MolNFT v1 · #120707 · protein
Crystal structure of mycobacterium tuberculosis wild-type malate synthase in complex with product malate
5H8U · Malate synthase G: “Crystal structure of mycobacterium tuberculosis wild-type malate synthase in complex with product malate”. X-ray diffraction, 3 ligands (LMR, GLV, MG), 13 pockets (best druggability 0.69). MolNFT v1 #120707 on…
- PDB
- 5H8U
- Type
- protein
- Length
- 1,436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate synthase G
- EC
- 2.3.3.9
- UniProt
- P9WK17
- Ligands
- LMR, GLV, MG
- Pockets
- 13 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate synthase G (EC 2.3.3.9) | protein | 720 | 46% helix, 18% strand | P9WK17 |
| B | Malate synthase G (EC 2.3.3.9) | protein | 716 | 44% helix, 16% strand | P9WK17 |
Ligands and binding sites
- LMR · (2S)-2-hydroxybutanedioic acid · ligand · chains A
- GLV · Glyoxylic acid · ligand · chains B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 525 | 0.69 | 0.79 | 43 | empty |
| 2 | 471 | 0.67 | 0.79 | 40 | empty |
| 3 | 243 | 0.67 | 0.84 | 52 | MG, LMR |
| 4 | 255 | 0.63 | 0.81 | 55 | MG, GLV |
| 5 | 119 | 0.50 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5H8U · Crystal structure of mycobacterium tuberculosis wild-type 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 1.00
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 5H8U · PDBe 5H8U · UniProt P9WK17
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