OCA Atlas for 1A4J

1A4J

Immunoglobulin

date

Jan 30, 1998

title

Diels Alder Catalytic Antibody Germline Precursor

authors

B.W.Spiller, F.E.Romesburg, P.G.Schultz, R.C.Stevens

compound

source

Molecule: Immunoglobulin, Diels Alder Catalytic Antibody (L Chain);
Chain: L, A
Fragment: Fab
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: Balbc
Cell_line: 25f2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: 25f2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P4xh

Molecule: Immunoglobulin, Diels Alder Catalytic Antibody (H Chain);
Chain: H, B
Fragment: Fab
Engineered: Yes

symmetry

Space Group: C 1 2 1

R_factor

0.229

R_Free

0.292

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
158.900	49.330	145.000	90.00	108.74	90.00

method

X-Ray Diffraction

resolution

2.10 Å

related structures

by homologous chain: 1FL5, 1JGL, 1WT5

Gene
Ontology

Chain	Function	Process	Component
A, L

Primary reference

Immunological origins of binding and catalysis in a Diels-Alderase antibody., Romesberg FE, Spiller B, Schultz PG, Stevens RC, Science 1998 Mar 20;279(5358):1929-33. PMID:9506942

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]

Biological Unit Coordinates (1a4j.pdb1.gz) 70 Kb

Biological Unit Coordinates (1a4j.pdb2.gz) 70 Kb

CSU: Contacts of Structural Units for 1A4J

Likely Quarternary Molecular Structure file(s) for 1A4J

Structure Factors (477 Kb)

Retrieve 1A4J in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1A4J from S2C, [Save to disk]

Re-refined 1a4j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1A4J 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 1A4J

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 1A4J, from MSDmotif at EBI

Genome occurence of 1A4J's fold from GeneCensus

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1a4ja1, region A:1-112 [Jmol] [rasmolscript] [script source]
- Domain d1a4ja2, region A:113-217 [Jmol] [rasmolscript] [script source]
- Domain d1a4jb1, region B:1-119 [Jmol] [rasmolscript] [script source]
- Domain d1a4jb2, region B:120-217 [Jmol] [rasmolscript] [script source]
- Domain d1a4jh1, region H:1-119 [Jmol] [rasmolscript] [script source]
- Domain d1a4jh2, region H:120-217 [Jmol] [rasmolscript] [script source]
- Domain d1a4jl1, region L:1-112 [Jmol] [rasmolscript] [script source]
- Domain d1a4jl2, region L:113-217 [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: [1a4j_B] [1a4j_H] [1a4j_L] [1a4j] [1a4j_A]

SWISS-PROT database: [P01834]

Domain organization of [IGKC_HUMAN] by SWISSPFAM

Domains found in 1A4J: [IG_like] [IGv ] by SMART

Other resources with information on 1A4J

Community annotation for 1A4J at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1A4J from the Database of Macromolecular Movements.

Images from IMB Jena Image Library of Biological Macromolecules.

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