MolNFT v1 · #106510 · protein

Pyridoxal kinase of entamoeba histolytica with ADP

4S1H: “Pyridoxal kinase of entamoeba histolytica with ADP”. X-ray diffraction, 2 ligands (ADP, MG), 7 pockets (best druggability 0.79). MolNFT v1 #106510 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4S1H
Type: protein
Length: 566 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal kinase
EC: 2.7.1.35
UniProt: C4LVZ4
Ligands: ADP, MG
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal kinase (EC 2.7.1.35)	protein	287	38% helix, 20% strand	C4LVZ4
B	Pyridoxal kinase (EC 2.7.1.35)	protein	279	37% helix, 20% strand	C4LVZ4

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 4 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	434	0.79	0.87	60	ADP, MG
2	438	0.76	0.85	59	MG, ADP
3	97	0.62	0.88	20	empty
4	89	0.41	0.78	16	empty
5	79	0.40	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 1849 Å² buried · 32 hydrogen bonds · protein-protein

Compared structures

4S1H · Pyridoxal kinase of Entamoeba histolytica with ADP · the same entry in another collection · 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 C4LVZ4
Elsewhere: RCSB PDB 4S1H · PDBe 4S1H · UniProt C4LVZ4

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