MolNFT v1 · #121166 · protein

Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1158

5HN7 · Farnesyl pyrophosphate synthase, putative: “Crystal structure of plasmodium vivax geranylgeranylpyrophosphate synthase complexed with bph-1158”. X-ray diffraction, 1 ligand (04M), 20 pockets (best druggability 0.83). MolNFT v1…

PDB: 5HN7
Type: protein
Length: 2,796 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Farnesyl pyrophosphate synthase, putative
UniProt: A5K4U6
Ligands: 04M
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 8 distinct chains · 73% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Farnesyl pyrophosphate synthase, putative	protein	347	74% helix, 1% strand	A5K4U6
B	Farnesyl pyrophosphate synthase, putative	protein	348	72% helix, 1% strand	A5K4U6
C	Farnesyl pyrophosphate synthase, putative	protein	357	72% helix, 1% strand	A5K4U6
D	Farnesyl pyrophosphate synthase, putative	protein	347	73% helix, 1% strand	A5K4U6
E	Farnesyl pyrophosphate synthase, putative	protein	358	72% helix, 1% strand	A5K4U6
F	Farnesyl pyrophosphate synthase, putative	protein	345	74% helix, 1% strand	A5K4U6
G	Farnesyl pyrophosphate synthase, putative	protein	346	75% helix, 1% strand	A5K4U6
H	Farnesyl pyrophosphate synthase, putative	protein	348	73% helix, 1% strand	A5K4U6

Ligands and binding sites

04M · 5-(morpholin-4-ylsulfonyl)-2-{[3-(octyloxy)benzyl]oxy}benzoic acid · ligand · 8 copies · chains A, E, B, C, D, G, F, H

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	714	0.83	0.87	84	04M
2	679	0.83	0.87	81	04M
3	955	0.82	0.84	93	04M
4	622	0.82	0.87	76	04M
5	494	0.82	0.88	64	04M

Interfaces

13 interfaces between chains.

B–C · 3455 Å² buried · 30 hydrogen bonds · protein-protein
A–E · 3442 Å² buried · 31 hydrogen bonds · protein-protein
F–H · 3358 Å² buried · 31 hydrogen bonds · protein-protein
D–G · 3308 Å² buried · 35 hydrogen bonds · protein-protein
B–G · 339 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent (covalent ligand).

Compared structures

5HN7 · Crystal structure of Plasmodium vivax geranylgeranylpyrophosphate synthase complexed with… · 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 5HN7 · PDBe 5HN7 · UniProt A5K4U6

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