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Malarial purine phosphoribosyltransferase

Analyse Malarial purine phosphoribosyltransferase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CJB
Type: protein
Length: 911 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (hypoxanthine-guanine phosphoribosyltransferase)
EC: 2.4.2.8
UniProt: P20035
Ligands: IRP, POP, MG
Pockets: 13 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Protein (hypoxanthine-guanine phosphoribosyltransferase) (EC 2.4.2.8)	protein	227	29% helix, 34% strand	P20035
C	Protein (hypoxanthine-guanine phosphoribosyltransferase) (EC 2.4.2.8)	protein	230	29% helix, 33% strand	P20035

Ligands and binding sites

IRP · (1S)-1(9-deazahypoxanthin-9yl)1,4-dideoxy-1,4-imino-D-ribitol-5-phosphate · ligand · 4 copies · chains A, B, C, D
POP · Pyrophosphate 2- · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 copies · chains A, B, C, D

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

Pockets

13 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	208	0.81	0.94	33	MG, IRP, POP
2	211	0.80	0.94	34	MG, IRP, POP
3	221	0.80	0.93	35	MG, IRP, POP
4	209	0.79	0.93	35	MG, IRP, POP
5	570	0.73	0.81	52	empty

Interfaces

2 interfaces between chains.

A–B · 1425 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 838 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1CJB · Malarial purine phosphoribosyltransferase · the same entry in another collection · chain A against A, TM-score 1.00
P20035 · AlphaFold monomer V2.0 prediction for hypoxanthine-guanine-xanthine… · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P20035
Elsewhere: RCSB PDB 1CJB · PDBe 1CJB · UniProt P20035

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