MolNFT v1 · #127338 · protein

Crystal structure of M. tuberculosis inha inhibited by PT511

5MTQ · Enoyl-[acyl-carrier-protein] reductase [NADH]: “Crystal structure of M. tuberculosis inha inhibited by PT511”. X-ray diffraction, 2 ligands (NAD, XT3), 20 pockets (best druggability 0.85). MolNFT v1 #127338 on GenesisL1: 3D…

PDB: 5MTQ
Type: protein
Length: 2,135 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, XT3
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, C, D, F	Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9)	protein	268	49% helix, 17% strand	P9WGR1
G	Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9)	protein	264	46% helix, 17% strand	P9WGR1
H	Enoyl-[acyl-carrier-protein] reductase [NADH] (EC 1.3.1.9)	protein	263	46% helix, 17% strand	P9WGR1

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, E, G, C, D, F, H
XT3 · 2-[4-[(4-cyclohexyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile · ligand · 8 copies · chains A, B, G, E, C, D, F, 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	859	0.85	0.87	69	NAD, XT3
2	1039	0.85	0.86	96	NAD, XT3
3	558	0.83	0.88	51	NAD, XT3
4	580	0.83	0.88	54	NAD, XT3
5	1141	0.83	0.84	57	empty

Interfaces

14 interfaces between chains.

F–H · 1558 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 1553 Å² buried · 19 hydrogen bonds · protein-protein
A–B · 1550 Å² buried · 21 hydrogen bonds · protein-protein
E–G · 1546 Å² buried · 20 hydrogen bonds · protein-protein
B–E · 1524 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5MTQ · Crystal structure of M. tuberculosis InhA inhibited by PT511 · the same entry in another collection · chain C against C, 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 H 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 5MTQ · PDBe 5MTQ · UniProt P9WGR1

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