MolNFT v1 · #124031 · protein

PDX1.3-adduct (arabidopsis)

5K2Z · Pyridoxal 5'-phosphate synthase subunit PDX1.3: “PDX1.3-adduct (arabidopsis)”. X-ray diffraction, 3 ligands (6R3, SO4, CL), 7 pockets (best druggability 0.76). MolNFT v1 #124031 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 5K2Z
Type: protein
Length: 1,109 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal 5'-phosphate synthase subunit PDX1.3
EC: 4.3.3.6
UniProt: Q8L940
Ligands: 6R3, SO4, CL
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	277	48% helix, 14% strand	Q8L940
B, D	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	278	47% helix, 14% strand	Q8L940
C	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	276	48% helix, 14% strand	Q8L940

Ligands and binding sites

6R3 · 2-azanylpenta-1,4-dien-3-one · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
CL · Chloride ion · ion · 2 copies · chains A, B, D
EDO · 1,2-ethanediol · additive · 4 copies · chains A, C, 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	635	0.76	0.82	72	EDO
2	457	0.70	0.81	56	empty
3	195	0.59	0.81	25	empty
4	195	0.57	0.81	25	empty
5	194	0.46	0.75	32	CL, EDO

Interfaces

5 interfaces between chains.

C–D · 1096 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 1085 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 611 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 60 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 25 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 covalent (covalent ligand).

Compared structures

5K2Z · PDX1.3-adduct (Arabidopsis) · the same entry in another collection · chain C against C, TM-score 1.00
Q8L940 · AlphaFold monomer V2.0 prediction for pyridoxal 5'-phosphate synthase subunit PDX1.3… · a predicted model of the same protein · chain C 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 Q8L940
Elsewhere: RCSB PDB 5K2Z · PDBe 5K2Z · UniProt Q8L940

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