Research workbench
Crystal structure of INHA(S94A) mutant in complex with pyridomycin
Analyse Crystal structure of INHA(S94A) mutant in complex with pyridomycin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BGE
- Type
- protein
- Length
- 1,558 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Enoyl-[acyl-carrier-protein] reductase [NADH]
- EC
- 1.3.1.9
- UniProt
- P9WGR1
- Ligands
- PYW
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 267 | 46% helix, 15% strand | P9WGR1 |
| C | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 254 | 44% helix, 16% strand | P9WGR1 |
| D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 252 | 45% helix, 17% strand | P9WGR1 |
| E | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 251 | 42% helix, 16% strand | P9WGR1 |
Ligands and binding sites
- PYW · Pyridomycin · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 789 | 0.79 | 0.82 | 53 | PYW |
| 2 | 810 | 0.79 | 0.82 | 52 | PYW |
| 3 | 785 | 0.78 | 0.82 | 57 | PYW |
| 4 | 614 | 0.72 | 0.79 | 47 | PYW |
| 5 | 492 | 0.66 | 0.77 | 44 | PYW |
Interfaces
8 interfaces between chains.
- E–F · 1595 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1462 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1449 Ų buried · 18 hydrogen bonds · protein-protein
- D–F · 648 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 387 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4BGE · Crystal structure of InhA(S94A) mutant in complex with pyridomycin · the same entry in another collection · chain E against E, TM-score 1.00
- P9WGR1 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH]… · a predicted model of the same protein · chain E against A, TM-score 0.98
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 P9WGR1
- Elsewhere: RCSB PDB 4BGE · PDBe 4BGE · UniProt P9WGR1
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