Research workbench
Crystal structure of mycobacterium tuberculosis malate synthase in complex with 2-hydroxy-4-(1H-indol-3-yl)-4-oxobut-2-enoic acid
Analyse Crystal structure of mycobacterium tuberculosis malate synthase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DRC
- Type
- protein
- Length
- 716 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate synthase G
- EC
- 2.3.3.9
- UniProt
- P9WK17
- Ligands
- 5ER, MG
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate synthase G (EC 2.3.3.9) | protein | 716 | 46% helix, 18% strand | P9WK17 |
Ligands and binding sites
- 5ER · (2Z)-2-hydroxy-4-(1H-indol-3-yl)-4-oxobut-2-enoic acid · ligand · 2 copies · chains A
- MG · Magnesium ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 185 | 0.70 | 0.87 | 42 | MG, 5ER |
| 2 | 368 | 0.61 | 0.77 | 42 | empty |
| 3 | 61 | 0.41 | 0.81 | 20 | empty |
| 4 | 62 | 0.37 | 0.79 | 18 | empty |
| 5 | 73 | 0.36 | 0.77 | 17 | MG |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5DRC · Crystal structure of Mycobacterium tuberculosis malate synthase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WK17 · AlphaFold monomer V2.0 prediction for malate synthase G (P9WK17) · a predicted model of the same protein · chain A 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 P9WK17
- Elsewhere: RCSB PDB 5DRC · PDBe 5DRC · UniProt P9WK17
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