1NDM Immune System Hydrolase date Dec 09, 2002
title Crystal Structure Of Fab Fragment Of Antibody Hyhel-26 Complexed With Lysozyme
authors R.A.Mariuzza, Y.Li, H.Li
compound source
Molecule: Antibody Kappa Light Chain
Chain: A
Fragment: Light Chain
Engineered: Yes
Other_details: First Chain Of Anti-Lysozyme Antibody Hyhel- 26;
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Immunoglobulin Gamma 1 Chain
Chain: B
Engineered: Yes
Other_details: Second Chain Of Anti-Lysozyme Antibody Hyhel-26;

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b

Molecule: Lysozyme C
Chain: C
Synonym: 1,4-Beta-N-Acetylmuramidase C; Allergen Gal D 4 Gal D Iv;
Ec: 3.2.1.17
Engineered: Yes
Mutation: Yes

Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
Expression_system: Saccharomyces Cerevisiae
Expression_system_common: Baker'S Yeast
Expression_system_taxid: 4932
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ppic9
symmetry Space Group: P 21 21 2
R_factor 0.208 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.680 164.020 40.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand
enzyme Hydrolase E.C.3.2.1.17 BRENDA
related structures by homologous chain: 1NC2, 1SY6, 1XEJ, 1YEK, 2LZ2
Gene
Ontology
ChainFunctionProcessComponent
A


C


Primary referenceX-ray snapshots of the maturation of an antibody response to a protein antigen., Li Y, Li H, Yang F, Smith-Gill SJ, Mariuzza RA, Nat Struct Biol 2003 Jun;10(6):482-8. PMID:12740607
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (104 Kb) [Save to disk]
  • Biological Unit Coordinates (1ndm.pdb1.gz) 100 Kb
  • CSU: Contacts of Structural Units for 1NDM
  • Likely Quarternary Molecular Structure file(s) for 1NDM
  • Structure Factors (241 Kb)
  • Retrieve 1NDM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NDM from S2C, [Save to disk]
  • Re-refined 1ndm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NDM 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 1NDM
  • 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 1NDM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ndma1, region A:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1ndma2, region A:108-214 [Jmol] [rasmolscript] [script source]
        - Domain d1ndmb1, region B:301-413 [Jmol] [rasmolscript] [script source]
        - Domain d1ndmb2, region B:414-521 [Jmol] [rasmolscript] [script source]
        - Domain d1ndmc_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1ndm 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: [1ndm_B] [1ndm_A] [1ndm] [1ndm_C]
  • SWISS-PROT database: [P01865] [P01837] [P00698]
  • Domain organization of [GCAM_MOUSE] [IGKC_MOUSE] [LYSC_CHICK] by SWISSPFAM
  • Domains found in 1NDM: [IG_like] [IGv] [LYZ1 ] by SMART
  • Other resources with information on 1NDM
  • Community annotation for 1NDM 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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