MolNFT v1 · #142133 · protein
Fit R10 Fab coordinates into the cryo-EM of EV71 in complex with D6
5ZUD · Capsid protein VP1: “Fit R10 Fab coordinates into the cryo-EM of EV71 in complex with D6”. Electron microscopy, 15 pockets (best druggability 0.80). MolNFT v1 #142133 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZUD
- Type
- protein
- Length
- 1,118 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein VP1; VP2; VP3; R10 antibody light chain; R10 antibody heavy chain
- UniProt
- G5CUH3, A0A1P8LK26, W8XVT2
- Pockets
- 15 · best druggability 0.80
Structure
electron microscopy · 5 distinct chains · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid protein VP1 | protein | 218 | 8% helix, 33% strand | G5CUH3 |
| B | VP2 | protein | 237 | 10% helix, 38% strand | A0A1P8LK26 |
| C | VP3 | protein | 239 | 11% helix, 34% strand | W8XVT2 |
| D | R10 antibody light chain | protein | 212 | 3% helix, 48% strand | — |
| E | R10 antibody heavy chain | protein | 212 | 6% helix, 54% strand | — |
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 811 | 0.80 | 0.83 | 68 | empty |
| 2 | 341 | 0.70 | 0.83 | 41 | empty |
| 3 | 402 | 0.58 | 0.75 | 53 | empty |
| 4 | 196 | 0.53 | 0.78 | 38 | empty |
| 5 | 147 | 0.51 | 0.79 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3077 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 1830 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1749 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1550 Ų buried · 18 hydrogen bonds · protein-protein
- C–E · 197 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5ZUD · Fit R10 Fab coordinates into the cryo-EM of EV71 in complex with D6 · 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 G5CUH3
- Every structure of UniProt A0A1P8LK26
- Every structure of UniProt W8XVT2
- Elsewhere: RCSB PDB 5ZUD · PDBe 5ZUD · UniProt G5CUH3 · UniProt A0A1P8LK26 · UniProt W8XVT2
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