Research workbench
The catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP, 3PG and magnesium trifluoride
Analyse The catalytically active fully closed conformation of human phosphoglycerate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WZB
- Type
- protein
- Length
- 405 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase 1
- EC
- 2.7.2.3
- UniProt
- P00558
- Ligands
- ADP, 3PG, MGF, MG, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 405 | 42% helix, 17% strand | P00558 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- 3PG · 3-phosphoglyceric acid · ligand · chains A
- MGF · Trifluoromagnesate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 542 | 0.71 | 0.80 | 62 | MG, ADP, 3PG, MGF |
| 2 | 87 | 0.33 | 0.74 | 16 | empty |
| 3 | 71 | 0.33 | 0.75 | 14 | empty |
Compared structures
- 2WZB · The catalytically active fully closed conformation of human phosphoglycerate kinase in… · the same entry in another collection · chain A against A, TM-score 1.00
- P00558 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase 1 (P00558) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 P00558
- Elsewhere: RCSB PDB 2WZB · PDBe 2WZB · UniProt P00558
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