MolNFT v1 · #123650 · protein
Crystal structure of glucosyl-3-phosphoglycerate synthase from mycobacterium tuberculosis in complex with phosphoglyceric acid (pga) - GPGS*PGA
5JQX: “Crystal structure of glucosyl-3-phosphoglycerate synthase from mycobacterium tuberculosis in complex with…”. X-ray diffraction, 1 ligand (3PG), 4 pockets (best druggability 0.80). MolNFT v1 #123650 on GenesisL1: 3D structure…
- PDB
- 5JQX
- Type
- protein
- Length
- 1,117 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosyl-3-phosphoglycerate synthase
- EC
- 2.4.1.266
- UniProt
- P9WMW9
- Ligands
- 3PG
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosyl-3-phosphoglycerate synthase (EC 2.4.1.266) | protein | 280 | 37% helix, 18% strand | P9WMW9 |
| B | Glucosyl-3-phosphoglycerate synthase (EC 2.4.1.266) | protein | 279 | 37% helix, 17% strand | P9WMW9 |
| C, D | Glucosyl-3-phosphoglycerate synthase (EC 2.4.1.266) | protein | 279 | 37% helix, 18% strand | P9WMW9 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.80 | 0.81 | 120 | 3PG |
| 2 | 467 | 0.76 | 0.85 | 55 | 3PG |
| 3 | 1104 | 0.76 | 0.78 | 112 | 3PG |
| 4 | 534 | 0.73 | 0.81 | 55 | 3PG |
Interfaces
3 interfaces between chains.
- A–B · 1414 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 482 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 433 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5JQX · Crystal structure of glucosyl-3-phosphoglycerate synthase from Mycobacterium tuberculosis… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WMW9 · AlphaFold monomer V2.0 prediction for glucosyl-3-phosphoglycerate synthase (P9WMW9) · a predicted model of the same protein · chain C 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 P9WMW9
- Elsewhere: RCSB PDB 5JQX · PDBe 5JQX · UniProt P9WMW9
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