3GCI	Hydrolase	date	Feb 22, 2009
title	Crystal Structure Of The Complex Formed Between A New Isoform Of Phospholipase A2 With C-Terminal Amyloid Beta Heptapeptide At 2 A Resolution
authors	Z.Mirza, G.Vikram, N.Singh, M.Sinha, A.Bhushan, S.Sharma, A.Srinivasan, P.Kaur, T.P.Singh
compound		source
Molecule: Phospholipase A2 Isoform 3 Chain: A Synonym: Phosphatidylcholine 2-Acylhydrolase Ec: 3.1.1.4		Organism_scientific: Naja Sagittifera Organism_common: Andaman Cobra Organism_taxid: 195058
Molecule: Heptapeptide From Amyloid Beta A4 Protein Chain: P Fragment: Unp Residues 707-713 Engineered: Yes		Synthetic: Yes Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Other_details: This Peptide Was Chemically Synthesized. This Sequence Occurs Naturally In Humans.
symmetry	Space Group: P 41	R_factor 0.184 R_Free 0.221
crystal cell	length a length b length c angle alpha angle beta angle gamma 42.679 42.679 65.817 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	2.04 Å
ligand	CA	enzyme	Hydrolase E.C.3.1.1.4 BRENDA
Gene Ontology	Chain Function Process Component A phospholipase A2 activity hydrolase activity metal ion binding lipid metabolic process lipid catabolic process extracellular region

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (26 Kb) [Save to disk] Biological Unit Coordinates (3gci.pdb1.gz) 21 Kb Biological Unit Coordinates (3gci.pdb2.gz) 2 Kb Biological Unit Coordinates (3gci.pdb3.gz) 22 Kb LPC: Ligand-Protein Contacts for 3GCI CSU: Contacts of Structural Units for 3GCI Likely Quarternary Molecular Structure file(s) for 3GCI Structure Factors (99 Kb) Retrieve 3GCI in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GCI from S2C, [Save to disk] Re-refined 3gci structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GCI 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 3GCI

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 3GCI, from MSDmotif at EBI Fold representative 3gci from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gci_A] [3gci_P] SWISS-PROT database: [P05067] [P60045] Belongs to the amyloid -protein peptide (app) family according to TCDB. Domain organization of [A4_HUMAN] [PA23_NAJSG] by SWISSPFAM Domain found in 3GCI: [PA2c ] by SMART Alignments of the sequence of 3GCI with the sequences similar proteins can be viewed for 3GCI's classification [A4_HUMAN] [PA23_NAJSG] 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 [A4_HUMAN] [PA23_NAJSG] at ProtoMap. Click on the Cluster number.

Other resources with information on 3GCI

Community annotation for 3GCI at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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