Research workbench

PDX1.2/PDX1.3 complex

Analyse PDX1.2/PDX1.3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6HX3
Type: protein
Length: 2,061 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2; Pyridoxal 5'-phosphate synthase…
EC: 4.3.3.6
UniProt: Q9ZNR6, Q8L940
Ligands: SO4
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 8 distinct chains · 21% helix, 74% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxal 5'-phosphate synthase-like subunit PDX1.2	protein	263	18% helix, 76% strand	Q9ZNR6
C	Pyridoxal 5'-phosphate synthase-like subunit PDX1.2	protein	256	22% helix, 72% strand	Q9ZNR6
E	Pyridoxal 5'-phosphate synthase-like subunit PDX1.2	protein	256	16% helix, 78% strand	Q9ZNR6
G	Pyridoxal 5'-phosphate synthase-like subunit PDX1.2	protein	257	18% helix, 77% strand	Q9ZNR6
B	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	263	19% helix, 76% strand	Q8L940
D	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	255	17% helix, 77% strand	Q8L940
F	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	255	28% helix, 66% strand	Q8L940
H	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	256	25% helix, 69% strand	Q8L940

Ligands and binding sites

SO4 · Sulfate ion · ion · 12 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

6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	883	0.79	0.82	175	empty
2	433	0.68	0.80	139	SO4
3	425	0.66	0.79	117	SO4
4	251	0.60	0.80	83	SO4
5	284	0.57	0.77	76	SO4

Interfaces

20 interfaces between chains.

G–H · 5886 Å² buried · 1,952 hydrogen bonds · protein-protein
C–D · 5855 Å² buried · 1,864 hydrogen bonds · protein-protein
A–B · 5829 Å² buried · 1,903 hydrogen bonds · protein-protein
E–F · 5738 Å² buried · 1,815 hydrogen bonds · protein-protein
G–B · 927 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide (disulfide).

Compared structures

6HX3 · PDX1.2/PDX1.3 complex · the same entry in another collection · chain H against H, 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 D 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 Q9ZNR6
Every structure of UniProt Q8L940
Elsewhere: RCSB PDB 6HX3 · PDBe 6HX3 · UniProt Q9ZNR6 · UniProt Q8L940

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