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capsid
Euk-VirPorcine_parvovirus_4
capsid__YP_004013958__Porcine_parvovirus_4__707546
Identity
- Accession:
- YP_004013958 ↗
- Protein ID:
- capsid
- Kingdom:
- euk
Quality
54.8
mean pLDDT
Taxonomy
Shotokuvirae›
Cossaviricota›
Quintoviricetes›
Piccovirales›
Parvoviridae›
Copiparvovirus›
Porcine_parvovirus_4
TaxID: 707546
Cluster
View cluster (92 members)3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 2-57
D2
medium
residues 157-234
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00740.24 best | VP1_2 | 34.5 | 1.20e-08 | 93.6% | 7.0% |
CATH (2)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6jpaA01 | 1.20.120.350 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C | 0.58 | 45.0 | 3.77e-01 | 85.9% | 85.5% |
| 1hp7A01 | 2.30.39.10 | Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 | 0.50 | 29.0 | 2.75e-01 | 82.1% | 45.3% |
ECOD (3)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3107916 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.91 | 86.0 | 5.57e-01 | 100.0% | 28.6% |
| 2990501 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.88 | 83.0 | 5.14e-01 | 100.0% | 26.7% |
| 5012054 | 310.3.1.0 ↗ | a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related | 0.51 | 31.0 | 3.29e-01 | 100.0% | 68.6% |
D3
medium
residues 235-310_345-380_625-643_658-681
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00740.24 best | VP1_2 | 66.8 | 2.10e-18 | 73.6% | 23.8% |
CATH (7)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4qc8A00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.93 | 90.0 | 6.01e-01 | 100.0% | 73.3% |
| 1s58A00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.92 | 89.0 | 5.90e-01 | 100.0% | 70.7% |
| 2g8gA00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.92 | 89.0 | 5.88e-01 | 100.0% | 74.4% |
| 1c8dA00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.92 | 89.0 | 5.80e-01 | 100.0% | 73.4% |
| 3zxaC01 | 2.60.120.20 | Mainly Beta › Sandwich › Jelly Rolls › | 0.63 | 43.0 | 4.03e-01 | 98.1% | 56.6% |
| 4lhsA01 | 2.60.120.260 | Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like | 0.57 | 33.0 | 3.38e-01 | 94.8% | 58.4% |
| 1wmdA02 | 2.60.120.380 | Mainly Beta › Sandwich › Jelly Rolls › | 0.51 | 31.0 | 3.57e-01 | 91.6% | 80.3% |
ECOD (21)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2990572 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.94 | 91.0 | 5.95e-01 | 100.0% | 74.5% |
| 2644354 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.93 | 90.0 | 5.92e-01 | 100.0% | 74.4% |
| 1195 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.92 | 89.0 | 5.90e-01 | 100.0% | 70.7% |
| 4884619 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.92 | 89.0 | 5.78e-01 | 100.0% | 71.7% |
| 2707659 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.92 | 89.0 | 5.87e-01 | 100.0% | 70.1% |
| 2142463 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.92 | 88.0 | 5.81e-01 | 100.0% | 71.5% |
| 3107798 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.91 | 88.0 | 5.79e-01 | 100.0% | 74.7% |
| 3107916 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.89 | 63.0 | 4.89e-01 | 72.3% | 41.4% |
| 4880563 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.82 | 64.0 | 5.95e-01 | 98.1% | 66.5% |
| 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) | 0.72 | 68.0 | 5.47e-01 | 100.0% | 71.4% |
| 178766 | 10.2.1.53 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › IHHNV_capsid | 0.71 | 67.0 | 5.29e-01 | 100.0% | 62.2% |
| 5033161 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.67 | 42.0 | 4.57e-01 | 96.1% | 73.8% |
| 3899364 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.58 | 29.0 | 3.37e-01 | 91.0% | 64.5% |
| 5039604 | 10.1.2.0 ↗ | beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) | 0.58 | 33.0 | 3.98e-01 | 94.8% | 86.0% |
| 3460039 | 10.12.1.16 ↗ | beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › 2OG-FeII_Oxy | 0.56 | 44.0 | 3.26e-01 | 96.8% | 33.6% |
| 4882276 | 10.2.1.1 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Rhv | 0.55 | 46.0 | 4.36e-01 | 98.1% | 74.2% |
| 3589068 | 11.1.4.30 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › GramPos_pilinD1 | 0.53 | 43.0 | 4.38e-01 | 93.5% | 85.8% |
| 3890321 | 10.32.1.5 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Ephrin_lbd | 0.53 | 35.0 | 3.61e-01 | 94.2% | 69.7% |
| 3466690 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.52 | 41.0 | 3.66e-01 | 94.8% | 59.5% |
| 3500088 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.50 | 38.0 | 3.77e-01 | 96.1% | 74.5% |
| 3889464 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.50 | 36.0 | 3.66e-01 | 96.1% | 74.7% |
D4
medium
residues 381-471_492-546_613-624_682-728