Research workbench
Crystal structure of mycobacterium tuberculosis malate synthase in complex with 5-(5-chlorothiophen-2-YL)ISOXAZOLE-3-carboxylic 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
- 5DX7
- Type
- protein
- Length
- 714 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
- 5H6, MG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate synthase G (EC 2.3.3.9) | protein | 714 | 46% helix, 16% strand | P9WK17 |
Ligands and binding sites
- 5H6 · 5-(5-chlorothiophen-2-yl)-1,2-oxazole-3-carboxylic acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.72 | 0.81 | 57 | MG, 5H6 |
| 2 | 123 | 0.52 | 0.81 | 31 | empty |
| 3 | 61 | 0.41 | 0.81 | 18 | empty |
| 4 | 77 | 0.39 | 0.79 | 18 | empty |
| 5 | 110 | 0.38 | 0.75 | 22 | empty |
Compared structures
- 5DX7 · 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 5DX7 · PDBe 5DX7 · UniProt P9WK17
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