MolNFT v1 · #18213 · protein
Structure of the ADP complex of the 3-phosphoglycerate kinase from bacillus stearothermophilus at 1.65 ångströms
1PHP: “Structure of the ADP complex of the 3-phosphoglycerate kinase from bacillus stearothermophilus at 1.65…”. X-ray diffraction, 2 ligands (ADP, MG), 3 pockets (best druggability 0.49). MolNFT v1 #18213 on GenesisL1: 3D structure…
- PDB
- 1PHP
- Type
- protein
- Length
- 394 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- P18912
- Ligands
- ADP, MG
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-phosphoglycerate kinase (EC 2.7.2.3) | protein | 394 | 42% helix, 17% strand | P18912 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.49 | 0.77 | 32 | empty |
| 2 | 110 | 0.42 | 0.77 | 31 | MG, ADP |
| 3 | 73 | 0.31 | 0.74 | 14 | empty |
Compared structures
- 1PHP · Structure of the ADP complex of the 3-phosphoglycerate kinase from bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P18912 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (P18912) · 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 P18912
- Elsewhere: RCSB PDB 1PHP · PDBe 1PHP · UniProt P18912
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