MolNFT v1 · #8864 · protein
Pig muscle 3-phosphoglycerate kinase complexed with 3-pg and mgadp.
1HDI: “Pig muscle 3-phosphoglycerate kinase complexed with 3-pg and mgadp.”. X-ray diffraction, 3 ligands (AMP, 3PG, MG), 4 pockets (best druggability 0.48). MolNFT v1 #8864 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HDI
- Type
- protein
- Length
- 413 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- Ligands
- AMP, 3PG, MG
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 413 | 40% helix, 18% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · 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
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 | 129 | 0.48 | 0.79 | 31 | AMP |
| 2 | 146 | 0.45 | 0.76 | 26 | empty |
| 3 | 174 | 0.43 | 0.74 | 26 | empty |
| 4 | 54 | 0.27 | 0.75 | 18 | 3PG |
Compared structures
- 1HDI · Pig muscle 3-PHOSPHOGLYCERATE KINASE complexed with 3-PG and MgADP. · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1HDI · PDBe 1HDI
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