Research workbench
Crystal structure of M. tuberculosis inha inhibited by PT514
Analyse Crystal structure of M. tuberculosis inha inhibited by PT514 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MTP
- Type
- protein
- Length
- 2,127 residues
- Chains
- 8
- 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
- P9WGR0
- Ligands
- NAD, 53K, NA, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, C, D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 268 | 48% helix, 17% strand | P9WGR0 |
| G, H | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 262 | 46% helix, 17% strand | P9WGR0 |
| F | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 263 | 46% helix, 17% strand | P9WGR0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, E, G, C, D, F, H
- 53K · 2-(2-methylphenoxy)-5-[(4-phenyl-1H-1,2,3-triazol-1-yl)methyl]phenol · ligand · 8 copies · chains A, B, G, E, C, D, H, F
- NA · Sodium ion · metal · 3 copies · chains D, F, H
- CL · Chloride ion · ion · 2 copies · chains A, G, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1031 | 0.86 | 0.87 | 119 | NAD, 53K |
| 2 | 559 | 0.84 | 0.89 | 53 | NAD, 53K |
| 3 | 591 | 0.83 | 0.88 | 54 | NAD, 53K |
| 4 | 839 | 0.83 | 0.85 | 81 | NAD, 53K |
| 5 | 596 | 0.83 | 0.87 | 56 | NAD, 53K |
Interfaces
14 interfaces between chains.
- E–G · 1560 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1559 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1558 Ų buried · 23 hydrogen bonds · protein-protein
- F–H · 1556 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1521 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5MTP · Crystal structure of M. tuberculosis InhA inhibited by PT514 · the same entry in another collection · chain H against H, TM-score 1.00
- P9WGR0 · AlphaFold monomer V2.0 prediction for enoyl-[acyl-carrier-protein] reductase [NADH]… · a predicted model of the same protein · chain G against A, TM-score 0.99
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 P9WGR0
- Elsewhere: RCSB PDB 5MTP · PDBe 5MTP · UniProt P9WGR0
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