Research workbench
The catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in complex with AMP-pcp and 3PG
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
- 2X14
- 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
- 3PG, ACP, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase 1 (EC 2.7.2.3) | protein | 405 | 40% helix, 18% strand | P00558 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · chains A
- ACP · Phosphomethylphosphonic acid adenylate ester · 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
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 | 634 | 0.73 | 0.80 | 68 | MG, 3PG, ACP |
| 2 | 85 | 0.32 | 0.73 | 16 | empty |
| 3 | 71 | 0.31 | 0.74 | 16 | empty |
Compared structures
- 2X14 · 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 0.77
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 2X14 · PDBe 2X14 · UniProt P00558
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