MolNFT v1 · #75114 · protein
The structure of yeast phosphoglycerate mutase at 0.28 nm resolution
3PGM · Phosphoglycerate mutase 1: “The structure of yeast phosphoglycerate mutase at 0.28 nm resolution”. X-ray diffraction, 2 ligands (3PG, SO4), 7 pockets (best druggability 0.62). MolNFT v1 #75114 on GenesisL1: 3D structure, binding…
- PDB
- 3PGM
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate mutase 1
- EC
- 2.7.5.3
- UniProt
- P00950
- Ligands
- 3PG, SO4
- Pockets
- 7 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphoglycerate mutase 1 (EC 2.7.5.3) | protein | 230 | 30% helix, 8% strand | P00950 |
Ligands and binding sites
- 3PG · 3-phosphoglyceric acid · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.62 | 0.81 | 34 | SO4, 3PG |
| 2 | 227 | 0.61 | 0.81 | 32 | SO4, 3PG |
| 3 | 124 | 0.49 | 0.80 | 24 | empty |
| 4 | 67 | 0.42 | 0.80 | 16 | empty |
| 5 | 90 | 0.41 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1033 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3PGM · The structure of yeast phosphoglycerate mutase at 0.28 nm resolution · the same entry in another collection · chain A against A, TM-score 1.00
- P00950 · AlphaFold monomer V2.0 prediction for phosphoglycerate mutase 1 (P00950) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P00950
- Elsewhere: RCSB PDB 3PGM · PDBe 3PGM · UniProt P00950
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