Research workbench

Type II dehydroquinase from mycobacterium tuberculosis complexed with citrazinic acid

Analyse Type II dehydroquinase from mycobacterium tuberculosis complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3N8K
Type: protein
Length: 3,391 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-dehydroquinate dehydratase
EC: 4.2.1.10
UniProt: P0A4Z6
Ligands: D1X, CL
Pockets: 11 · best druggability 0.67

Structure

x-ray diffraction · 7 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	142	46% helix, 18% strand	P0A4Z6
C	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	142	46% helix, 18% strand	P0A4Z6
D, E, G	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	143	47% helix, 17% strand	P0A4Z6
F, H, I, J, K, L, N, O, P, R, S, T, U, V, W	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	141	49% helix, 18% strand	P0A4Z6
M	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	151	45% helix, 17% strand	P0A4Z6
Q	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	136	38% helix, 18% strand	P0A4Z6
X	3-dehydroquinate dehydratase (EC 4.2.1.10)	protein	134	44% helix, 19% strand	P0A4Z6

Ligands and binding sites

D1X · 2,6-dioxo-1,2,3,6-tetrahydropyridine-4-carboxylic acid · ligand · 22 copies · chains A, L, B, E, C, D, G, F, H, J, I, K, N, Q, O, P, S, M, X, R, T, V, U, W
CL · Chloride ion · ion · 26 copies · chains A, G, B, F, C, H, D, I, E, K, J, L, M, S, N, R, O, T, P, U, Q, W, V, X

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

Pockets

11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	822	0.67	0.74	67	CL
2	333	0.63	0.79	53	empty
3	260	0.63	0.81	28	empty
4	247	0.61	0.81	40	empty
5	290	0.59	0.78	51	empty

Interfaces

39 interfaces between chains.

N–R · 1103 Å² buried · 19 hydrogen bonds · protein-protein
B–F · 1091 Å² buried · 17 hydrogen bonds · protein-protein
Q–W · 1090 Å² buried · 21 hydrogen bonds · protein-protein
V–X · 1083 Å² buried · 25 hydrogen bonds · protein-protein
O–T · 1071 Å² buried · 19 hydrogen bonds · protein-protein

Compared structures

3N8K · Type II dehydroquinase from Mycobacterium tuberculosis complexed with citrazinic acid · the same entry in another collection · chain A 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 P0A4Z6
Elsewhere: RCSB PDB 3N8K · PDBe 3N8K · UniProt P0A4Z6

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.