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Apo-PDX1.3 (arabidopsis)

Analyse Apo-PDX1.3 (arabidopsis) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5K3V
Type: protein
Length: 1,104 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: SO4, CL
Pockets: 9 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 48% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	276	48% helix, 14% strand	Q8L940
B	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	274	47% helix, 13% strand	Q8L940
C, D	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	277	47% helix, 13% strand	Q8L940

Ligands and binding sites

SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, D
CL · Chloride ion · ion · 5 copies · chains A, C, D, B
EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1078	0.80	0.81	110	EDO
2	87	0.73	0.96	27	SO4
3	83	0.72	0.96	26	SO4
4	86	0.71	0.95	28	SO4
5	149	0.63	0.86	35	SO4

Interfaces

5 interfaces between chains.

B–D · 1080 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 1065 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 612 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 68 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 30 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

5K3V · apo-PDX1.3 (Arabidopsis) · the same entry in another collection · chain A against A, 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 B 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 5K3V · PDBe 5K3V · UniProt Q8L940

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