Research workbench
Crystal structure of glucosyl-3-phosphoglycerate synthase from mycobacterium tuberculosis in complex with MN2+, uridine-diphosphate- glucose (udp-glc) and 3-(PHOSPHONOOXY)PROPANOIC acid (ppa) - gpgs MN2+ udp-glc ppa
Analyse Crystal structure of glucosyl-3-phosphoglycerate synthase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y7F
- Type
- protein
- Length
- 279 residues
- Chains
- 1
- 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
- 48X, UPG, MN, SO4
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucosyl-3-phosphoglycerate synthase (EC 2.4.1.266) | protein | 279 | 41% helix, 18% strand | P9WMW9 |
Ligands and binding sites
- 48X · 3-(phosphonooxy)propanoic acid · ligand · chains A
- UPG · Uridine-5'-diphosphate-glucose · ligand · chains A
- MN · Manganese (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 515 | 0.76 | 0.83 | 52 | MN, 48X, UPG |
Compared structures
- 4Y7F · 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 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 P9WMW9
- Elsewhere: RCSB PDB 4Y7F · PDBe 4Y7F · UniProt P9WMW9
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