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VP1_structural_protein

Euk-Vir

bat_polyomavirus_4b

VP1_structural_protein__YP_009174991__bat_polyomavirus_4b__2758138

Identity

Accession:: YP_009174991 ↗
Protein ID:: VP1_structural_protein
Kingdom:: euk

Quality

72.4 mean pLDDT

Taxonomy

Shotokuvirae› Cossaviricota› Papovaviricetes› Sepolyvirales› Polyomaviridae› Alphapolyomavirus› bat_polyomavirus_4b

TaxID: 2758138

Cluster

View cluster (117 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 50-168_243-364

PDB

Domain cluster: rep: VP1__YP_009325930__Betapolyomavirus_securanorvegicus__1919247__D30-309

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00718.29 best	Polyoma_coat	123.1	1.80e-35	50.2%	40.5%
PF00718.29	Polyoma_coat	177.5	4.60e-52	45.2%	35.8%

CATH (13)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1sidF00	2.60.175.10	Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus	0.91	77.0	6.53e-01	85.5%	80.8%
3s7vC00	2.60.175.10	Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus	0.83	69.0	6.64e-01	84.6%	100.0%
1zx5A02	2.60.120.10	Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls	0.65	22.0	3.80e-01	79.3%	89.2%
2pn5A08	2.60.120.1540	Mainly Beta › Sandwich › Jelly Rolls ›	0.61	29.0	4.08e-01	81.3%	93.7%
1dzlA00	2.60.175.20	Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Major capsid L1 (late) superfamily, Papillomavirus	0.59	56.0	4.46e-01	100.0%	96.0%
4oq8A00	2.60.120.220	Mainly Beta › Sandwich › Jelly Rolls › Satellite virus coat domain	0.59	32.0	4.07e-01	79.7%	87.5%
1qwrA02	2.60.120.10	Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls	0.58	19.0	3.18e-01	76.3%	79.8%
2b39A10	2.60.120.1540	Mainly Beta › Sandwich › Jelly Rolls ›	0.57	28.0	3.89e-01	80.9%	94.8%
5ewnA01	2.60.120.20	Mainly Beta › Sandwich › Jelly Rolls ›	0.53	40.0	4.45e-01	86.7%	100.0%
1o6uA02	2.60.120.680	Mainly Beta › Sandwich › Jelly Rolls › GOLD domain	0.52	25.0	3.50e-01	73.0%	97.2%
4kq7A01	2.60.120.1390	Mainly Beta › Sandwich › Jelly Rolls › Protein of unknown function DUF2961	0.52	32.0	3.88e-01	81.7%	92.0%
3qs2A00	2.60.40.3290	Mainly Beta › Sandwich › Immunoglobulin-like › Fimbrial protein EcpA	0.51	36.0	4.21e-01	80.1%	100.0%
2hb0B02	2.60.40.2040	Mainly Beta › Sandwich › Immunoglobulin-like › CFA/I fimbrial subunit E, pilin domain	0.51	35.0	3.99e-01	92.9%	93.8%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
961478	10.2.1.6 ↗	beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat	0.91	69.0	6.81e-01	77.2%	100.0%
2666438	10.2.1.6 ↗	beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat	0.90	77.0	6.64e-01	86.7%	85.6%
423236	10.2.1.6 ↗	beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat	0.81	68.0	6.53e-01	85.1%	100.0%
3406853	10.4.1.0 ↗	beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain	0.61	31.0	4.30e-01	80.9%	96.7%
3241691	10.4.1.0 ↗	beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain	0.56	32.0	4.12e-01	80.5%	95.7%
3876166	10.32.1.203 ↗	beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Seipin	0.55	33.0	4.16e-01	76.3%	99.3%
4944752	10.1.2.0 ↗	beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED)	0.55	29.0	3.93e-01	73.9%	99.2%
3309020	10.32.1.0 ↗	beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like	0.54	28.0	3.71e-01	75.9%	91.2%
3805836	10.32.1.0 ↗	beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like	0.52	28.0	3.61e-01	92.5%	89.6%
3473996	10.2.1.0 ↗	beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins)	0.52	41.0	3.97e-01	83.0%	95.7%
3805853	10.32.1.192 ↗	beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › C-JID	0.52	30.0	3.30e-01	75.1%	66.7%

D2 medium residues 169-242

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00718.29 best	Polyoma_coat	75.1	7.10e-21	100.0%	22.0%

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1sidF00	2.60.175.10	Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus	0.97	90.0	5.53e-01	100.0%	20.3%
3s7vC00	2.60.175.10	Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus	0.89	77.0	5.03e-01	100.0%	25.0%
2dlpA00	2.30.30.40	Mainly Beta › Roll › SH3 type barrels. › SH3 Domains	0.53	41.0	3.95e-01	90.5%	74.1%

ECOD (3)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2666438	10.2.1.6 ↗	beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat	0.98	92.0	5.65e-01	100.0%	21.2%
961478	10.2.1.6 ↗	beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat	0.97	91.0	5.97e-01	100.0%	28.5%
3662385	4.1.1.304 ↗	beta barrels › SH3 › SH3 › SH3 › SH3-C_UBE2O	0.52	44.0	4.41e-01	93.2%	100.0%