OCA Atlas for 1CDN

1CDN

Calcium-Binding Protein

date

Aug 04, 1995

title

Solution Structure Of (Cd2+)1-Calbindin D9k Reveals Details Stepwise Structural Changes Along The Apo--> (Ca2+)Ii1--> ( Binding Pathway

authors

M.Akke, S.Forsen, W.J.Chazin

compound

source

Molecule: Calbindin D9k
Chain: A
Synonym: Intestinal Calcium-Binding Protein, Icbp, Icabp, C S100d;
Engineered: Yes
Mutation: Yes
Other_details: Bovine Minor A Form, Cadmium-Half-Saturated, Ion Is Bound In C-Terminal Site

Organism_scientific: Bos Taurus
Organism_common: Cattle
Organism_taxid: 9913
Gene: Icabp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Picb1
Expression_system_gene: Icabp

method

Solution NMR

Gene
Ontology

Chain	Function	Process	Component
A

Primary reference

Solution structure of (Cd2+)1-calbindin D9k reveals details of the stepwise structural changes along the Apo-->(Ca2+)II1-->(Ca2+)I,II2 binding pathway., Akke M, Forsen S, Chazin WJ, J Mol Biol 1995 Sep 8;252(1):102-21. PMID:7666423

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (477 Kb) [Save to disk]

Biological Unit Coordinates (1cdn.pdb1.gz) 20 Kb

CSU: Contacts of Structural Units for 1CDN

Original NMR restraints for 1CDN from PDB

Experimental data, such as chemical shifts, at BioMagResBank (BMRB)

NMR Restraints Grid from BioMagResBank (BMRB)

Retrieve 1CDN in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1CDN from S2C, [Save to disk]

View 1CDN 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 1CDN

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1CDN, from MSDmotif at EBI

Genome occurence of 1CDN's fold from GeneCensus

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1cdn__, region [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: [1cdn_A] [1cdn]

SWISS-PROT database: [P02633]

Domain organization of [S100G_BOVIN] by SWISSPFAM

Domain found in 1CDN: [S_100 ] by SMART

Other resources with information on 1CDN

Community annotation for 1CDN at PDBWiki (http://pdbwiki.org)

NMR Ensemble (OLDERADO: core, domain and representative structure database)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1CDN from the Database of Macromolecular Movements.

Images from IMB Jena Image Library of Biological Macromolecules.

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