MolNFT v1 · #120207 · protein
Crystal structure of EV71 3C in complex with N69S 1.8K
5GSW · 3C protein: “Crystal structure of EV71 3C in complex with N69S 1.8K”. X-ray diffraction, 1 ligand (5GI), 11 pockets (best druggability 0.56). MolNFT v1 #120207 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5GSW
- Type
- protein
- Length
- 904 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C protein
- UniProt
- E7E815
- Ligands
- 5GI
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E | 3C protein | protein | 181 | 13% helix, 49% strand | E7E815 |
| B | 3C protein | protein | 180 | 12% helix, 52% strand | E7E815 |
Ligands and binding sites
- 5GI · ~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]propan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide · ligand · 5 copies · chains A, E, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.56 | 0.82 | 35 | empty |
| 2 | 131 | 0.51 | 0.80 | 21 | empty |
| 3 | 141 | 0.50 | 0.79 | 24 | empty |
| 4 | 181 | 0.47 | 0.76 | 23 | empty |
| 5 | 175 | 0.45 | 0.75 | 43 | 5GI |
Interfaces
6 interfaces between chains.
- A–E · 650 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 581 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 461 Ų buried · 3 hydrogen bonds · protein-protein
- C–E · 313 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5GSW · Crystal structure of EV71 3C in complex with N69S 1.8k · the same entry in another collection · chain D against D, 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 E7E815
- Elsewhere: RCSB PDB 5GSW · PDBe 5GSW · UniProt E7E815
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