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Crystal structure of 3-dehydroquinate dehydratase from mycobacterium tuberculosis in complex with inhibitor 4

Analyse Crystal structure of 3-dehydroquinate dehydratase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3N86
Type: protein
Length: 3,394 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-dehydroquinate dehydratase
UniProt: P0A4Z6
Ligands: RJP
Pockets: 20 · best druggability 0.76

Structure

x-ray diffraction · 4 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, L, M, N, O, Q, S, T, U, X	3-dehydroquinate dehydratase	protein	141	48% helix, 19% strand	P0A4Z6
J, W	3-dehydroquinate dehydratase	protein	143	45% helix, 19% strand	P0A4Z6
K, P, R	3-dehydroquinate dehydratase	protein	142	50% helix, 19% strand	P0A4Z6
V	3-dehydroquinate dehydratase	protein	144	44% helix, 17% strand	P0A4Z6

Ligands and binding sites

RJP · (1R,5R)-1,5-dihydroxy-4-oxo-3-[3-oxo-3-(phenylamino)propyl]cyclohex-2-ene-1-carboxylic acid · ligand · 24 copies · chains A, L, B, E, C, D, G, F, H, J, I, K, M, X, N, Q, O, P, S, R, T, V, U, W

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.76	0.97	24	RJP
2	101	0.76	0.97	24	RJP
3	179	0.76	0.92	30	RJP
4	112	0.75	0.95	30	RJP
5	94	0.75	0.97	24	RJP

Interfaces

36 interfaces between chains.

B–F · 1025 Å² buried · 16 hydrogen bonds · protein-protein
P–U · 1022 Å² buried · 20 hydrogen bonds · protein-protein
N–R · 1022 Å² buried · 15 hydrogen bonds · protein-protein
V–X · 1021 Å² buried · 21 hydrogen bonds · protein-protein
J–L · 1015 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

3N86 · Crystal structure of 3-dehydroquinate dehydratase from Mycobacterium tuberculosis in… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt P0A4Z6
Elsewhere: RCSB PDB 3N86 · PDBe 3N86 · UniProt P0A4Z6

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