MolNFT v1 · #137145 · protein
1.36 ångström resolution crystal structure of malate synthase G from pseudomonas aeruginosa in complex with glycolic acid.
5VFB: “1.36 ångström resolution crystal structure of malate synthase G from pseudomonas aeruginosa in complex with…”. X-ray diffraction, 4 ligands (GOA, NI, NA), 12 pockets (best druggability 0.76). MolNFT v1 #137145 on GenesisL1: 3D…
- PDB
- 5VFB
- Type
- protein
- Length
- 1,448 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
- Q9I636
- Ligands
- GOA, NI, NA, CL
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Malate synthase G (EC 2.3.3.9) | protein | 724 | 45% helix, 19% strand | Q9I636 |
Ligands and binding sites
- GOA · Glycolic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 602 | 0.76 | 0.82 | 59 | NA |
| 2 | 385 | 0.69 | 0.82 | 32 | CL |
| 3 | 299 | 0.65 | 0.81 | 53 | NI, GOA |
| 4 | 279 | 0.65 | 0.81 | 49 | NI, GOA |
| 5 | 397 | 0.65 | 0.78 | 34 | CL |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5VFB · 1.36 Angstrom Resolution Crystal Structure of Malate Synthase G from Pseudomonas… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9I636 · AlphaFold monomer V2.0 prediction for malate synthase G (Q9I636) · 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 Q9I636
- Elsewhere: RCSB PDB 5VFB · PDBe 5VFB · UniProt Q9I636
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