Research workbench
Crystal structure of M. tuberculosis mend bound to thdp and MN2+
Analyse Crystal structure of M. tuberculosis mend bound to thdp and MN2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ESD
- Type
- protein
- Length
- 2,152 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
- TPP, MN
- 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 | 539 | 39% helix, 19% strand | P9WK11 |
| B | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 532 | 39% helix, 19% strand | P9WK11 |
| C | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 540 | 40% helix, 18% strand | P9WK11 |
| D | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1- carboxylate synthase (EC 2.2.1.9) | protein | 541 | 40% helix, 17% strand | P9WK11 |
Ligands and binding sites
- TPP · Thiamine diphosphate · ligand · 4 copies · chains A, D, B, C
- MN · Manganese (II) ion · metal · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 676 | 0.86 | 0.90 | 83 | empty |
| 2 | 598 | 0.85 | 0.90 | 89 | empty |
| 3 | 649 | 0.83 | 0.88 | 84 | TPP, MN |
| 4 | 619 | 0.83 | 0.88 | 83 | TPP |
| 5 | 400 | 0.78 | 0.87 | 57 | MN, TPP |
Interfaces
6 interfaces between chains.
- A–D · 3309 Ų buried · 47 hydrogen bonds · protein-protein
- B–C · 3271 Ų buried · 52 hydrogen bonds · protein-protein
- A–C · 1580 Ų buried · 44 hydrogen bonds · protein-protein
- B–D · 1556 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 831 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5ESD · Crystal Structure of M. tuberculosis MenD bound to ThDP and Mn2+ · 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 5ESD · PDBe 5ESD · UniProt P9WK11
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