Research workbench
M.TB mend bound to intermediate I and inhibitor
Analyse M.TB mend bound to intermediate I and inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O0G
- Type
- protein
- Length
- 2,130 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, TOG, AKG, MG, CL
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% 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 | 530 | 38% helix, 19% strand | P9WK11 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 538 | 39% helix, 18% strand | P9WK11 |
| B | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 530 | 39% helix, 19% strand | P9WK11 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 532 | 39% helix, 18% strand | P9WK11 |
Ligands and binding sites
- DNA · 1,4-dihydroxy-2-naphthoic acid · ligand · 4 copies · chains A, D, B, C
- TOG · 4-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy) phosphoryl]oxyethyl]-1,3-thiazol-3-ium-2-yl]-4-oxidanyl-butanoic acid · ligand · 2 copies · chains A, D, B, C
- AKG · 2-oxoglutaric acid · ligand · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains D, C
- CL · Chloride ion · ion · chains D
- FMT · Formic acid · additive · 8 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains D, B, C
- GOL · Glycerol · additive · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 546 | 0.83 | 0.90 | 91 | DNA |
| 2 | 459 | 0.83 | 0.90 | 81 | ACT, FMT, AKG, TOG, MG |
| 3 | 497 | 0.81 | 0.88 | 81 | FMT, TOG, MG |
| 4 | 411 | 0.81 | 0.89 | 62 | DNA, FMT, PGE, GOL |
| 5 | 97 | 0.68 | 0.92 | 23 | DNA |
Interfaces
6 interfaces between chains.
- A–D · 3288 Ų buried · 56 hydrogen bonds · protein-protein
- B–C · 3143 Ų buried · 50 hydrogen bonds · protein-protein
- D–B · 1567 Ų buried · 44 hydrogen bonds · protein-protein
- A–C · 1526 Ų buried · 47 hydrogen bonds · protein-protein
- D–C · 710 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6O0G · M.tb MenD bound to Intermediate I and Inhibitor · the same entry in another collection · chain C against C, 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 A 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 P9WK11
- Elsewhere: RCSB PDB 6O0G · PDBe 6O0G · UniProt P9WK11
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