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Crystal structure of trypanosoma brucei hypoxanthine-guanine-xanthine phosphoribosyltranferase in complex with imp

Analyse Crystal structure of trypanosoma brucei hypoxanthine-guanine-xanthine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6MXD
Type: protein
Length: 866 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypoxanthine-guanine phosphoribosyltransferase, putative
UniProt: Q38CA1
Ligands: IMP, MG
Pockets: 9 · best druggability 0.57

Structure

x-ray diffraction · 3 distinct chains · 23% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Hypoxanthine-guanine phosphoribosyltransferase, putative	protein	217	23% helix, 34% strand	Q38CA1
B	Hypoxanthine-guanine phosphoribosyltransferase, putative	protein	216	23% helix, 31% strand	Q38CA1
C	Hypoxanthine-guanine phosphoribosyltransferase, putative	protein	216	23% helix, 31% strand	Q38CA1

Ligands and binding sites

IMP · Inosinic acid · ligand · 4 copies · chains A, B, C, D
MG · Magnesium ion · metal · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	322	0.57	0.76	34	IMP, MG
2	275	0.54	0.76	31	IMP, MG
3	321	0.54	0.75	27	empty
4	210	0.51	0.76	26	IMP
5	203	0.49	0.75	24	empty

Interfaces

4 interfaces between chains.

A–B · 2255 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 1035 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 937 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 218 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

6MXD · Crystal structure of Trypanosoma brucei hypoxanthine-guanine-xanthine… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q38CA1
Elsewhere: RCSB PDB 6MXD · PDBe 6MXD · UniProt Q38CA1

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