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S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with inhibitor bph-210

Analyse S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Z7H
Type: protein
Length: 605 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Geranylgeranyl pyrophosphate synthetase
EC: 2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29
UniProt: Q12051
Ligands: GG3, MG
Pockets: 7 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 76% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29)	protein	308	76% helix, 1% strand	Q12051
B	Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.30, 2.5.1.1, 2.5.1.10, 2.5.1.29)	protein	297	76% helix, 1% strand	Q12051

Ligands and binding sites

GG3 · {1-hydroxy-3-[methyl(4-phenylbutyl)amino]propane-1,1-diyl}bis(phosphonic acid) · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · chains A

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

Pockets

7 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	647	0.79	0.84	66	MG, GG3
2	727	0.77	0.82	64	GG3
3	81	0.37	0.76	16	empty
4	66	0.32	0.75	16	empty
5	75	0.29	0.72	17	empty

Interfaces

1 interface between chains.

A–B · 3409 Å² buried · 29 hydrogen bonds · protein-protein

Compared structures

2Z7H · S. cerevisiae geranylgeranyl pyrophosphate synthase in complex with inhibitor BPH-210 · the same entry in another collection · chain A against A, TM-score 1.00
Q12051 · AlphaFold monomer V2.0 prediction for geranylgeranyl pyrophosphate synthase (Q12051) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q12051
Elsewhere: RCSB PDB 2Z7H · PDBe 2Z7H · UniProt Q12051

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