MolNFT v1 · #92535 · protein
Human coxsackievirus B3 strain rd coat protein
4GB3 · Coat protein 1: “Human coxsackievirus B3 strain rd coat protein”. X-ray diffraction, 2 ligands (PLM, MYR), 11 pockets (best druggability 0.78). MolNFT v1 #92535 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GB3
- Type
- protein
- Length
- 822 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein 1; Coat protein 2; Coat protein 3; Coat protein 4
- UniProt
- F8VA14
- Ligands
- PLM, MYR
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Coat protein 1 | protein | 273 | 10% helix, 31% strand | F8VA14 |
| 2 | Coat protein 2 | protein | 256 | 13% helix, 35% strand | F8VA14 |
| 3 | Coat protein 3 | protein | 238 | 10% helix, 30% strand | F8VA14 |
| 4 | Coat protein 4 | protein | 55 | 11% helix, 16% strand | F8VA14 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.78 | 0.86 | 60 | PLM |
| 2 | 68 | 0.49 | 0.84 | 23 | empty |
| 3 | 82 | 0.47 | 0.82 | 23 | empty |
| 4 | 119 | 0.46 | 0.78 | 21 | empty |
| 5 | 114 | 0.45 | 0.78 | 20 | empty |
Interfaces
6 interfaces between chains.
- 1–3 · 4313 Ų buried · 68 hydrogen bonds · protein-protein
- 1–2 · 2127 Ų buried · 29 hydrogen bonds · protein-protein
- 2–3 · 1639 Ų buried · 18 hydrogen bonds · protein-protein
- 1–4 · 1145 Ų buried · 17 hydrogen bonds · protein-protein
- 3–4 · 956 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 lipid (myristoylation).
Compared structures
- 4GB3 · Human coxsackievirus B3 strain RD coat protein · the same entry in another collection · chain 1 against 1, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt F8VA14
- Elsewhere: RCSB PDB 4GB3 · PDBe 4GB3 · UniProt F8VA14
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