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ORF56

Euk-Vir

Macaca_nemestrina_rhadinovirus_2

ORF56__YP_010084604__Macaca_nemestrina_rhadinovirus_2__123630

Identity

Accession:: YP_010084604 ↗
Protein ID:: ORF56
Kingdom:: euk

Quality

83.0 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Rhadinovirus› Macaca_nemestrina_rhadinovirus_2

TaxID: 123630

Cluster

View cluster (58 members)

3D Structure

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Domains

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

D1 high residues 716-835

PDB

Domain cluster: rep: helicase-primase_primase_subunit__NP_944382__Psittacid_alphaherpesvirus_1__50294__D1138-1286

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03121.21 best	Herpes_UL52	95.4	2.10e-27	62.5%	97.3%

D2 medium residues 12-123_139-160

PDB

Domain cluster: rep: helicase-primase_primase_subunit__YP_010085930__Wood_mouse_herpesvirus__432370__D12-162

D3 medium residues 161-249

PDB

Domain cluster: rep: helicase-primase_primase_subunit__YP_401662__Human_gammaherpesvirus_4__10376__D153-223

D4 medium residues 250-337

PDB

Domain cluster: rep: ORF56__YP_001129409__Human_gammaherpesvirus_8__37296__D254-341

D5 medium residues 338-435

PDB

Domain cluster: representative

CATH (16)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1dq3A04	3.10.28.10	Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases	0.68	35.0	3.36e-01	81.6%	42.1%
7qssA01	3.10.28.10	Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases	0.67	35.0	2.83e-01	81.6%	26.1%
3k6hA01	3.40.109.10	Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase	0.61	42.0	3.55e-01	70.4%	76.0%
3gkuA03	3.30.1370.50	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain	0.60	31.0	3.53e-01	79.6%	66.2%
3pxpA02	3.30.450.180	Alpha Beta › 2-Layer Sandwich › Beta-Lactamase ›	0.60	44.0	3.54e-01	78.6%	77.4%
4hh2B03	3.30.450.20	Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain	0.58	43.0	4.33e-01	78.6%	96.0%
1d06A00	3.30.450.20	Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain	0.57	43.0	3.96e-01	79.6%	80.8%
2pt7G02	3.30.1370.180	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 ›	0.57	29.0	3.37e-01	78.6%	67.2%
2anrA02	3.30.1370.10	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1	0.56	32.0	3.57e-01	83.7%	70.7%
5axgA03	2.60.40.1180	Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II	0.56	31.0	2.87e-01	80.6%	41.3%
1s67L00	3.30.450.20	Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain	0.55	42.0	3.99e-01	80.6%	89.1%
2lrrA00	3.30.1370.50	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › R3H-like domain	0.54	28.0	3.23e-01	81.6%	67.1%
3hheA02	3.30.70.260	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain	0.52	31.0	3.43e-01	82.7%	74.4%
2nqcA00	2.60.40.10	Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins	0.51	27.0	2.78e-01	82.7%	47.4%
1yk3B00	3.40.630.30	Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT)	0.51	36.0	3.01e-01	75.5%	66.3%
4ofkB00	2.60.40.10	Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins	0.50	27.0	2.72e-01	81.6%	46.2%

ECOD (14)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3454258	320.1.1.0 ↗	a+b two layers › R3H domain-like › R3H domain › R3H domain	0.66	32.0	3.50e-01	77.6%	55.3%
4993850	242.1.1.0 ↗	a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases	0.64	34.0	3.54e-01	83.7%	52.6%
4580823	242.1.1.2 ↗	a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2	0.61	33.0	3.07e-01	80.6%	40.0%
4128067	242.1.1.5 ↗	a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N	0.61	34.0	3.34e-01	83.7%	49.1%
4155057	242.1.1.2 ↗	a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2	0.61	32.0	3.31e-01	80.6%	50.5%
5041289	2484.1.1.22 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF99	0.60	38.0	3.11e-01	84.7%	34.4%
4291325	306.9.1.1 ↗	a+b two layers › Glucose permease domain IIB-like › MecA substrate binding domain › MecA substrate binding domain › MecA	0.58	40.0	4.39e-01	81.6%	88.7%
5004445	328.8.1.1 ↗	a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2	0.57	36.0	3.23e-01	82.7%	46.7%
4969882	328.8.1.0 ↗	a+b two layers › IF3-like › Schlafen 8 › Schlafen 8	0.57	37.0	3.36e-01	84.7%	49.2%
4981204	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.56	38.0	3.97e-01	79.6%	76.4%
5004330	328.8.1.1 ↗	a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2	0.55	34.0	3.26e-01	82.7%	50.8%
3989900	213.1.1.1 ↗	a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_1	0.53	38.0	3.29e-01	75.5%	69.4%
4937824	328.8.1.1 ↗	a+b two layers › IF3-like › Schlafen 8 › Schlafen 8 › SLFN_AlbA_2	0.52	38.0	3.38e-01	83.7%	52.4%
4361067	301.8.1.1 ↗	a+b three layers › Bacillus chorismate mutase-like › 4'-phosphopantetheinyl transferase › 4'-phosphopantetheinyl transferase › ACPS	0.51	40.0	3.72e-01	83.7%	99.2%

D6 medium residues 468-503_556-578_628-650

PDB

Domain cluster: rep: helicase-primase_primase_subunit__YP_009118446__Equid_gammaherpesvirus_5__10371__D515-537_680-714

D7 medium residues 504-555_579-627_651-696

PDB

Domain cluster: rep: primase__YP_009345453__Noumeavirus__1955558__D12-194