MolNFT v1 · #157389 · protein

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

6MXC · Hypoxanthine-guanine phosphoribosyltransferase: “Crystal structure of trypanosoma brucei hypoxanthine-guanine-xanthine phosphoribosyltranferase in complex…”. X-ray diffraction, 2 ligands (5GP, MG), 16 pockets (best druggability…

PDB: 6MXC
Type: protein
Length: 1,304 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypoxanthine-guanine phosphoribosyltransferase
UniProt: Q38CA1
Ligands: 5GP, MG
Pockets: 16 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 24% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypoxanthine-guanine phosphoribosyltransferase	protein	218	24% helix, 32% strand	Q38CA1
B	Hypoxanthine-guanine phosphoribosyltransferase	protein	217	24% helix, 32% strand	Q38CA1
C	Hypoxanthine-guanine phosphoribosyltransferase	protein	220	24% helix, 32% strand	Q38CA1
D	Hypoxanthine-guanine phosphoribosyltransferase	protein	215	24% helix, 33% strand	Q38CA1
E	Hypoxanthine-guanine phosphoribosyltransferase	protein	216	24% helix, 32% strand	Q38CA1
F	Hypoxanthine-guanine phosphoribosyltransferase	protein	218	24% helix, 33% strand	Q38CA1

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 6 copies · chains A, B, C, D, E, F
MG · Magnesium ion · metal · 11 copies · chains A, B, C, D, E, F

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

Pockets

16 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	848	0.77	0.81	80	empty
2	395	0.68	0.81	51	empty
3	419	0.64	0.78	40	5GP, MG
4	337	0.62	0.79	51	empty
5	344	0.60	0.77	34	5GP, MG

Interfaces

5 interfaces between chains.

A–B · 2307 Å² buried · 46 hydrogen bonds · protein-protein
E–F · 2273 Å² buried · 39 hydrogen bonds · protein-protein
C–D · 2241 Å² buried · 46 hydrogen bonds · protein-protein
A–C · 646 Å² buried · 8 hydrogen bonds · protein-protein
B–E · 599 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6MXC · Crystal structure of Trypanosoma brucei hypoxanthine-guanine-xanthine… · 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 Q38CA1
Elsewhere: RCSB PDB 6MXC · PDBe 6MXC · UniProt Q38CA1

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