2Q80	Transferase	date	Jun 08, 2007
title	Crystal Structure Of Human Geranylgeranyl Pyrophosphate Synt To Ggpp
authors	K.L.Kavanagh, J.E.Dunford, G.Bunkoczi, C.Smee, F.Von Delft, C.Arr J.Weigelt, A.Edwards, M.Sundstrom, U.Oppermann, Structural Geno Consortium (Sgc)
compound		source
Molecule: Geranylgeranyl Pyrophosphate Synthetase Chain: A, B, C, D, E, F Ec: 2.5.1.1, 2.5.1.10, 2.5.1.29 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ggps1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pnic28-Bsa4
symmetry	Space Group: P 41 21 2	R_factor 0.202 R_Free 0.253
crystal cell	length a length b length c angle alpha angle beta angle gamma 141.248 141.248 211.705 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	GRG, MG	enzyme	Transferase E.C.2.5.1.1 BRENDA
note	2Q80 supersedes 2FVI
Gene Ontology	Chain Function Process Component F, A, D, C, E, B dimethylallyltranstransferas... farnesyltranstransferase act... geranyltranstransferase acti... transferase activity metal ion binding cholesterol biosynthetic pro... isoprenoid metabolic process... isoprenoid biosynthetic proc... geranyl diphosphate biosynth... geranylgeranyl diphosphate b... small molecule metabolic pro... farnesyl diphosphate biosynt... cytoplasm cytosol
Primary reference	The crystal structure of human geranylgeranyl pyrophosphate synthase reveals a novel hexameric arrangement and inhibitory product binding., Kavanagh KL, Dunford JE, Bunkoczi G, Russell RG, Oppermann U, J Biol Chem. 2006 Aug 4;281(31):22004-12. Epub 2006 May 11. PMID:16698791

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (286 Kb) [Save to disk] Biological Unit Coordinates (2q80.pdb1.gz) 274 Kb LPC: Ligand-Protein Contacts for 2Q80 CSU: Contacts of Structural Units for 2Q80 Likely Quarternary Molecular Structure file(s) for 2Q80 Structure Factors (766 Kb) Retrieve 2Q80 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Q80 from S2C, [Save to disk] Re-refined 2q80 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Q80 in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 2Q80

Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 2Q80, from MSDmotif at EBI Fold representative 2q80 from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2q80_A] [2q80_B] [2q80_C] [2q80_D] [2q80_E] [2q80_F] SWISS-PROT database: [O95749] Domain organization of [GGPPS_HUMAN] by SWISSPFAM Alignments of the sequence of 2Q80 with the sequences similar proteins can be viewed for 2Q80's classification [GGPPS_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list. A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [GGPPS_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2Q80

Community annotation for 2Q80 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2010 Bioinformatics Unit Weizmann Institute of Science

---