MolNFT v1 · #127363 · protein
Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active dodecameric form induced by the presence of the N-terminal wdpnwd motif
5MUF · SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial: “Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its enzymatically active…”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability…
- PDB
- 5MUF
- Type
- protein
- Length
- 629 residues
- Chains
- 3
- 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
- 8 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16) | protein | 210 | 33% helix, 20% strand | Q96HS1 |
| C | SERINE/THREONINE-protein phosphatase PGAM5, mitochondrial (EC 3.1.3.16) | protein | 209 | 33% helix, 19% strand | Q96HS1 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.60 | 0.82 | 20 | empty |
| 2 | 159 | 0.58 | 0.82 | 19 | empty |
| 3 | 314 | 0.56 | 0.76 | 40 | PO4 |
| 4 | 293 | 0.56 | 0.77 | 36 | PO4 |
| 5 | 260 | 0.48 | 0.73 | 30 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1505 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 873 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5MUF · Crystal structure of human phosphoglycerate mutase family member 5 (PGAM5) in its… · the same entry in another collection · chain A against A, TM-score 1.00
- Q96HS1 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein phosphatase PGAM5… · a predicted model of the same protein · chain C 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
- Every structure of UniProt Q96HS1
- Elsewhere: RCSB PDB 5MUF · PDBe 5MUF · UniProt Q96HS1
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