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Crystal structure of pyridoxal kinase complexed with ADP and plp

Analyse Crystal structure of pyridoxal kinase complexed with ADP and plp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RFU
Type: protein
Length: 2,496 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal kinase
EC: 2.7.1.35
UniProt: P82197
Ligands: PLP, ADP, ZN
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Pyridoxal kinase (EC 2.7.1.35)	protein	312	41% helix, 21% strand	P82197

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
ADP · Adenosine-5'-diphosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1057	0.85	0.86	122	ZN, PLP, ADP
2	491	0.80	0.87	55	ZN, PLP, ADP
3	532	0.79	0.85	67	ZN, PLP, ADP
4	490	0.79	0.86	59	ZN, PLP, ADP
5	534	0.79	0.85	61	ZN, PLP, ADP

Interfaces

11 interfaces between chains.

C–H · 2119 Å² buried · 47 hydrogen bonds · protein-protein
B–F · 2096 Å² buried · 45 hydrogen bonds · protein-protein
A–E · 2063 Å² buried · 39 hydrogen bonds · protein-protein
D–G · 2053 Å² buried · 36 hydrogen bonds · protein-protein
A–B · 429 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1RFU · Crystal structure of pyridoxal kinase complexed with ADP and PLP · the same entry in another collection · chain H against H, TM-score 1.00
P82197 · AlphaFold monomer V2.0 prediction for pyridoxal kinase (P82197) · 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 P82197
Elsewhere: RCSB PDB 1RFU · PDBe 1RFU · UniProt P82197

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