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M.TB mend with inhibitor

Analyse M.TB mend with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O0N
Type: protein
Length: 2,072 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase
EC: 2.2.1.9
UniProt: P9WK11
Ligands: DNA
Pockets: 20 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9)	protein	523	38% helix, 19% strand	P9WK11
B	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9)	protein	519	38% helix, 19% strand	P9WK11
C	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9)	protein	514	38% helix, 18% strand	P9WK11
D	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9)	protein	516	39% helix, 18% strand	P9WK11

Ligands and binding sites

DNA · 1,4-dihydroxy-2-naphthoic acid · ligand · 4 copies · chains A, B, 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, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	433	0.78	0.87	50	DNA
2	417	0.78	0.87	46	DNA
3	401	0.78	0.87	62	empty
4	203	0.71	0.88	43	empty
5	352	0.70	0.82	60	empty

Interfaces

6 interfaces between chains.

A–D · 2432 Å² buried · 33 hydrogen bonds · protein-protein
B–C · 2113 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1541 Å² buried · 41 hydrogen bonds · protein-protein
B–D · 1521 Å² buried · 40 hydrogen bonds · protein-protein
C–D · 390 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6O0N · M.tb MenD with Inhibitor · the same entry in another collection · chain D against D, TM-score 1.00
P9WK11 · AlphaFold monomer V2.0 prediction for 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-c… · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P9WK11
Elsewhere: RCSB PDB 6O0N · PDBe 6O0N · UniProt P9WK11

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