Research workbench
Crystallographic analysis of phosphoglycerate kinase from the hyperthermophilic bacterium thermotoga maritima
Analyse Crystallographic analysis of phosphoglycerate kinase from the hyperthermophilic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VPE
- Type
- protein
- Length
- 398 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- P36204
- Ligands
- ANP, 3PG, MG
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 398 | 41% helix, 18% strand | P36204 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- 3PG · 3-phosphoglyceric acid · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.65 | 0.79 | 54 | MG, ANP, 3PG |
| 2 | 138 | 0.51 | 0.80 | 28 | empty |
| 3 | 54 | 0.38 | 0.80 | 18 | empty |
Compared structures
- 1VPE · Crystallographic analysis of phosphoglycerate kinase from the hyperthermophilic bacterium… · the same entry in another collection · chain A against A, TM-score 1.00
- P36204 · AlphaFold monomer V2.0 prediction for bifunctional PGK/TIM (P36204) · a predicted model of the same protein · chain A against A, TM-score 0.84
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 P36204
- Elsewhere: RCSB PDB 1VPE · PDBe 1VPE · UniProt P36204
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