Research workbench
Crystal structure of PFHAD1 in complex with mannose-6-phosphate
Analyse Crystal structure of PFHAD1 in complex with mannose-6-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZEV
- Type
- protein
- Length
- 560 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- PFHAD1
- UniProt
- Q8IJ74
- Ligands
- M6P, MG, PO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | PFHAD1 | protein | 290 | 43% helix, 22% strand | Q8IJ74 |
| B | PFHAD1 | protein | 270 | 44% helix, 20% strand | Q8IJ74 |
Ligands and binding sites
- M6P · 6-O-phosphono-alpha-D-mannopyranose · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.76 | 0.97 | 21 | MG, M6P |
| 2 | 403 | 0.66 | 0.79 | 35 | MG, PO4 |
| 3 | 67 | 0.50 | 0.85 | 17 | empty |
| 4 | 164 | 0.45 | 0.75 | 24 | empty |
| 5 | 70 | 0.44 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4ZEV · Crystal structure of PfHAD1 in complex with mannose-6-phosphate · 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
- Every structure of UniProt Q8IJ74
- Elsewhere: RCSB PDB 4ZEV · PDBe 4ZEV · UniProt Q8IJ74
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