2Z6W	Isomerase Immunosuppressant	date	Aug 09, 2007
title	Crystal Structure Of Human Cyclophilin D In Complex With Cyc
authors	K.Kajitani, M.Fujihashi, Y.Kobayashi, S.Shimizu, Y.Tsujimoto, K.M
compound		source
Molecule: Peptidyl-Prolyl Cis-Trans Isomerase Chain: A, B Fragment: Residues 2-165 Synonym: Ppiase, Rotamase, Cyclophilin D Ec: 5.2.1.8 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ppif, Cyp3 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21(De3) Expression_system_vector_type: Plasmid Expression_system_plasmid: Pet-21a
Molecule: Cyclosporin A Chain: M, N Synonym: Ciclosporin, Ciclosporine Engineered: Yes		Synthetic: Yes Organism_scientific: Tolypocladium Inflatum Organism_taxid: 29910
symmetry	Space Group: P 21 21 21	R_factor 0.129 R_Free 0.153
crystal cell	length a length b length c angle alpha angle beta angle gamma 38.882 69.313 112.077 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	0.96 Å
ligand	ABA, BMT, CIT, DAL, MLE, MVA, SAR	enzyme	Isomerase E.C.5.2.1.8 BRENDA
Primary reference	Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution., Kajitani K, Fujihashi M, Kobayashi Y, Shimizu S, Tsujimoto Y, Miki K, Proteins. 2008 Mar;70(4):1635-9. PMID:18076075

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (146 Kb) [Save to disk] Biological Unit Coordinates (2z6w.pdb1.gz) 70 Kb Biological Unit Coordinates (2z6w.pdb2.gz) 72 Kb LPC: Ligand-Protein Contacts for 2Z6W CSU: Contacts of Structural Units for 2Z6W Likely Quarternary Molecular Structure file(s) for 2Z6W Structure Factors (1275 Kb) Retrieve 2Z6W in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2Z6W from S2C, [Save to disk] Re-refined 2z6w structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2Z6W 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 2Z6W

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 2Z6W, from MSDmotif at EBI Fold representative 2z6w from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2z6w_A] [2z6w_B] [2z6w_M] [2z6w_N] SWISS-PROT database: [P30405] Domain organization of [PPIF_HUMAN] by SWISSPFAM Alignments of the sequence of 2Z6W with the sequences similar proteins can be viewed for 2Z6W's classification [PPIF_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 [PPIF_HUMAN] at ProtoMap. Click on the Cluster number.

Other resources with information on 2Z6W

Community annotation for 2Z6W at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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