Research workbench
Crystal structure of M. tuberculosis inha inhibited by PT512
Analyse Crystal structure of M. tuberculosis inha inhibited by PT512 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MTR
- Type
- protein
- Length
- 2,126 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
- P9WGR1
- Ligands
- NAD, XT0, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 268 | 47% helix, 17% strand | P9WGR1 |
| E | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 265 | 46% helix, 17% strand | P9WGR1 |
| G | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 260 | 45% helix, 17% strand | P9WGR1 |
| H | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 261 | 45% helix, 17% strand | P9WGR1 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, E, G, C, D, F, H
- XT0 · 2-[4-[(4-cyclopentyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile · ligand · 8 copies · chains A, B, E, G, C, D, F, H
- CL · Chloride ion · ion · 2 copies · chains C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.83 | 0.88 | 54 | NAD, XT0 |
| 2 | 567 | 0.83 | 0.88 | 54 | NAD, XT0 |
| 3 | 597 | 0.83 | 0.88 | 56 | NAD, XT0 |
| 4 | 585 | 0.83 | 0.87 | 54 | NAD, XT0 |
| 5 | 591 | 0.83 | 0.87 | 55 | NAD, XT0 |
Interfaces
12 interfaces between chains.
- A–B · 1566 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1563 Ų buried · 24 hydrogen bonds · protein-protein
- F–H · 1555 Ų buried · 22 hydrogen bonds · protein-protein
- E–G · 1554 Ų buried · 25 hydrogen bonds · protein-protein
- C–H · 1518 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5MTR · Crystal structure of M. tuberculosis InhA inhibited by PT512 · the same entry in another collection · chain H against H, 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 G 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 5MTR · PDBe 5MTR · UniProt P9WGR1
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