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ORF56

Euk-Vir

Retroperitoneal_fibromatosis-associated_herpesvirus

ORF56__YP_010084419__Retroperitoneal_fibromatosis-associated_herpesvirus__111469

Identity

Accession:
YP_010084419 ↗
Protein ID:
ORF56
Kingdom:
euk

Quality

87.9 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Rhadinovirus› Retroperitoneal_fibromatosis-associated_herpesvirus

TaxID: 111469

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 487-694
PDB
Domain cluster: rep: primase__YP_009345453__Noumeavirus__1955558__D12-194
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2f5gA00 3.30.70.1290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Transposase IS200-like 0.69 37.0 4.65e-01 94.7% 83.8%
3h20A02 3.30.70.1790 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RepB DNA-primase, N-terminal domain 0.67 35.0 4.73e-01 91.3% 98.1%
4j37A01 3.30.70.580 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Pseudouridine synthase I, catalytic domain, N-terminal subdomain 0.65 34.0 4.56e-01 91.8% 95.4%
4fprB00 3.30.70.2910 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 38.0 4.77e-01 95.2% 94.5%
3qjlA01 3.30.70.1890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 37.0 4.68e-01 87.5% 100.0%
3i4hX01 3.30.70.1890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 39.0 4.73e-01 90.9% 100.0%
4c98A01 3.30.70.1890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.62 32.0 4.37e-01 93.3% 98.1%
1pbuA00 3.30.70.1010 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Translation elongation factor EF1B, gamma chain, conserved domain 0.61 38.0 4.24e-01 80.8% 78.4%
2yq1C00 3.30.70.390 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Epstein Barr virus nuclear antigen-1, DNA-binding domain 0.61 30.0 3.72e-01 87.5% 73.3%
2f7vA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.59 32.0 4.26e-01 95.2% 100.0%
3gnnA01 3.90.1170.20 Alpha Beta › Alpha-Beta Complex › Aldehyde Oxidoreductase; domain 3 › Quinolinate phosphoribosyl transferase, N-terminal domain 0.58 31.0 3.69e-01 90.9% 74.6%
3pfeA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 36.0 4.37e-01 89.9% 100.0%
1rjjA00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 30.0 3.91e-01 91.8% 92.8%
4wiqA02 3.30.70.1040 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dystroglycan, domain 2 0.56 33.0 4.15e-01 87.0% 96.0%
1t0tV02 3.30.70.1030 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Apc35880; domain 1 0.55 29.0 3.77e-01 91.8% 91.0%
3znuA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.55 27.0 3.80e-01 92.8% 100.0%
1tvgA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.54 25.0 2.99e-01 97.1% 61.8%
1ybtB00 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.54 36.0 3.91e-01 100.0% 80.2%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.51 27.0 3.58e-01 93.3% 93.7%
4jb9H01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 30.0 3.66e-01 98.6% 92.4%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3719042 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.81 63.0 6.07e-01 99.0% 71.7%
3608399 862.1.1.7 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › PPL5 0.81 63.0 6.02e-01 99.5% 70.6%
3677440 862.1.1.11 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › AEP_C962R 0.77 65.0 6.09e-01 99.0% 73.9%
4673704 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.77 63.0 5.65e-01 99.5% 63.6%
4001493 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.76 62.0 5.87e-01 97.1% 72.5%
3626314 862.1.1.11 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › AEP_C962R 0.76 62.0 5.82e-01 98.1% 70.4%
3512046 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.75 64.0 5.96e-01 99.0% 72.5%
3802060 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.75 65.0 6.06e-01 100.0% 74.1%
3937694 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.73 64.0 5.88e-01 100.0% 72.5%
3715696 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.69 64.0 5.69e-01 98.6% 71.9%
3492512 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.66 62.0 5.30e-01 100.0% 70.0%
4967179 304.51.1.13 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas6_I-A 0.64 37.0 4.76e-01 89.9% 100.0%
5004227 862.1.1.0 ↗ a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.64 45.0 4.24e-01 100.0% 59.6%
3735316 304.9.1.1 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_1 0.62 31.0 3.50e-01 100.0% 61.3%
4984501 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 0.61 38.0 4.67e-01 90.9% 100.0%
4971629 304.51.1.9 ↗ a+b two layers › Alpha-beta plaits › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › CRISPR transcript (pre-crRNA) processing endoribonuclease-related › Cas6_N 0.61 37.0 4.65e-01 90.9% 100.0%
3730399 304.43.1.0 ↗ a+b two layers › Alpha-beta plaits › Hypothetical protein TT1725 › Hypothetical protein TT1725 0.61 38.0 4.66e-01 91.3% 97.7%
3180157 304.4.1.0 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.61 39.0 4.73e-01 91.8% 97.8%
3786175 304.46.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain › EF1G 0.60 38.0 4.19e-01 80.3% 78.5%
3487626 304.47.1.0 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain 0.59 39.0 4.73e-01 90.4% 100.0%
3187975 304.112.1.3 ↗ a+b two layers › Alpha-beta plaits › Argonaute, N-terminal domain › Argonaute, N-terminal domain › ArgoN 0.58 29.0 3.98e-01 91.8% 98.0%
4994692 304.44.1.1 ↗ a+b two layers › Alpha-beta plaits › Ribosomal protein S10 › Ribosomal protein S10 › Ribosomal_S10 0.57 31.0 4.04e-01 91.3% 96.4%
356037 304.4.1.13 ↗ a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › SOR 0.57 36.0 4.12e-01 89.9% 85.9%
3181858 304.20.1.0 ↗ a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain 0.57 40.0 4.52e-01 70.7% 95.5%
3924928 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 28.0 3.80e-01 98.6% 91.4%
4965450 304.25.1.1 ↗ a+b two layers › Alpha-beta plaits › Bacterial exopeptidase dimerisation domain › Bacterial exopeptidase dimerisation domain › M20_dimer 0.56 31.0 4.09e-01 96.6% 100.0%
3236985 390.1.1.0 ↗ few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.56 23.0 3.39e-01 79.8% 85.6%
4187036 306.7.1.0 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain 0.55 28.0 3.82e-01 95.7% 93.6%
3273461 304.46.1.1 ↗ a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain › EF1G 0.55 40.0 4.43e-01 85.1% 95.6%
3990209 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.54 25.0 3.37e-01 96.6% 84.8%
3538462 11.1.1.385 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ASH 0.54 26.0 3.24e-01 98.1% 74.8%
3406520 390.1.1.1 ↗ few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like › PAN_1 0.53 25.0 3.21e-01 79.8% 76.5%
3575333 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.53 26.0 2.52e-01 98.1% 38.4%
3589587 886.1.1.2 ↗ a+b duplicates or obligate multimers › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › Probable bacterial effector-binding domain › GyrI-like 0.52 43.0 4.45e-01 87.0% 95.5%
4962205 302.4.1.0 ↗ a+b two layers › Reverse ferredoxin › a+b domain in Acetophenone carboxylase (Apc) alpha subunit › a+b domain in Acetophenone carboxylase (Apc) alpha subunit 0.51 29.0 3.85e-01 91.8% 100.0%
4996591 309.1.2.2 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_bind_4 0.50 36.0 3.91e-01 97.6% 87.4%
D2 high residues 709-833
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 91.3 3.90e-26 60.0% 97.3%
D3 medium residues 1-154
PDB
Domain cluster: rep: helicase-primase_primase_subunit__YP_010085930__Wood_mouse_herpesvirus__432370__D12-162
D4 medium residues 155-249
PDB
Domain cluster: rep: helicase-primase_primase_subunit__YP_401662__Human_gammaherpesvirus_4__10376__D153-223
D5 medium residues 250-340_695-708
PDB
Domain cluster: rep: ORF56__YP_001129409__Human_gammaherpesvirus_8__37296__D254-341
D6 medium residues 341-486
PDB
Domain cluster: rep: helicase-primase_primase_subunit__YP_182338__Gallid_alphaherpesvirus_1__10386__D431-468_522-592_634-660