MolNFT v1 · #56487 · protein
Crystal structure of human phosphoglycerate kinase bound to D-ADP
2ZGV · Phosphoglycerate kinase 1: “Crystal structure of human phosphoglycerate kinase bound to D-ADP”. X-ray diffraction, 1 ligand (ADP), 4 pockets (best druggability 0.45). MolNFT v1 #56487 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2ZGV
- Type
- protein
- Length
- 403 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
- Pockets
- 4 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 403 | 39% helix, 18% strand | P00558 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.45 | 0.81 | 25 | ADP |
| 2 | 121 | 0.40 | 0.75 | 20 | empty |
| 3 | 55 | 0.30 | 0.75 | 11 | empty |
| 4 | 66 | 0.28 | 0.74 | 19 | empty |
Compared structures
- 2ZGV · Crystal Structure of human phosphoglycerate kinase bound to D-ADP · 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 0.99
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 P00558
- Elsewhere: RCSB PDB 2ZGV · PDBe 2ZGV · UniProt P00558
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