1RUM Immune System date Dec 11, 2003
title Crystal Structure (F) Of H2o2-Soaked Cationic Cyclization An Fab At Ph 8.5 With A Data Set Collected At Ssrl Beamline 9-
authors X.Zhu, P.Wentworth Jr., A.D.Wentworth, A.Eschenmoser, R.A.Lerner I.A.Wilson
compound source
Molecule: Immunoglobulin Igg2a, Light Chain
Chain: L
Fragment: Fab
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: 129g1x+

Molecule: Immunoglobulin Igg2a, Heavy Chain
Chain: H
Fragment: Fab

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Strain: 129g1x+
symmetry Space Group: P 41 21 2
length a length b length c angle alpha angle beta angle gamma
64.386 64.386 266.983 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.48 Å
ligand 4HT, BEZ, GOL enzyme
related structures by homologous chain: 1Q9Q, 1Q9R, 1UAC

Primary referenceProbing the antibody-catalyzed water-oxidation pathway at atomic resolution., Zhu X, Wentworth P Jr, Wentworth AD, Eschenmoser A, Lerner RA, Wilson IA, Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2247-52. PMID:14982995
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (169 Kb) [Save to disk]
  • Biological Unit Coordinates (1rum.pdb1.gz) 164 Kb
  • LPC: Ligand-Protein Contacts for 1RUM
  • CSU: Contacts of Structural Units for 1RUM
  • Likely Quarternary Molecular Structure file(s) for 1RUM
  • Structure Factors (837 Kb)
  • Retrieve 1RUM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RUM from S2C, [Save to disk]
  • Re-refined 1rum structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RUM 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 1RUM
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Conformational Epitope Prediction for 1RUM 1RUMH 1RUML from the CEP Server.
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RUM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rumh1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rumh2, region H:114-231 [Jmol] [rasmolscript] [script source]
        - Domain d1ruml1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1ruml2, region L:108-214 [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: [1rum] [1rum_L] [1rum_H]
  • SWISS-PROT database: [P01865]
  • Domain organization of [GCAM_MOUSE] by SWISSPFAM
  • Domains found in 1RUM: [IG_like] [IGv ] by SMART
  • Other resources with information on 1RUM
  • Community annotation for 1RUM 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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