←Back to structures

VP2

Euk-Vir

New_Jersey_polyomavirus-2013

VP2__YP_009030018__New_Jersey_polyomavirus-2013__1497391

Identity

Accession:: YP_009030018 ↗
Protein ID:: VP2
Kingdom:: euk

Quality

65.8 mean pLDDT

Taxonomy

Shotokuvirae› Cossaviricota› Papovaviricetes› Sepolyvirales› Polyomaviridae› Alphapolyomavirus› New_Jersey_polyomavirus-2013

TaxID: 1497391

Cluster

View cluster (96 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 2-80

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00761.26 best	Polyoma_coat2	47.4	3.40e-12	100.0%	23.6%

CATH (39)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1qsdA00	1.20.58.90	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.79	41.0	3.70e-01	100.0%	39.2%
3c24A02	1.10.3640.10	Mainly Alpha › Orthogonal Bundle › putative oxidoreductase fold › Semialdehyde dehydrogenase-like, C-terminal	0.67	36.0	3.37e-01	100.0%	41.0%
3hc1A00	1.10.3210.10	Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432	0.64	44.0	2.97e-01	72.2%	63.1%
1etkA00	1.10.10.60	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like	0.61	36.0	3.76e-01	100.0%	61.3%
1evsA00	1.20.1250.10	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; ›	0.59	52.0	4.11e-01	98.7%	76.7%
1j5wA02	1.20.58.180	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2	0.59	42.0	4.33e-01	75.9%	81.8%
1ydxA02	1.10.287.1120	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein	0.59	40.0	3.87e-01	70.9%	84.4%
3vfzB00	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.58	38.0	4.23e-01	83.5%	85.7%
1mhyG01	1.20.1280.10	Mainly Alpha › Up-down Bundle › Monooxygenase › Methane monooxygenase, gamma chain, domain 1	0.58	40.0	4.29e-01	79.7%	86.8%
4hehA01	1.10.1240.10	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain	0.58	41.0	4.05e-01	81.0%	71.1%
2ch7A00	1.10.287.950	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein	0.57	41.0	2.70e-01	82.3%	19.1%
6w0pA02	1.50.10.10	Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase ›	0.57	46.0	2.92e-01	89.9%	20.0%
4izzB02	1.10.10.1680	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › HetR, N-terminal DNA-binding domain	0.56	38.0	4.01e-01	82.3%	79.4%
4pcqA01	1.10.10.10	Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	0.56	33.0	3.89e-01	70.9%	90.0%
8hk0B03	1.20.140.10	Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3	0.56	45.0	3.84e-01	89.9%	95.7%
2e18A00	3.40.50.620	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs	0.56	48.0	3.45e-01	98.7%	66.0%
4gc0A02	1.20.1250.20	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › MFS general substrate transporter like domains	0.55	42.0	3.10e-01	92.4%	29.2%
3wirA02	1.50.10.10	Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase ›	0.55	45.0	2.91e-01	91.1%	22.8%
4u7iA00	1.20.58.80	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit	0.55	38.0	3.70e-01	74.7%	77.4%
1lliA00	1.10.260.40	Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains	0.54	35.0	3.46e-01	81.0%	58.4%
4bw5C00	1.10.287.70	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.54	48.0	3.45e-01	100.0%	33.9%
1m62A00	1.20.58.120	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain	0.54	38.0	3.72e-01	74.7%	77.0%
2q5zB00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.54	42.0	4.05e-01	92.4%	73.4%
8ctsB01	1.10.287.70	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.54	43.0	4.26e-01	100.0%	81.6%
1xdpA01	1.20.58.310	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Polyphosphate kinase N-terminal domain	0.54	38.0	3.52e-01	74.7%	80.0%
7xcnM01	1.10.1240.10	Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain	0.54	39.0	3.93e-01	81.0%	76.9%
3layF00	1.20.120.1490	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) ›	0.53	38.0	3.88e-01	92.4%	75.6%
1sumB02	1.20.58.220	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2	0.53	42.0	3.68e-01	84.8%	78.8%
1nmrA01	1.10.1900.10	Mainly Alpha › Orthogonal Bundle › c-terminal domain of poly(a) binding protein › c-terminal domain of poly(a) binding protein	0.53	35.0	3.61e-01	92.4%	71.1%
2gl2B00	1.10.287.1700	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.53	40.0	3.64e-01	82.3%	75.2%
4lzjA02	1.10.8.1080	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 ›	0.52	35.0	3.58e-01	70.9%	84.8%
2go7A02	1.10.150.240	Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2	0.52	35.0	3.81e-01	79.7%	83.6%
1t72A02	1.20.58.220	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2	0.51	41.0	3.83e-01	86.1%	80.6%
3zh9B03	1.20.272.10	Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 ›	0.51	41.0	3.48e-01	86.1%	95.2%
2e9xD01	1.20.58.1030	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.51	40.0	3.34e-01	84.8%	65.7%
2icwG01	1.20.120.390	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1	0.51	41.0	3.64e-01	92.4%	96.8%
1f45B00	1.20.1250.10	Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; ›	0.51	44.0	3.79e-01	100.0%	73.7%
3v5uA01	6.10.280.80	Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › NCX, peripheral helical region	0.51	39.0	4.04e-01	100.0%	86.8%
3fblA00	1.20.58.800	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.50	38.0	3.78e-01	83.5%	79.3%

ECOD (31)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3620861	174.1.1.0 ↗	few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain	0.68	60.0	5.06e-01	100.0%	82.2%
3282529	632.1.1.3 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid	0.66	40.0	3.67e-01	87.3%	45.7%
4069535	7015.1.1.1 ↗	alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › DHHC	0.65	52.0	4.07e-01	91.1%	73.5%
3798353	174.1.1.0 ↗	few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain	0.64	57.0	4.63e-01	100.0%	88.7%
3336731	7015.1.1.1 ↗	alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › DHHC	0.63	50.0	4.12e-01	91.1%	73.8%
4142297	7015.1.1.0 ↗	alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain	0.63	50.0	4.23e-01	91.1%	78.6%
3967501	632.18.1.1 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901 › DUF4398	0.61	39.0	3.68e-01	100.0%	53.7%
3682662	7015.1.1.0 ↗	alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain	0.61	50.0	4.37e-01	94.9%	93.1%
3734386	7015.1.1.0 ↗	alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain	0.61	48.0	4.10e-01	91.1%	79.3%
3706056	604.22.1.0 ↗	alpha bundles › Spectrin repeat-like › tubulin binding cofactor C N-terminal domain › tubulin binding cofactor C N-terminal domain	0.60	43.0	4.24e-01	74.7%	74.1%
4959128	632.18.1.0 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › hypothetical protein PA2901 › hypothetical protein PA2901	0.60	38.0	3.97e-01	70.9%	68.0%
4953182	3877.1.1.0 ↗	alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC	0.60	41.0	3.19e-01	91.1%	31.7%
3188597	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.60	43.0	4.15e-01	75.9%	82.2%
5028679	632.22.1.0 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats	0.58	37.0	3.44e-01	83.5%	50.5%
4995305	604.5.1.2 ↗	alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU	0.57	42.0	4.00e-01	78.5%	87.4%
3935017	604.12.1.0 ↗	alpha bundles › Spectrin repeat-like › MIT domain › MIT domain	0.57	42.0	4.23e-01	78.5%	86.3%
3984938	101.1.6.0 ↗	alpha arrays › HTH › HTH › TrpR	0.56	39.0	3.89e-01	70.9%	95.0%
3271308	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.56	39.0	3.51e-01	75.9%	56.7%
4930709	3877.1.1.0 ↗	alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC	0.55	46.0	3.51e-01	93.7%	71.8%
4927173	632.11.1.0 ↗	alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like	0.55	40.0	3.94e-01	96.2%	70.6%
3357244	4106.1.1.1 ↗	few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC	0.55	44.0	4.02e-01	87.3%	72.4%
3640621	186.1.1.0 ↗	alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N	0.54	42.0	4.00e-01	97.5%	70.5%
3502800	622.1.1.1 ↗	alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › HSCB_C	0.54	42.0	4.09e-01	84.8%	80.0%
5079886	159.1.1.0 ↗	alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060	0.53	41.0	4.17e-01	84.8%	88.0%
3651776	4106.1.1.1 ↗	few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC	0.53	43.0	3.31e-01	91.1%	42.6%
4927596	604.5.1.0 ↗	alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895)	0.52	43.0	3.65e-01	89.9%	56.9%
3698039	4106.1.1.1 ↗	few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC	0.52	44.0	3.77e-01	94.9%	79.8%
3216590	188.1.1.0 ↗	alpha arrays › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain › Nuclear receptor ligand-binding domain	0.51	42.0	3.16e-01	96.2%	78.7%
3880	611.5.1.1 ↗	alpha bundles › N-cbl like › Superantigen MAM N-terminal domain › Superantigen MAM N-terminal domain › MA-Mit	0.51	42.0	3.65e-01	92.4%	96.8%
4327633	4336.1.1.1 ↗	alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › Com_YlbF	0.51	43.0	3.97e-01	100.0%	78.2%
3221921	3939.1.1.0 ↗	alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain	0.51	40.0	3.76e-01	87.3%	98.0%

D2 high residues 105-219

PDB

Domain cluster: rep: VP2_minor_capsid_protein__YP_007188587__Alphapolyomavirus_chlopygerythrus__1891719__D131-219

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00761.26 best	Polyoma_coat2	42.1	1.30e-10	33.0%	9.9%