1VDF	Extracellular Matrix Protein	date	Sep 12, 1996
title	Assembly Domain Of Cartilage Oligomeric Matrix Protein
authors	V.N.Malashkevich
compound		source
Molecule: Cartilage Oligomeric Matrix Protein Chain: A, B, C, D, E Fragment: Assembly Domain Synonym: Comp Engineered: Yes Other_details: Pentameric Coiled-Coil		Organism_scientific: Rattus Norvegicus Organism_common: Norway Rat Organism_taxid: 10116 Cell_line: Bl21 Tissue: Cartilage Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_strain: Bl21 (De3) Expression_system_plasmid: Pet-3b
symmetry	Space Group: P 1 21 1	R_factor 0.176 R_Free NULL
crystal cell	length a length b length c angle alpha angle beta angle gamma 38.470 49.470 54.980 90.00 103.84 90.00
method	X-Ray Diffraction	resolution	2.05 Å
ligand	CL	enzyme
related structures	by homologous chain: 1FBM, 1MZ9
Primary reference	The crystal structure of a five-stranded coiled coil in COMP: a prototype ion channel?, Malashkevich VN, Kammerer RA, Efimov VP, Schulthess T, Engel J, Science 1996 Nov 1;274(5288):761-5. PMID:8864111

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk] Biological Unit Coordinates (1vdf.pdb1.gz) 42 Kb LPC: Ligand-Protein Contacts for 1VDF CSU: Contacts of Structural Units for 1VDF Likely Quarternary Molecular Structure file(s) for 1VDF Retrieve 1VDF in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1VDF from S2C, [Save to disk]

View 1VDF 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.

Visual 3D analysis of 1VDF

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1VDF, from MSDmotif at EBI Genome occurence of 1VDF's fold from GeneCensus Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1vdfa_, region A [Jmol] [rasmolscript] [script source]     - Domain d1vdfb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1vdfc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1vdfd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1vdfe_, region E [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1vdf_A] [1vdf] [1vdf_C] [1vdf_B] [1vdf_D] [1vdf_E] SWISS-PROT database: [P35444] Domain organization of [COMP_RAT] by SWISSPFAM

Other resources with information on 1VDF

Community annotation for 1VDF at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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