Research workbench
Human phosphomannomutase 2 (PMM2) wild-type soaked with the activator glucose 1,6-bisphosphate
Analyse Human phosphomannomutase 2 (PMM2) wild-type soaked with the activator glucose… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O4G
- Type
- protein
- Length
- 484 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphomannomutase 2
- EC
- 5.4.2.8
- UniProt
- O15305
- Ligands
- G16, MG, NA, CL
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Phosphomannomutase 2 (EC 5.4.2.8) | protein | 242 | 40% helix, 20% strand | O15305 |
Ligands and binding sites
- G16 · 1,6-di-O-phosphono-alpha-D-glucopyranose · ligand · chains A
- MG · Magnesium ion · metal · 4 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.52 | 0.75 | 39 | G16 |
| 2 | 170 | 0.46 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 952 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7O4G · Human phosphomannomutase 2 (PMM2) wild-type soaked with the activator glucose… · the same entry in another collection · chain A against A, TM-score 1.00
- O15305 · AlphaFold monomer V2.0 prediction for phosphomannomutase 2 (O15305) · 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 O15305
- Elsewhere: RCSB PDB 7O4G · PDBe 7O4G · UniProt O15305
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