 0.53 36.0 3.29e-01 94.3% 50.8%
4937824 328.8.1.1 ↗ a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2 0.53 40.0 3.45e-01 95.5% 50.3%
4168395 3019.1.1.1 ↗ beta sandwiches › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › gp11/flagellar cap protein FliD insertion domain › Flagellin_IN 0.52 43.0 3.94e-01 93.2% 71.7%
3875198 11.1.1.108 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_2 0.52 29.0 2.76e-01 94.3% 41.8%
4279545 306.9.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › MecA substrate binding domain › MecA substrate binding domain › MecA 0.51 39.0 4.04e-01 92.0% 91.3%
3716228 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.51 38.0 3.29e-01 78.4% 71.4%
3165390 304.24.1.36 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › SPOR 0.51 37.0 3.86e-01 98.9% 83.7%
3283806 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.51 36.0 3.14e-01 73.9% 89.3%
3460420 304.51.1.0 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related 0.50 37.0 3.55e-01 78.4% 91.4%
D7 medium residues 436-485
PDB
Domain cluster: rep: ORF56__YP_001129409__Human_gammaherpesvirus_8__37296__D437-488