Research workbench
Crystal structure of human pyridoxal 5'-phosphate phosphatase with its substrate
Analyse Crystal structure of human pyridoxal 5'-phosphate phosphatase with its substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CFT
- Type
- protein
- Length
- 292 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphate phosphatase
- EC
- 3.1.3.74
- UniProt
- Q96GD0
- Ligands
- PLP, CA
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal phosphate phosphatase (EC 3.1.3.74) | protein | 292 | 40% helix, 20% strand | Q96GD0 |
Ligands and binding sites
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 | 225 | 0.67 | 0.85 | 34 | PLP, CA |
| 2 | 59 | 0.32 | 0.76 | 19 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 2CFT · Crystal structure of human pyridoxal 5'-phosphate phosphatase with its substrate · the same entry in another collection · chain A against A, TM-score 1.00
- Q96GD0 · AlphaFold monomer V2.0 prediction for pyridoxal phosphate phosphatase (Q96GD0) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q96GD0
- Elsewhere: RCSB PDB 2CFT · PDBe 2CFT · UniProt Q96GD0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.