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Crystal structure of mycobacterium tuberculosis argc in complex with nicotinamide adenine dinucleotide phosphate (NADP+) and 5-methoxy-3- indoleacetic acid

Analyse Crystal structure of mycobacterium tuberculosis argc in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7NOT
Type: protein
Length: 2,752 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N-acetyl-gamma-glutamyl-phosphate reductase
EC: 1.2.1.38
UniProt: P9WPZ9
Ligands: MYI, NAP
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38)	protein	344	32% helix, 22% strand	P9WPZ9

Ligands and binding sites

MYI · (5-methoxy-1H-indol-3-yl)acetic acid · ligand · 4 copies · chains A, B, C, D
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	442	0.87	0.94	88	empty
2	833	0.86	0.88	139	empty
3	684	0.77	0.82	84	MYI
4	461	0.70	0.81	44	NAP, MYI
5	632	0.70	0.78	68	NAP, MYI

Interfaces

13 interfaces between chains.

E–H · 1788 Å² buried · 17 hydrogen bonds · protein-protein
B–C · 1753 Å² buried · 14 hydrogen bonds · protein-protein
A–D · 1733 Å² buried · 18 hydrogen bonds · protein-protein
F–G · 1726 Å² buried · 19 hydrogen bonds · protein-protein
C–D · 1184 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7NOT · Crystal structure of Mycobacterium tuberculosis ArgC in complex with nicotinamide adenine… · the same entry in another collection · chain H against H, TM-score 1.00
P9WPZ9 · AlphaFold monomer V2.0 prediction for N-acetyl-gamma-glutamyl- phosphate reductase… · a predicted model of the same protein · chain B against A, TM-score 1.00

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 P9WPZ9
Elsewhere: RCSB PDB 7NOT · PDBe 7NOT · UniProt P9WPZ9

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