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Crystal structure of plasmodium vivax hypoxanthine guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3- ((S)-2-hydroxy-2-PHOSPHONOETHYL)OXY-1-N-(phosphonopropionyl) pyrrolidine

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

PDB: 6BO7
Type: protein
Length: 2,612 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypoxanthine phosphoribosyltransferase
EC: 2.4.2.8
UniProt: A0A1G4HBT9
Ligands: YPG, MG
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 7 distinct chains · 29% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8)	protein	220	29% helix, 29% strand	A0A1G4HBT9
C	Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8)	protein	219	29% helix, 30% strand	A0A1G4HBT9
D, G, H, J	Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8)	protein	218	29% helix, 30% strand	A0A1G4HBT9
E	Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8)	protein	211	29% helix, 28% strand	A0A1G4HBT9
F	Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8)	protein	220	30% helix, 30% strand	A0A1G4HBT9
I, K	Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8)	protein	217	29% helix, 29% strand	A0A1G4HBT9
L	Hypoxanthine phosphoribosyltransferase (EC 2.4.2.8)	protein	216	29% helix, 28% strand	A0A1G4HBT9

Ligands and binding sites

YPG · [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-yl]-3-oxidanylidene-propyl]phosphonic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
MG · Magnesium ion · metal · 27 copies · chains A, B, C, D, E, I, F, G, H, J, K, L

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1142	0.89	0.90	120	empty
2	1008	0.89	0.90	103	empty
3	500	0.84	0.90	72	empty
4	540	0.84	0.90	61	empty
5	358	0.66	0.80	47	MG, YPG

Interfaces

21 interfaces between chains.

F–J · 1733 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1683 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 1670 Å² buried · 5 hydrogen bonds · protein-protein
H–K · 1640 Å² buried · 12 hydrogen bonds · protein-protein
E–I · 1555 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

6BO7 · Crystal structure of Plasmodium vivax hypoxanthine guanine phosphoribosyltransferase in… · 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 A0A1G4HBT9
Elsewhere: RCSB PDB 6BO7 · PDBe 6BO7 · UniProt A0A1G4HBT9

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