MolNFT v1 · #118132 · protein
Crystal structure of M. tuberculosis mend bound to MG2+ and covalent intermediate I (a thdp and decarboxylated 2-oxoglutarate adduct)
5ESS · 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1…: “Crystal structure of M. tuberculosis mend bound to MG2+ and covalent intermediate I (a thdp and…”. X-ray diffraction, 3 ligands (TOG, DPO, MG), 20 pockets (best druggability…
- PDB
- 5ESS
- Type
- protein
- Length
- 2,173 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
- TOG, DPO, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 18% 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 | 551 | 38% helix, 19% strand | P9WK11 |
| B | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 537 | 39% helix, 19% strand | P9WK11 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 543 | 39% helix, 18% strand | P9WK11 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 542 | 39% helix, 18% strand | P9WK11 |
Ligands and binding sites
- 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 B, C, A, D
- DPO · Diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 3 copies · chains A, C, D
- FMT · Formic acid · additive · 10 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 3 copies · chains D
- GOL · Glycerol · additive · chains 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.86 | 0.91 | 89 | empty |
| 2 | 620 | 0.85 | 0.90 | 89 | empty |
| 3 | 611 | 0.83 | 0.88 | 83 | FMT, TOG, MG |
| 4 | 460 | 0.83 | 0.90 | 72 | FMT, TOG, MG |
| 5 | 849 | 0.81 | 0.84 | 82 | MG, DPO |
Interfaces
6 interfaces between chains.
- A–D · 3444 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 3442 Ų buried · 52 hydrogen bonds · protein-protein
- B–D · 1567 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 1554 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 847 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5ESS · Crystal Structure of M. tuberculosis MenD bound to Mg2+ and covalent intermediate I (a… · 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 0.98
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 5ESS · PDBe 5ESS · UniProt P9WK11
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