OCA Atlas for 1JF1

1JF1

Immune System

date

Jun 19, 2001

title

Crystal Structure Of Hla-A20201 In Complex With A Decameric Altered Peptide Ligand From The Mart-1melan-A

authors

P.Sliz, O.Michielin, J.C.Cerottini, I.Luescher, P.Romero, M.Karplus, D.C.Wiley

compound

source

Molecule: Hla Class I Histocompatibility Antigen, A-2 Alpha Chain;
Chain: A
Fragment: Heavy Chain
Synonym: Hla-A20201; Mhc Class I Histocompatibility Antigen Hla-A2 Alpha Chain; Mhc Class I Antigen; Lymphocyte Antigen; Mhc Class I Hla-A;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Beta-2-Microglobulin
Chain: B
Fragment: Beta-Chain Of Major Histocompatibility Complex Class I Molecules;
Synonym: Hla-A20201
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Decameric Peptide Ligand From The Mart-1melan-A
Chain: C
Engineered: Yes
Mutation: Yes

Synthetic: Yes
Other_details: Standard Solid-Phase Peptide Synthesis

symmetry

Space Group: P 21 21 21

R_factor

0.182

R_Free

0.225

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
49.020	75.250	121.640	90.00	90.00	90.00

method

X-Ray Diffraction

resolution

1.85 Å

ligand

enzyme

related structures

by homologous chain: 1I7U, 1JGD

Gene
Ontology

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

Primary reference

Crystal structures of two closely related but antigenically distinct HLA-A2/melanocyte-melanoma tumor-antigen peptide complexes., Sliz P, Michielin O, Cerottini JC, Luescher I, Romero P, Karplus M, Wiley DC, J Immunol 2001 Sep 15;167(6):3276-84. PMID:11544315

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]

Biological Unit Coordinates (1jf1.pdb1.gz) 71 Kb

LPC: Ligand-Protein Contacts for 1JF1

CSU: Contacts of Structural Units for 1JF1

Likely Quarternary Molecular Structure file(s) for 1JF1

Structure Factors (322 Kb)

Retrieve 1JF1 in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1JF1 from S2C, [Save to disk]

Re-refined 1jf1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1JF1 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 1JF1

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 1JF1, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1jf1a2, region A:1-181 [Jmol] [rasmolscript] [script source]
- Domain d1jf1a1, region A:182-275 [Jmol] [rasmolscript] [script source]
- Domain d1jf1b_, region B [Jmol] [rasmolscript] [script source]
- Domain d1m1jf1, region F:142-393 [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: [1jf1_B] [1jf1_A] [1jf1] [1jf1_C]

SWISS-PROT database: [P01892] [P61769]

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

Domain found in 1JF1: [IGc1 ] by SMART

Other resources with information on 1JF1

Community annotation for 1JF1 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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