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RV1086 citronellyl pyrophosphate complex

Analyse RV1086 citronellyl pyrophosphate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2VG0
Type: protein
Length: 454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Short-chain Z-isoprenyl diphosphate synthetase
EC: 2.5.1.68
UniProt: O53434
Ligands: GPP
Pockets: 3 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Short-chain Z-isoprenyl diphosphate synthetase (EC 2.5.1.68)	protein	227	50% helix, 15% strand	O53434

Ligands and binding sites

GPP · Geranyl diphosphate · ligand · 2 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	99	0.79	0.99	32	empty
2	221	0.69	0.86	29	GPP
3	218	0.67	0.85	27	GPP

Interfaces

1 interface between chains.

A–B · 1888 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

2VG0 · Rv1086 citronellyl pyrophosphate complex · 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 O53434
Elsewhere: RCSB PDB 2VG0 · PDBe 2VG0 · UniProt O53434

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