MolNFT v1 · #73395 · protein
Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in complex with phosphate
3O0T · SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial: “Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in complex with phosphate”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability…
- PDB
- 3O0T
- Type
- protein
- Length
- 383 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial
- EC
- 3.1.3.16
- UniProt
- Q96HS1
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16) | protein | 193 | 38% helix, 21% strand | Q96HS1 |
| B | SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16) | protein | 190 | 39% helix, 20% strand | Q96HS1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.61 | 0.83 | 20 | EDO |
| 2 | 180 | 0.61 | 0.82 | 20 | EDO |
| 3 | 233 | 0.52 | 0.76 | 42 | PO4, EDO |
| 4 | 77 | 0.38 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1148 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3O0T · Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in complex… · the same entry in another collection · chain B against B, TM-score 1.00
- Q96HS1 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PGAM5… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q96HS1
- Elsewhere: RCSB PDB 3O0T · PDBe 3O0T · UniProt Q96HS1
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