MolNFT v1 · #53592 · protein
The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in complex with ADP, 3PG and aluminium trifluoride
2WZD · Phosphoglycerate kinase 1: “The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in complex…”. X-ray diffraction, 5 ligands (AF3, ADP, 3PG), 3 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 2WZD
- 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
- AF3, ADP, 3PG, MG, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 405 | 42% helix, 18% strand | P00558 |
Ligands and binding sites
- AF3 · Aluminum fluoride · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- 3PG · 3-phosphoglyceric acid · 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 | 635 | 0.74 | 0.80 | 74 | MG, AF3, ADP, 3PG |
| 2 | 65 | 0.32 | 0.75 | 16 | empty |
| 3 | 69 | 0.31 | 0.74 | 15 | empty |
Compared structures
- 2WZD · The catalytically active fully closed conformation of human phosphoglycerate kinase K219A… · 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 0.76
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 2WZD · PDBe 2WZD · UniProt P00558
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