MolNFT v1 · #174575 · protein
Cryo-EM structure of mature coxsackievirus A10 in complex with KRM1 at pH 7.4
7BZT · Capsid protein VP1: “Cryo-EM structure of mature coxsackievirus A10 in complex with KRM1 at pH 7.4”. Electron microscopy, 2 ligands (SPH, NAG), 16 pockets (best druggability 0.79). MolNFT v1 #174575 on GenesisL1: 3D structure…
- PDB
- 7BZT
- Type
- protein
- Length
- 1,094 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; Capsid protein VP2; Capsid protein VP3; Capsid protein VP4; KRM1
- UniProt
- G0YPI2
- Ligands
- SPH, NAG
- Pockets
- 16 · best druggability 0.79
Structure
electron microscopy · 5 distinct chains · 8% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 272 | 6% helix, 25% strand | — |
| B | Capsid protein VP2 | protein | 246 | 11% helix, 31% strand | G0YPI2 |
| C | Capsid protein VP3 | protein | 239 | 12% helix, 32% strand | G0YPI2 |
| D | Capsid protein VP4 | protein | 44 | 9% helix, 2% strand | G0YPI2 |
| E | KRM1 | protein | 293 | 3% helix, 27% strand | — |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.79 | 0.81 | 100 | SPH |
| 2 | 123 | 0.67 | 0.90 | 27 | empty |
| 3 | 163 | 0.56 | 0.81 | 29 | empty |
| 4 | 171 | 0.51 | 0.78 | 25 | empty |
| 5 | 118 | 0.51 | 0.81 | 26 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3802 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 2263 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 1766 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1039 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 841 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7BZT · Cryo-EM structure of mature Coxsackievirus A10 in complex with KRM1 at pH 7.4 · the same entry in another collection · chain A against A, 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 G0YPI2
- Elsewhere: RCSB PDB 7BZT · PDBe 7BZT · UniProt G0YPI2
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