MolNFT v1 · #116883 · protein
Crystal structure of mycobacterium tuberculosis malate synthase in complex with 2-hydroxy-4-(1H-indol-5-yl)-4-oxobut-2-enoic acid inhibitor
5DRI · Malate synthase G: “Crystal structure of mycobacterium tuberculosis malate synthase in complex with…”. X-ray diffraction, 2 ligands (5EQ, MG), 4 pockets (best druggability 0.70). MolNFT v1 #116883 on GenesisL1: 3D structure, binding…
- PDB
- 5DRI
- Type
- protein
- Length
- 708 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
- A5U3K4
- Ligands
- 5EQ, MG
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate synthase G (EC 2.3.3.9) | protein | 708 | 45% helix, 16% strand | A5U3K4 |
Ligands and binding sites
- 5EQ · (2Z)-2-hydroxy-4-(1H-indol-5-yl)-4-oxobut-2-enoic 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
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 184 | 0.70 | 0.87 | 39 | MG, 5EQ |
| 2 | 439 | 0.66 | 0.79 | 37 | empty |
| 3 | 155 | 0.56 | 0.81 | 31 | empty |
| 4 | 59 | 0.38 | 0.80 | 20 | empty |
Compared structures
- 5DRI · Crystal structure of Mycobacterium tuberculosis malate synthase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- A5U3K4 · AlphaFold monomer V2.0 prediction for malate synthase G (A5U3K4) · 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 A5U3K4
- Elsewhere: RCSB PDB 5DRI · PDBe 5DRI · UniProt A5U3K4
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