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Crystal structure of plasmodial plp synthase

Analyse Crystal structure of plasmodial plp synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ADT
Type: protein
Length: 535 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyridoxine biosynthetic enzyme PDX1 homologue, putative
UniProt: Q4Z0E8
Ligands: PO4
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyridoxine biosynthetic enzyme PDX1 homologue, putative	protein	273	44% helix, 14% strand	Q4Z0E8
B	Pyridoxine biosynthetic enzyme PDX1 homologue, putative	protein	262	42% helix, 15% strand	Q4Z0E8

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, B

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	253	0.65	0.82	39	PO4
2	234	0.63	0.82	39	PO4
3	74	0.40	0.79	15	empty
4	124	0.39	0.74	19	empty
5	64	0.35	0.78	18	empty

Interfaces

1 interface between chains.

A–B · 446 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4ADT · Crystal structure of plasmodial PLP synthase · 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 Q4Z0E8
Elsewhere: RCSB PDB 4ADT · PDBe 4ADT · UniProt Q4Z0E8

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