MolNFT v1 · #17911 · protein
Structure of escherichia COLI malate synthase G:PYRUVATE:ACETYL- coenzyme a abortive ternary complex at 1.95 ångström resolution
1P7T: “Structure of escherichia COLI malate synthase G:PYRUVATE:ACETYL- coenzyme a abortive ternary complex at 1.95…”. X-ray diffraction, 3 ligands (ACO, PYR, MG), 10 pockets (best druggability 0.74). MolNFT v1 #17911 on GenesisL1: 3D…
- PDB
- 1P7T
- Type
- protein
- Length
- 1,411 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
- P37330
- Ligands
- ACO, PYR, MG
- Pockets
- 10 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Malate synthase G (EC 2.3.3.9) | protein | 706 | 49% helix, 19% strand | P37330 |
| B | Malate synthase G (EC 2.3.3.9) | protein | 705 | 49% helix, 18% strand | P37330 |
Ligands and binding sites
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains A, B
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · 2 copies · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1023 | 0.74 | 0.77 | 85 | PEG |
| 2 | 517 | 0.69 | 0.79 | 38 | empty |
| 3 | 528 | 0.67 | 0.78 | 43 | empty |
| 4 | 327 | 0.66 | 0.81 | 57 | MG, ACO, PYR |
| 5 | 258 | 0.63 | 0.81 | 41 | MG, ACO, PYR |
Interfaces
1 interface between chains.
- A–B · 883 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (oxidation).
Compared structures
- 1P7T · Structure of Escherichia coli malate synthase G:pyruvate:acetyl-Coenzyme A abortive… · the same entry in another collection · chain A against A, TM-score 1.00
- P37330 · AlphaFold monomer V2.0 prediction for malate synthase G (P37330) · 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 P37330
- Elsewhere: RCSB PDB 1P7T · PDBe 1P7T · UniProt P37330
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