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Crystal structure of plasmodium vivax putative polyprenyl pyrophosphate synthase in complex with geranylgeranyl diphosphate

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

PDB: 3PH7
Type: protein
Length: 1,376 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Farnesyl pyrophosphate synthase
UniProt: A5K4U6
Ligands: GRG
Pockets: 15 · best druggability 0.82

Structure

x-ray diffraction · 4 distinct chains · 72% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Farnesyl pyrophosphate synthase	protein	347	73% helix, 1% strand	A5K4U6
B	Farnesyl pyrophosphate synthase	protein	359	71% helix, 1% strand	A5K4U6
C	Farnesyl pyrophosphate synthase	protein	331	71% helix, 1% strand	A5K4U6
D	Farnesyl pyrophosphate synthase	protein	339	73% helix, 1% strand	A5K4U6

Ligands and binding sites

GRG · Geranylgeranyl diphosphate · ligand · 4 copies · chains A, B, C, D

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

Pockets

15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	640	0.82	0.87	79	GRG
2	1096	0.79	0.80	121	GRG
3	507	0.76	0.84	67	GRG
4	678	0.75	0.81	81	GRG
5	332	0.64	0.80	32	empty

Interfaces

6 interfaces between chains.

A–B · 3562 Å² buried · 30 hydrogen bonds · protein-protein
C–D · 3227 Å² buried · 25 hydrogen bonds · protein-protein
B–D · 303 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 130 Å² buried · 1 hydrogen bond · protein-protein
A–C · 112 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

3PH7 · Crystal structure of Plasmodium vivax putative polyprenyl pyrophosphate synthase 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 A5K4U6
Elsewhere: RCSB PDB 3PH7 · PDBe 3PH7 · UniProt A5K4U6

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