MolNFT v1 · #113418 · protein
Crystal structure of murine chronophin (pyridoxal phosphate phosphatase) in complex with a pnp-derived inhibitor
5AES: “Crystal structure of murine chronophin (pyridoxal phosphate phosphatase) in complex with a pnp-derived…”. X-ray diffraction, 2 ligands (5B0, MG), 2 pockets (best druggability 0.68). MolNFT v1 #113418 on GenesisL1: 3D structure…
- PDB
- 5AES
- 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
- UniProt
- P60487
- Ligands
- 5B0, MG
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyridoxal phosphate phosphatase (EC 3.1.3.74) | protein | 291 | 41% helix, 21% strand | P60487 |
| B | Pyridoxal phosphate phosphatase (EC 3.1.3.74) | protein | 291 | 41% helix, 21% strand | P60487 |
Ligands and binding sites
- 5B0 · {2-[5-hydroxy-4-(hydroxymethyl)-6-methylpyridin-3-yl]ethyl}phosphonic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 198 | 0.68 | 0.87 | 33 | MG, 5B0, GOL |
| 2 | 244 | 0.66 | 0.84 | 32 | MG, 5B0 |
Interfaces
1 interface between chains.
- A–B · 996 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5AES · 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 0.99
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 5AES · PDBe 5AES · UniProt P60487
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