OCA Atlas for 1CD1

1CD1

Cd1

date

Apr 02, 1997

title

Cd1(Mouse) Antigen Presenting Molecule

authors

Z.H.Zeng, B.W.Segelke, I.A.Wilson

compound

source

Molecule: Cd1
Chain: A, C
Fragment: Alpha1, Alpha2, Alpha3, Beta2-Microglobulin
Synonym: Mcd1d.1
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: C57bl6
Cell_line: Sc2
Cell: Cortical Thymocytes, Dendritic Cells
Cellular_location: Extracellular
Gene: Cd1.1
Expression_system: Drosophila Melanogaster
Expression_system_common: Fruit Fly
Expression_system_taxid: 7227
Expression_system_plasmid: Prmha-3
Expression_system_gene: Cd1.1

Molecule: Cd1
Chain: B, D
Fragment: Alpha1, Alpha2, Alpha3, Beta2-Microglobulin
Synonym: Mcd1d.1
Engineered: Yes

symmetry

Space Group: P 1 21 1

R_factor

0.192

R_Free

0.330

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
59.340	76.200	103.400	90.00	102.29	90.00

method

X-Ray Diffraction

resolution

2.67 Å

related structures

by homologous chain: 1EXU, 1FFO

Gene
Ontology

Chain	Function	Process	Component
A, C
D, B

Primary reference

Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove., Zeng Z, Castano AR, Segelke BW, Stura EA, Peterson PA, Wilson IA, Science 1997 Jul 18;277(5324):339-45. PMID:9219685

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (117 Kb) [Save to disk]

Biological Unit Coordinates (1cd1.pdb1.gz) 57 Kb

Biological Unit Coordinates (1cd1.pdb2.gz) 57 Kb

CSU: Contacts of Structural Units for 1CD1

Likely Quarternary Molecular Structure file(s) for 1CD1

Retrieve 1CD1 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1CD1 from S2C, [Save to disk]

View 1CD1 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 1CD1

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1CD1, from MSDmotif at EBI

Genome occurence of 1CD1's fold from GeneCensus

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1cd1a1, region A:186-279 [Jmol] [rasmolscript] [script source]
- Domain d1cd1a2, region A:7-185 [Jmol] [rasmolscript] [script source]
- Domain d1cd1b_, region B [Jmol] [rasmolscript] [script source]
- Domain d1cd1c1, region C:186-279 [Jmol] [rasmolscript] [script source]
- Domain d1cd1c2, region C:7-185 [Jmol] [rasmolscript] [script source]
- Domain d1cd1d_, region D [Jmol] [rasmolscript] [script source]
- Domain d1e1cd1, region D:20-475 [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: [1cd1_C] [1cd1_A] [1cd1_B] [1cd1_D] [1cd1]

SWISS-PROT database: [P01887] [P11609]

Domain organization of [B2MG_MOUSE] [CD1D1_MOUSE] by SWISSPFAM

Domain found in 1CD1: [IGc1 ] by SMART

Other resources with information on 1CD1

Community annotation for 1CD1 at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1CD1 from the Database of Macromolecular Movements.

Images from IMB Jena Image Library of Biological Macromolecules.

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