MolNFT v1 · #143362 · protein
Crystal structure of mycobacterium tuberculosis malate synthase in complex with 2-naphthyldiketoacid
6AXB · Malate synthase G: “Crystal structure of mycobacterium tuberculosis malate synthase in complex with 2-naphthyldiketoacid”. X-ray diffraction, 2 ligands (C0V, MG), 5 pockets (best druggability 0.70). MolNFT v1 #143362 on GenesisL1…
- PDB
- 6AXB
- Type
- protein
- Length
- 715 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
- C0V, MG
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate synthase G (EC 2.3.3.9) | protein | 715 | 47% helix, 18% strand | A5U3K4 |
Ligands and binding sites
- C0V · (2Z)-2-hydroxy-4-(naphthalen-2-yl)-4-oxobut-2-enoic acid · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · 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 | 247 | 0.70 | 0.85 | 47 | MG, C0V |
| 2 | 374 | 0.61 | 0.77 | 35 | empty |
| 3 | 111 | 0.50 | 0.81 | 30 | PEG |
| 4 | 64 | 0.39 | 0.80 | 21 | empty |
| 5 | 60 | 0.37 | 0.80 | 18 | empty |
Compared structures
- 6AXB · 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 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 A5U3K4
- Elsewhere: RCSB PDB 6AXB · PDBe 6AXB · UniProt A5U3K4
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