←Back to structures

DNA_packaging_terminase_subunit_2

Euk-Vir

Gallid_alphaherpesvirus_2

DNA_packaging_terminase_subunit_2__YP_001033957__Gallid_alphaherpesvirus_2__10390

Identity

Accession:: YP_001033957 ↗
Protein ID:: DNA_packaging_terminase_subunit_2
Kingdom:: euk

Quality

76.7 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Mardivirus› Gallid_alphaherpesvirus_2

TaxID: 10390

Cluster

View cluster (77 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 medium residues 19-132

PDB

Domain cluster: rep: transport_protein__YP_004207847__Cricetid_gammaherpesvirus_2__1605972__D1-97

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	124.0	7.80e-36	98.2%	17.1%

D2 medium residues 133-200_531-566

PDB

Domain cluster: rep: DNA_packaging_terminase_subunit_2__YP_007969816__Elephantid_betaherpesvirus_1__146015__D118-183_479-495

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	75.6	3.40e-21	67.3%	10.7%
PF01366.24	PRTP	29.0	4.30e-07	35.6%	5.3%

CATH (15)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3pe0A02	1.20.58.60	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.75	53.0	5.35e-01	74.0%	87.7%
2jqqA00	1.20.58.1240	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.73	64.0	5.55e-01	94.2%	89.0%
2lm9A00	1.20.58.970	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.70	50.0	5.22e-01	75.0%	99.0%
1zoyA03	1.20.58.100	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain	0.68	50.0	4.86e-01	77.9%	70.9%
1hciA01	1.20.58.60	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.62	46.0	4.34e-01	78.8%	83.3%
4ceiA03	6.10.250.2380	Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.60	42.0	4.15e-01	79.8%	67.9%
4gzrB00	1.10.287.1060	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like	0.58	41.0	4.61e-01	92.3%	98.7%
4o8sA02	1.20.58.1790	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › JHP933, helical tail domain	0.58	48.0	4.82e-01	92.3%	97.2%
3dt5A00	1.10.3940.10	Mainly Alpha › Orthogonal Bundle › AF_0924 fold › AF_0924 domain	0.56	39.0	3.78e-01	73.1%	91.6%
1kt1A03	1.25.40.10	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain	0.54	49.0	4.24e-01	100.0%	93.7%
2jexA01	1.10.287.30	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › E2 (early) protein, N terminal domain, subdomain 1	0.54	39.0	4.00e-01	95.2%	81.2%
4ehoB03	3.30.450.270	Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PHY domain	0.54	40.0	3.41e-01	79.8%	99.4%
5cygB00	3.40.50.1580	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain	0.54	41.0	3.12e-01	84.6%	71.1%
1x9mA01	3.30.420.10	Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H	0.51	44.0	3.45e-01	95.2%	83.2%
4h33A00	1.10.287.70	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.50	41.0	4.33e-01	92.3%	98.9%

ECOD (19)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3220023	174.1.1.0 ↗	few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain	0.67	49.0	4.37e-01	77.9%	70.0%
3608382	109.3.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat	0.66	57.0	4.66e-01	95.2%	93.8%
3484940	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.66	51.0	4.98e-01	82.7%	93.9%
3324543	4121.1.1.2 ↗	a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like	0.63	48.0	3.58e-01	82.7%	50.5%
3499265	3542.1.1.3 ↗	alpha arrays › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Presenilin family intramembrane aspartate proteases › Peptidase_A22B	0.60	50.0	3.56e-01	92.3%	83.6%
3174371	5050.1.1.0 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter	0.60	44.0	3.39e-01	76.9%	37.5%
1268318	604.1.1.1 ↗	alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin	0.60	46.0	4.48e-01	82.7%	94.1%
3354458	109.4.1.361 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › NPH3	0.59	52.0	4.02e-01	97.1%	69.1%
4025088	109.4.1.418 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Condensin2nSMC	0.58	49.0	3.03e-01	93.3%	20.9%
4082175	3001.1.1.1 ↗	alpha arrays › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › Tetrahydrodipicolinate-N-succinlytransferase, N-terminal 3-helical domain › THDPS_N_2	0.58	41.0	4.40e-01	94.2%	89.4%
3263125	150.1.1.0 ↗	alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin	0.58	41.0	3.49e-01	74.0%	64.4%
3820897	109.4.1.1682 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PHM7_cyt	0.58	37.0	4.45e-01	88.5%	97.1%
3575264	604.12.1.61 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Clc-like	0.55	50.0	4.83e-01	100.0%	97.4%
3171863	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.55	43.0	3.35e-01	94.2%	36.7%
4954786	605.1.1.0 ↗	alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase	0.55	42.0	4.59e-01	93.3%	100.0%
3873955	7016.1.1.0 ↗	extended segments › Palmitoyltransferase DHHC C-terminal domain › Palmitoyltransferase DHHC C-terminal domain › Palmitoyltransferase DHHC C-terminal domain	0.55	48.0	4.18e-01	96.2%	81.3%
3372303	5050.1.1.55 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr, MFS_1	0.54	41.0	3.07e-01	80.8%	51.4%
5023340	4070.1.1.0 ↗	alpha arrays › FtsH protease domain-like › FtsH protease domain-like › FtsH protease domain-like	0.53	45.0	3.64e-01	94.2%	53.3%
4944558	1075.1.2.0 ↗	alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain	0.50	40.0	3.33e-01	89.4%	90.2%

D3 medium residues 238-276_338-427

PDB

Domain cluster: rep: DNA_packaging_terminase_subunit_2__YP_053077__Equid_alphaherpesvirus_1__10326__D247-267_332-417

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	84.1	9.00e-24	74.4%	13.1%

D4 medium residues 567-590_704-783

PDB

Domain cluster: rep: terminase_subunit_2__YP_009179297__Elephant_endotheliotropic_herpesvirus_4__548914__D513-536_648-697

D5 medium residues 591-703

PDB

Domain cluster: rep: orf7__YP_009044394__Alcelaphine_gammaherpesvirus_2__138184__D511-616

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF01366.24 best	PRTP	143.8	7.80e-42	82.3%	14.2%