Research workbench
Crystal structure of murine chronophin (pyridoxal phosphate phosphatase) in complex with beryllium trifluoride
Analyse Crystal structure of murine chronophin (pyridoxal phosphate phosphatase) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BX2
- Type
- protein
- Length
- 582 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyridoxal phosphate phosphatase
- EC
- 3.1.3.74, 3.1.3.3
- UniProt
- P60487
- Ligands
- BEF, MG
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal phosphate phosphatase (EC 3.1.3.74, 3.1.3.3) | protein | 292 | 41% helix, 21% strand | P60487 |
| B | Pyridoxal phosphate phosphatase (EC 3.1.3.74, 3.1.3.3) | protein | 290 | 41% helix, 20% strand | P60487 |
Ligands and binding sites
- BEF · Beryllium trifluoride ion · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.67 | 0.86 | 34 | MG, BEF, GOL |
| 2 | 230 | 0.63 | 0.83 | 32 | MG, BEF, GOL |
| 3 | 61 | 0.36 | 0.79 | 21 | empty |
| 4 | 59 | 0.28 | 0.74 | 17 | empty |
| 5 | 64 | 0.27 | 0.72 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1005 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4BX2 · Crystal Structure of murine Chronophin (Pyridoxal Phosphate Phosphatase) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P60487 · AlphaFold monomer V2.0 prediction for pyridoxal phosphate phosphatase (P60487) · a predicted model of the same protein · 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 P60487
- Elsewhere: RCSB PDB 4BX2 · PDBe 4BX2 · UniProt P60487
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