1I8M Immune System Dna date Mar 14, 2001
title Crystal Structure Of A Recombinant Anti-Single-Stranded Dna Fragment Complexed With Dt5
authors J.J.Tanner, A.A.Komissarov, S.L.Deutscher
compound source
Molecule: 5'-D(Tptptptpt)-3'
Chain: T
Engineered: Yes
Synthetic: Yes

Molecule: 5'-D(Ptpt)-3'
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Antibody Light Chain Fab
Chain: L, A
Synonym: Anti-Single-Stranded Dna Antigen-Binding Fab Fragm
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh12s
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcomb36-His

Molecule: Antibody Heavy Chain Fab
Chain: H, B
Synonym: Anti-Single-Stranded Dna Antigen-Binding Fab Fragm
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Dh12s
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcomb36-His
symmetry Space Group: P 65 2 2
R_factor 0.220 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
171.840 171.840 144.568 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.10 Å
ligand SO4 enzyme
related structures by homologous chain: 1DQM, 1MH5, 1U8H, 1WT5
Primary referenceCrystal structure of an antigen-binding fragment bound to single-stranded DNA., Tanner JJ, Komissarov AA, Deutscher SL, J Mol Biol 2001 Dec 7;314(4):807-22. PMID:11733999
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (143 Kb) [Save to disk]
  • Biological Unit Coordinates (1i8m.pdb1.gz) 71 Kb
  • Biological Unit Coordinates (1i8m.pdb2.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 1I8M
  • CSU: Contacts of Structural Units for 1I8M
  • Likely Quarternary Molecular Structure file(s) for 1I8M
  • Structure Factors (1471 Kb)
  • Retrieve 1I8M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1I8M from S2C, [Save to disk]
  • Re-refined 1i8m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1I8M 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 1I8M
  • 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 1I8M, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1i8ma1, region A:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1i8ma2, region A:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1i8mb1, region B:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1i8mb2, region B:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1i8mh1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1i8mh2, region H:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1i8ml1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1i8ml2, region L:108-213 [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: [1i8m_L] [1i8m] [1i8m_D] [1i8m_A] [1i8m_B] [1i8m_T] [1i8m_H]
  • SWISS-PROT database: [P01837] [Q7TS98] [Q924Q6]
  • Domain organization of [IGKC_MOUSE] [Q7TS98_MOUSE] [Q924Q6_MOUSE] by SWISSPFAM
  • Domains found in 1I8M: [IG_like] [IGv ] by SMART
  • Other resources with information on 1I8M
  • Community annotation for 1I8M 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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