OCA Atlas for 3GJF

3GJF

Immune System

date

Mar 08, 2009

title

Rational Development Of High-Affinity T-Cell Receptor-Like A

authors

G.Stewart-Jones, A.Wadle, A.Hombach, E.Shenderov, G.Held, E.Fisch S.Kleber, F.Stenner-Liewen, S.Bauer, A.Mcmichael, A.Knuth, H.Abk A.A.Hombach, V.Cerundolo, E.Y.Jones, C.Renner

compound

source

Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha
Chain: A, D
Fragment: Unp Residues 25-300
Synonym: Mhc Class I Antigen A2
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pett22b+

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

Molecule: Nyeso-1 Peptide
Chain: C, F
Engineered: Yes

Synthetic: Yes
Other_details: Peptide From Human Tumours

Molecule: Antibody Light Chain
Chain: L, K
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Hb2151
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phen

Molecule: Antibody Heavy Chain
Chain: H, M
Engineered: Yes

symmetry

Space Group: P 1 21 1

R_factor

0.202

R_Free

0.251

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
71.601	111.841	124.715	90.00	93.49	90.00

method

X-Ray Diffraction

resolution

1.90 Å

Gene
Ontology

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

Primary reference

Rational development of high-affinity T-cell receptor-like antibodies., Stewart-Jones G, Wadle A, Hombach A, Shenderov E, Held G, Fischer E, Kleber S, Stenner-Liewen F, Bauer S, McMichael A, Knuth A, Abken H, Hombach AA, Cerundolo V, Jones EY, Renner C, Proc Natl Acad Sci U S A. 2009 Apr 7;106(14):5784-8. Epub 2009 Mar 23. PMID:19307587

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (290 Kb) [Save to disk]

Biological Unit Coordinates (3gjf.pdb1.gz) 145 Kb

Biological Unit Coordinates (3gjf.pdb2.gz) 144 Kb

CSU: Contacts of Structural Units for 3GJF

Likely Quarternary Molecular Structure file(s) for 3GJF

Structure Factors (1131 Kb)

Retrieve 3GJF in mmCIF format [Save to disk]

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

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

View 3GJF 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 3GJF

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

3D motif for 3GJF, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gjf_L] [3gjf_M] [3gjf_B] [3gjf_E] [3gjf_D] [3gjf_C] [3gjf_F] [3gjf_K] [3gjf] [3gjf_A] [3gjf_H]

SWISS-PROT database: [P01892] [P61769]

Domain organization of [1A02_HUMAN] [B2MG_HUMAN] by SWISSPFAM

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

Other resources with information on 3GJF

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

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]