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Crystal structure of farnesyl diphosphate synthase from rhodobacter capsulatus SB1003

Analyse Crystal structure of farnesyl diphosphate synthase from rhodobacter capsulatus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3LVS
Type: protein
Length: 544 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Farnesyl diphosphate synthase
Ligands: PO4
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 75% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Farnesyl diphosphate synthase	protein	270	75% helix, 1% strand	—
B	Farnesyl diphosphate synthase	protein	274	75% helix, 1% strand	—

Ligands and binding sites

PO4 · Phosphate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

8 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	601	0.72	0.79	58	PO4
2	460	0.72	0.82	62	PO4
3	70	0.36	0.77	22	GOL
4	60	0.34	0.77	15	PO4
5	54	0.32	0.77	19	empty

Interfaces

1 interface between chains.

A–B · 1715 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

3LVS · Crystal structure of farnesyl diphosphate synthase from rhodobacter capsulatus sb1003 · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 3LVS · PDBe 3LVS

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