MolNFT v1 · #116808 · protein
Crystal structure of EV71 3C proteinase in complex with compound 7
5DP6: “Crystal structure of EV71 3C proteinase in complex with compound 7”. X-ray diffraction, 1 ligand (5EB), 5 pockets (best druggability 0.82). MolNFT v1 #116808 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DP6
- Type
- protein
- Length
- 716 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C proteinase
- UniProt
- A9XG43
- Ligands
- 5EB
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C proteinase | protein | 178 | 11% helix, 54% strand | A9XG43 |
| B, C | 3C proteinase | protein | 179 | 7% helix, 54% strand | A9XG43 |
| D | 3C proteinase | protein | 180 | 12% helix, 53% strand | A9XG43 |
Ligands and binding sites
- 5EB · ethyl (2Z,4S)-4-{[N-(3-cyclopropylpropanoyl)-L-phenylalanyl]amino}-5-[(3S)-2-oxopyrrolidin-3-yl]pent-2-enoate · ligand · 2 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.82 | 0.83 | 73 | 5EB |
| 2 | 813 | 0.80 | 0.83 | 63 | 5EB |
| 3 | 438 | 0.64 | 0.77 | 36 | empty |
| 4 | 121 | 0.43 | 0.77 | 24 | empty |
| 5 | 75 | 0.40 | 0.79 | 21 | empty |
Interfaces
4 interfaces between chains.
- A–B · 612 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 496 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 495 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 477 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5DP6 · Crystal Structure of EV71 3C Proteinase in complex with compound 7 · 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 A9XG43
- Elsewhere: RCSB PDB 5DP6 · PDBe 5DP6 · UniProt A9XG43
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