OCA Atlas for 1D6V

1D6V

Immune System

date

Oct 15, 1999

title

Conformation Effects In Biological Catalysis Introduced By O Antibody Maturation

authors

E.C.Mundorff, M.A.Hanson, P.G.Schultz, R.C.Stevens

compound

source

Molecule: Chimeric Germline Precursor Of Oxy-Cope Catalytic Az-28 (Light Chain);
Chain: L
Fragment: Chimeric Fab Fragment (Unp Q7ts98 Reisues 23-129, Residues 1-104);
Engineered: Yes
Other_details: The Protein Was Produced As A Chimeric Fab F The Variable Domains (Chains A,L 1-107, Chains B,H 1-113) A The Constant Domains (Chains A, L 108-211 And Chains B,H 11 Human.;

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Gene: Igkc
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Chimeric Germline Precursor Of Oxy-Cope Catalytic Az-28 (Heavy Chain);
Chain: H
Fragment: Chimeric Fab Fragment (Unp K7t9i5 Residues 1-112, Residues 120-220);
Engineered: Yes
Other_details: The Protein Was Produced As A Chimeric Fab F The Variable Domains (Chains A,L 1-107, Chains B,H 1-113) A The Constant Domains (Chains A, L 108-211 And Chains B,H 11 Human.

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

symmetry

Space Group: P 1 21 1

R_factor

0.224

R_Free

0.264

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma
52.718	64.446	73.870	90.00	99.09	90.00

method

X-Ray Diffraction

resolution

2.00 Å

ligand

CD, HOP

enzyme

related structures

by homologous chain: 1DZB, 1K4C, 1YY8, 2F5B

Gene
Ontology

Chain	Function	Process	Component
L

Primary reference

Conformational effects in biological catalysis: an antibody-catalyzed oxy-cope rearrangement., Mundorff EC, Hanson MA, Varvak A, Ulrich H, Schultz PG, Stevens RC, Biochemistry 2000 Feb 1;39(4):627-32. PMID:10651626

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (77 Kb) [Save to disk]

Biological Unit Coordinates (1d6v.pdb1.gz) 72 Kb

LPC: Ligand-Protein Contacts for 1D6V

CSU: Contacts of Structural Units for 1D6V

Likely Quarternary Molecular Structure file(s) for 1D6V

Retrieve 1D6V in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 1D6V from S2C, [Save to disk]

View 1D6V 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 1D6V

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

3D motif for 1D6V, from MSDmotif at EBI

Classification of representative domains in scop (Structural Classification of Proteins)
- Domain d1d6vh1, region H:1-113 [Jmol] [rasmolscript] [script source]
- Domain d1d6vh2, region H:114-214 [Jmol] [rasmolscript] [script source]
- Domain d1d6vl1, region L:1-107 [Jmol] [rasmolscript] [script source]
- Domain d1d6vl2, region L:108-211 [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: [1d6v_L] [1d6v] [1d6v_H]

SWISS-PROT database: [P01857] [P01834]

Domain organization of [IGHG1_HUMAN] [IGKC_HUMAN] by SWISSPFAM

Domains found in 1D6V: [IG_like] [IGv ] by SMART

Other resources with information on 1D6V

Community annotation for 1D6V at PDBWiki (http://pdbwiki.org)

MMDB (Entrez's Structure Database)

Movements, Movies and Images

Domain movements in 1D6V from the Database of Macromolecular Movements.

Images from IMB Jena Image Library of Biological Macromolecules.

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