1D5B Immune System date Oct 06, 1999
title Unliganded Mature Oxy-Cope Catalytic Antibody
authors E.C.Mundorff, M.A.Hanson, P.G.Schultz, R.C.Stevens
compound source
Molecule: Chimeric Oxy-Cope Catalytic Antibody Az-28 (Light
Chain: A, 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 113 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
Expression_system_plasmid: Paz-28

Molecule: Chimeric Oxy-Cope Catalytic Antibody Az-28 (Heavy
Chain: B, 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 113 Human.

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mouse, Human
Organism_taxid: 10090, 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Paz-28
symmetry Space Group: P 21 21 21
R_factor 0.232 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.420 80.670 134.750 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand CD enzyme
related structures by homologous chain: 1AD9, 1CFQ, 1EGJ
Gene
Ontology
ChainFunctionProcessComponent
A, L


Primary referenceConformational 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] (133 Kb) [Save to disk]
  • Biological Unit Coordinates (1d5b.pdb1.gz) 127 Kb
  • Biological Unit Coordinates (1d5b.pdb2.gz) 65 Kb
  • Biological Unit Coordinates (1d5b.pdb3.gz) 65 Kb
  • LPC: Ligand-Protein Contacts for 1D5B
  • CSU: Contacts of Structural Units for 1D5B
  • Likely Quarternary Molecular Structure file(s) for 1D5B
  • Structure Factors (157 Kb)
  • Retrieve 1D5B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1D5B from S2C, [Save to disk]
  • Re-refined 1d5b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1D5B 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 1D5B
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1D5B, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1d5ba1, region A:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1d5ba2, region A:108-211 [Jmol] [rasmolscript] [script source]
        - Domain d1d5bb1, region B:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1d5bb2, region B:114-214 [Jmol] [rasmolscript] [script source]
        - Domain d1d5bh1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1d5bh2, region H:114-214 [Jmol] [rasmolscript] [script source]
        - Domain d1d5bl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1d5bl2, region L:108-211 [Jmol] [rasmolscript] [script source]
  • Fold representative 1d5b from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1d5b_A] [1d5b] [1d5b_L] [1d5b_B] [1d5b_H]
  • SWISS-PROT database: [P01857] [P01834]
  • Domain organization of [IGHG1_HUMAN] [IGKC_HUMAN] by SWISSPFAM
  • Domains found in 1D5B: [IG_like] [IGv ] by SMART
  • Other resources with information on 1D5B
  • Community annotation for 1D5B at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1D5B from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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