Research workbench
The complete reaction cycle of human phosphoglycerate kinase: the open ternary complex with 3PG and AMP-pnp
Analyse The complete reaction cycle of human phosphoglycerate kinase: the open ternary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XE8
- Type
- protein
- Length
- 413 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
- Pockets
- 3 · best druggability 0.50
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 | 413 | 42% helix, 18% strand | P00558 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · chains A
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 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 | 113 | 0.50 | 0.81 | 29 | ACP |
| 2 | 127 | 0.42 | 0.76 | 27 | 3PG |
| 3 | 83 | 0.35 | 0.75 | 13 | empty |
Compared structures
- 2XE8 · The complete reaction cycle of human phosphoglycerate kinase: The open ternary complex… · 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 0.97
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 2XE8 · PDBe 2XE8 · UniProt P00558
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