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Crystal structure of M. tuberculosis mend with thdp, MG2+ and isochorismate bound
Analyse Crystal structure of M. tuberculosis mend with thdp, MG2+ and isochorismate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ESO
- Type
- protein
- Length
- 2,150 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
- ISC, TPP, MG
- Pockets
- 20 · best druggability 0.83
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 | 529 | 39% helix, 19% strand | P9WK11 |
| B | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 535 | 39% helix, 19% strand | P9WK11 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 543 | 40% helix, 17% strand | P9WK11 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 543 | 40% helix, 17% strand | P9WK11 |
Ligands and binding sites
- ISC · (5S,6S)-5-[(1-carboxyethenyl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylic acid · ligand · 2 copies · chains A, D, B, C
- TPP · Thiamine diphosphate · ligand · 2 copies · chains B, C, A, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 6 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.83 | 0.88 | 86 | ISC, MG, FMT, TPP |
| 2 | 409 | 0.82 | 0.90 | 68 | ISC, MG, TPP |
| 3 | 324 | 0.80 | 0.91 | 52 | empty |
| 4 | 333 | 0.79 | 0.90 | 50 | FMT |
| 5 | 245 | 0.75 | 0.89 | 37 | empty |
Interfaces
6 interfaces between chains.
- B–C · 3356 Ų buried · 48 hydrogen bonds · protein-protein
- A–D · 3254 Ų buried · 49 hydrogen bonds · protein-protein
- B–D · 1556 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 1535 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 791 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5ESO · Crystal Structure of M. tuberculosis MenD with ThDP, Mg2+ and Isochorismate bound · 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 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 5ESO · PDBe 5ESO · UniProt P9WK11
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