MolNFT v1 · #183179 · protein

Crystal structure of arabidopsis thaliana PDX1K166R-I333 complex

7NHE · Pyridoxal 5'-phosphate synthase subunit PDX1.3: “Crystal structure of arabidopsis thaliana PDX1K166R-I333 complex”. X-ray diffraction, 2 ligands (KPR, PO4), 12 pockets (best druggability 0.74). MolNFT v1 #183179 on GenesisL1: 3D…

PDB: 7NHE
Type: protein
Length: 1,084 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: KPR, PO4
Pockets: 12 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 49% 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	272	49% helix, 14% strand	Q8L940
B	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	271	49% helix, 13% strand	Q8L940
C	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	271	49% helix, 14% strand	Q8L940
D	Pyridoxal 5'-phosphate synthase subunit PDX1.3 (EC 4.3.3.6)	protein	270	49% helix, 13% strand	Q8L940

Ligands and binding sites

KPR · [(~{E},4~{S})-4-azanyl-3-oxidanylidene-pent-1-enyl] dihydrogen phosphate · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 4 copies · chains A, D, B, C

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	74	0.74	0.98	27	KPR
2	66	0.73	0.98	23	KPR
3	74	0.72	0.97	24	KPR
4	149	0.67	0.88	41	PO4
5	173	0.66	0.86	29	empty

Interfaces

5 interfaces between chains.

A–D · 998 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 996 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 983 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 975 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 449 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

7NHE · Crystal structure of Arabidopsis thaliana Pdx1K166R-I333 complex · the same entry in another collection · chain D against D, 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 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 Q8L940
Elsewhere: RCSB PDB 7NHE · PDBe 7NHE · UniProt Q8L940

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