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RV1086 E,E-farnesyl diphosphate complex

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

PDB: 2VG1
Type: protein
Length: 456 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: FPP, PO4
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 51% 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	228	51% helix, 15% strand	O53434

Ligands and binding sites

FPP · Farnesyl diphosphate · ligand · chains A, B
PO4 · Phosphate ion · ion · 2 copies · chains A, B
GOL · Glycerol · additive · 6 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	246	0.69	0.85	33	PO4, FPP
2	218	0.65	0.83	27	PO4, GOL

Interfaces

1 interface between chains.

A–B · 1827 Å² buried · 25 hydrogen bonds · protein-protein

Compared structures

2VG1 · Rv1086 E,E-farnesyl diphosphate 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 2VG1 · PDBe 2VG1 · UniProt O53434

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