MolNFT v1 · #104699 · protein
The structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase RV2419C complexes with VO3
4QIH: “The structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase RV2419C complexes with VO3”. X-ray diffraction, 1 ligand (VN3), 2 pockets (best druggability 0.68). MolNFT v1 #104699 on GenesisL1: 3D structure, binding sites…
- PDB
- 4QIH
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucosyl-3-phosphoglycerate phosphatase
- EC
- 3.1.3.-, 3.1.3.70
- UniProt
- P9WIC6
- Ligands
- VN3
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.-, 3.1.3.70) | protein | 209 | 42% helix, 19% strand | P9WIC6 |
| B | Glucosyl-3-phosphoglycerate phosphatase (EC 3.1.3.-, 3.1.3.70) | protein | 201 | 43% helix, 19% strand | P9WIC6 |
Ligands and binding sites
- VN3 · Vanadate ion · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.68 | 0.81 | 39 | VN3 |
| 2 | 336 | 0.65 | 0.80 | 42 | empty |
Interfaces
1 interface between chains.
- A–B · 826 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4QIH · The structure of mycobacterial glucosyl-3-phosphoglycerate phosphatase Rv2419c complexes… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WIC6 · AlphaFold monomer V2.0 prediction for glucosyl-3-phosphoglycerate phosphatase (P9WIC6) · 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 P9WIC6
- Elsewhere: RCSB PDB 4QIH · PDBe 4QIH · UniProt P9WIC6
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