MolNFT v1 · #155198 · protein
Crystal structure of yggs family pyridoxal phosphate-dependent enzyme pipy from fusobacterium nucleatum
6KZW · Pyridoxal phosphate homeostasis protein: “Crystal structure of yggs family pyridoxal phosphate-dependent enzyme pipy from fusobacterium nucleatum”. X-ray diffraction, 1 ligand (PO4), 9 pockets (best druggability 0.54). MolNFT v1…
- PDB
- 6KZW
- Type
- protein
- Length
- 665 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphate homeostasis protein
- UniProt
- A0A117MW82
- Ligands
- PO4
- Pockets
- 9 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Pyridoxal phosphate homeostasis protein | protein | 223 | 45% helix, 19% strand | A0A117MW82 |
| B | Pyridoxal phosphate homeostasis protein | protein | 219 | 46% helix, 18% strand | A0A117MW82 |
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
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 217 | 0.54 | 0.78 | 35 | PO4 |
| 2 | 190 | 0.50 | 0.76 | 37 | PO4 |
| 3 | 140 | 0.47 | 0.77 | 26 | PO4 |
| 4 | 115 | 0.47 | 0.79 | 25 | empty |
| 5 | 87 | 0.45 | 0.80 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–C · 633 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 544 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 6KZW · Crystal structure of YggS family pyridoxal phosphate-dependent enzyme PipY from… · 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 A0A117MW82
- Elsewhere: RCSB PDB 6KZW · PDBe 6KZW · UniProt A0A117MW82
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