MolNFT v1 · #55875 · protein

Human pyridoxal kinase

2YXT: “Human pyridoxal kinase”. X-ray diffraction, 2 ligands (NA, PO4), 7 pockets (best druggability 0.77). MolNFT v1 #55875 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2YXT
Type: protein
Length: 608 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal kinase
EC: 2.7.1.35
UniProt: O00764
Ligands: NA, PO4
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal kinase (EC 2.7.1.35)	protein	304	40% helix, 20% strand	O00764
B	Pyridoxal kinase (EC 2.7.1.35)	protein	304	40% helix, 23% strand	O00764

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B
PO4 · Phosphate ion · ion · 6 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 14 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.77	0.99	16	empty
2	874	0.76	0.80	66	NA, PO4, MPD
3	841	0.76	0.80	66	NA, MPD
4	109	0.61	0.87	17	empty
5	78	0.46	0.82	19	empty

Interfaces

1 interface between chains.

A–B · 2216 Å² buried · 40 hydrogen bonds · protein-protein

Compared structures

2YXT · Human Pyridoxal Kinase · the same entry in another collection · chain A against A, TM-score 1.00
O00764 · AlphaFold monomer V2.0 prediction for pyridoxal kinase (O00764) · 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 O00764
Elsewhere: RCSB PDB 2YXT · PDBe 2YXT · UniProt O00764

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