MolNFT v1 · #171405 · protein
Structure of EV71 in complex with a protective antibody 38-1-10A Fab
6Z3Q · VP1: “Structure of EV71 in complex with a protective antibody 38-1-10A Fab”. Electron microscopy, 1 ligand (SPH), 16 pockets (best druggability 0.79). MolNFT v1 #171405 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z3Q
- Type
- protein
- Length
- 1,066 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; VP2; VP3; VP4; Heavy chain; Light chain
- EC
- 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48
- UniProt
- A0A2L1GIK5, D4QGA2, D4QGA3, Q6YLE3
- Ligands
- SPH
- Pockets
- 16 · best druggability 0.79
Structure
electron microscopy · 6 distinct chains · 11% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | VP1 (EC 3.4.22.29, 3.6.1.15, 3.4.22.28, 2.7.7.48) | protein | 295 | 14% helix, 27% strand | A0A2L1GIK5 |
| B | VP2 | protein | 245 | 13% helix, 36% strand | D4QGA2 |
| C | VP3 | protein | 242 | 12% helix, 31% strand | D4QGA3 |
| D | VP4 | protein | 58 | 12% helix, 9% strand | Q6YLE3 |
| H | Heavy chain | protein | 120 | 5% helix, 44% strand | — |
| L | Light chain | protein | 106 | 3% helix, 51% strand | — |
Ligands and binding sites
- SPH · Sphingosine · ligand · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.79 | 0.87 | 66 | SPH |
| 2 | 662 | 0.74 | 0.80 | 97 | empty |
| 3 | 121 | 0.54 | 0.83 | 25 | empty |
| 4 | 166 | 0.53 | 0.79 | 25 | empty |
| 5 | 55 | 0.49 | 0.86 | 16 | empty |
Interfaces
11 interfaces between chains.
- A–C · 3991 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 2585 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 1707 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1548 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1117 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6Z3Q · Structure of EV71 in complex with a protective antibody 38-1-10A Fab · 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 A0A2L1GIK5
- Every structure of UniProt D4QGA2
- Every structure of UniProt D4QGA3
- Every structure of UniProt Q6YLE3
- Elsewhere: RCSB PDB 6Z3Q · PDBe 6Z3Q · UniProt A0A2L1GIK5 · UniProt D4QGA2 · UniProt D4QGA3 · UniProt Q6YLE3
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