MolNFT v1 · #60549 · protein
Atomic resolution structures of escherichia COLI and bacillis anthracis malate synthase a: comparison with isoform G and implications for structure based drug design
3CV2: “Atomic resolution structures of escherichia COLI and bacillis anthracis malate synthase a: comparison with…”. X-ray diffraction, 3 ligands (OXL, COA, MG), 14 pockets (best druggability 0.76). MolNFT v1 #60549 on GenesisL1: 3D…
- PDB
- 3CV2
- Type
- protein
- Length
- 1,049 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Malate synthase a
- EC
- 2.3.3.9
- UniProt
- P08997
- Ligands
- OXL, COA, MG
- Pockets
- 14 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate synthase a (EC 2.3.3.9) | protein | 524 | 51% helix, 13% strand | P08997 |
| B | Malate synthase a (EC 2.3.3.9) | protein | 525 | 51% helix, 13% strand | P08997 |
Ligands and binding sites
- OXL · Oxalate ion · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · 2 copies · chains A, 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
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1044 | 0.76 | 0.78 | 80 | empty |
| 2 | 156 | 0.67 | 0.87 | 38 | OXL, MG |
| 3 | 245 | 0.64 | 0.82 | 50 | OXL, MG |
| 4 | 238 | 0.61 | 0.80 | 38 | empty |
| 5 | 127 | 0.58 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 3CV2 · Atomic Resolution Structures of Escherichia coli and Bacillis anthracis Malate Synthase… · the same entry in another collection · chain A against A, TM-score 1.00
- P08997 · AlphaFold monomer V2.0 prediction for malate synthase a (P08997) · 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 P08997
- Elsewhere: RCSB PDB 3CV2 · PDBe 3CV2 · UniProt P08997
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