MolNFT v1 · #59620 · protein
Crystal structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-cdp
3C3C · Phosphoglycerate kinase 1: “Crystal structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-cdp”. X-ray diffraction, 3 ligands (3PG, CDP, MG), 8 pockets (best druggability 0.71). MolNFT v1 #59620 on GenesisL1…
- PDB
- 3C3C
- Type
- protein
- Length
- 801 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase 1
- EC
- 2.7.2.3
- UniProt
- P00558
- Ligands
- 3PG, CDP, MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 403 | 37% helix, 19% strand | P00558 |
| B | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 398 | 35% helix, 19% strand | P00558 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains A, B
- CDP · Cytidine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1027 | 0.71 | 0.75 | 75 | empty |
| 2 | 214 | 0.50 | 0.76 | 37 | 3PG |
| 3 | 96 | 0.46 | 0.80 | 30 | empty |
| 4 | 91 | 0.45 | 0.80 | 24 | CDP |
| 5 | 107 | 0.39 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 246 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3C3C · Crystal Structure of human phosphoglycerate kinase bound to 3-phosphoglycerate and L-CDP · 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 B against A, TM-score 0.95
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 3C3C · PDBe 3C3C · UniProt P00558
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