OCA Atlas for 3KPS

3KPS

Immune System

date

Nov 16, 2009

title

Crystal Structure Of The Lc13 Tcr In Complex With Hla B4405 Eeylqafty A Self Peptide From The Abcd3 Protein

authors

W.A.Macdonald, Z.Chen, S.Gras, J.K.Archbold, F.E.Tynan, C.S.Cleme M.Bharadwaj, L.Kjer-Nielsen, P.M.Saunders, M.C.Wilce, F.Crawfor B.Stadinsky, D.Jackson, A.G.Brooks, A.W.Purcell, J.W.Kappler, S.R.Burrows, J.Rossjohn, J.Mccluskey

compound

source

Molecule: Hla Class I Histocompatibility Antigen, B-44 Alph
Chain: A
Synonym: Mhc Class I Antigen B44, Bw-44
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hla-B, Hlab
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Beta-2-Microglobulin
Chain: B
Synonym: Beta-2-Microglobulin Form Pi 5.3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: B2m, Cdabp0092, Hdcma22p
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Eeylqafty, Self Peptide From The Atp Binding Cass Protein Abcd3;
Chain: C
Engineered: Yes

Synthetic: Yes

Molecule: Lc13 Tcr Alpha Chain
Chain: D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30

Molecule: Lc13 Tcr Beta Chain
Chain: E
Engineered: Yes

symmetry

Space Group: C 1 2 1

R_factor

0.193

R_Free

0.269

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
142.518	54.237	121.766	90.00	114.43	90.00

method

X-Ray Diffraction

resolution

2.70 Å

Gene
Ontology

Chain	Function	Process	Component
B		cellular response to iron io...

Primary reference

T cell allorecognition via molecular mimicry., Macdonald WA, Chen Z, Gras S, Archbold JK, Tynan FE, Clements CS, Bharadwaj M, Kjer-Nielsen L, Saunders PM, Wilce MC, Crawford F, Stadinsky B, Jackson D, Brooks AG, Purcell AW, Kappler JW, Burrows SR, Rossjohn J, McCluskey J, Immunity. 2009 Dec 18;31(6):897-908. PMID:20064448

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (138 Kb) [Save to disk]

Biological Unit Coordinates (3kps.pdb1.gz) 133 Kb

CSU: Contacts of Structural Units for 3KPS

Structure Factors (286 Kb)

Retrieve 3KPS in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 3KPS from S2C, [Save to disk]

Re-refined 3kps structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3KPS 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 3KPS

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 3KPS, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3kps_C] [3kps_B] [3kps_D] [3kps] [3kps_E] [3kps_A]

SWISS-PROT database: [P30481] [P61769] [P01848]

Domain organization of [1B44_HUMAN] [B2MG_HUMAN] [TCA_HUMAN] by SWISSPFAM

Domains found in 3KPS: [IG_like] [IGc1] [IGv ] by SMART

Other resources with information on 3KPS

Community annotation for 3KPS at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

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