MolNFT v1 · #120385 · protein

Crystal structure of human pyridoxal 5'-phosphate phosphatase (chronophin) mutant - C221S

5GYN · Pyridoxal phosphate phosphatase: “Crystal structure of human pyridoxal 5'-phosphate phosphatase (chronophin) mutant - C221S”. X-ray diffraction, 1 ligand (MG), 1 pocket (best druggability 0.71). MolNFT v1 #120385 on GenesisL1: 3D…

PDB: 5GYN
Type: protein
Length: 295 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal phosphate phosphatase
EC: 3.1.3.3, 3.1.3.74
UniProt: Q96GD0
Ligands: MG
Pockets: 1 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal phosphate phosphatase (EC 3.1.3.3, 3.1.3.74)	protein	295	40% helix, 19% strand	Q96GD0

Ligands and binding sites

MG · Magnesium ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	301	0.71	0.85	36	MG

Compared structures

5GYN · Crystal structure of human pyridoxal 5'-phosphate phosphatase (Chronophin) mutant - C221S · 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 5GYN · PDBe 5GYN · UniProt Q96GD0

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