Research workbench
Cryo-EM structure of mature coxsackievirus A10 in complex with KRM1 at pH 5.5
Analyse Cryo-EM structure of mature coxsackievirus A10 in complex with KRM1 at pH 5.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BZU
- Type
- protein
- Length
- 1,093 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
- NAG
- Pockets
- 16 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 8% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 272 | 8% helix, 26% strand | — |
| B | Capsid protein VP2 | protein | 246 | 9% helix, 33% strand | G0YPI2 |
| C | Capsid protein VP3 | protein | 239 | 11% helix, 31% strand | G0YPI2 |
| D | Capsid protein VP4 | protein | 43 | 9% helix, 2% strand | G0YPI2 |
| E | KRM1 | protein | 293 | 3% helix, 28% strand | — |
Ligands and binding sites
- 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 | 303 | 0.78 | 0.89 | 55 | empty |
| 2 | 131 | 0.71 | 0.91 | 28 | empty |
| 3 | 55 | 0.69 | 0.97 | 30 | empty |
| 4 | 672 | 0.67 | 0.76 | 86 | empty |
| 5 | 146 | 0.54 | 0.81 | 23 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3724 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2289 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 1733 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 1018 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 844 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7BZU · Cryo-EM structure of mature Coxsackievirus A10 in complex with KRM1 at pH 5.5 · 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 7BZU · PDBe 7BZU · UniProt G0YPI2
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