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Crystal structure of M. tuberculosis inha inhibited by PT501
Analyse Crystal structure of M. tuberculosis inha inhibited by PT501 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UGS
- Type
- protein
- Length
- 1,608 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
- XT5, NAD, NA, CL
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G, C, D | Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9) | protein | 268 | 44% helix, 16% strand | P9WGR1 |
Ligands and binding sites
- XT5 · 5-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-(2-methylphenoxy)phenol · ligand · 7 copies · chains A, B, E, G, C, D
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 6 copies · chains A, B, E, G, C, D
- NA · Sodium ion · metal · chains B
- CL · Chloride ion · ion · 10 copies · chains A, B, G, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.84 | 0.89 | 52 | NAD, XT5 |
| 2 | 635 | 0.84 | 0.88 | 60 | NAD, XT5 |
| 3 | 729 | 0.83 | 0.86 | 63 | NAD, XT5, CL |
| 4 | 693 | 0.83 | 0.86 | 70 | NAD, XT5 |
| 5 | 1177 | 0.83 | 0.84 | 60 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1559 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1557 Ų buried · 21 hydrogen bonds · protein-protein
- E–G · 1553 Ų buried · 23 hydrogen bonds · protein-protein
- B–E · 1513 Ų buried · 20 hydrogen bonds · protein-protein
- A–G · 1505 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5UGS · Crystal structure of M. tuberculosis InhA inhibited by PT501 · 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 A against A, TM-score 0.97
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 5UGS · PDBe 5UGS · UniProt P9WGR1
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