1QKZ Immune System date Aug 17, 1999
title Fab Fragment (Mn14c11.6) In Complex With A Peptide Antigen D From Neisseria Meningitidis P1.7 Serosubtype Antigen And Do From Streptococcal Protein G
authors J.P.Derrick, I.Feavers, M.C.J.Maiden
compound source
Molecule: Protein G-Prime
Chain: A
Fragment: Domain II
Engineered: Yes
Mutation: Yes
Organism_scientific: Streptococcus Sp.
Organism_taxid: 1320
Strain: Group G
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Modified Puc18

Molecule: Antibody
Chain: H
Fragment: Fab

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Cell_line: Mn14c11.6 Murine Hybridoma
Cell: Hybridoma

Molecule: Antibody
Chain: L
Fragment: Fab

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Cell_line: Mn14c11.6 Murine Hybridoma
Cell: Hybridoma

Molecule: Major Outer Membrane Protein P1.16
Chain: P
Fragment: Residues 4-13
Engineered: Yes

Synthetic: Yes
Organism_scientific: Neisseria Meningitidis
Organism_taxid: 487
symmetry Space Group: P 1 21 1
R_factor 0.205 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.482 63.099 89.374 90.00 81.54 90.00
method X-Ray Diffractionresolution 1.95 Å
related structures by homologous chain: 1E4W, 1EM7, 1GPO, 1PGB, 1SM3
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of an Fab fragment in complex with a meningococcal serosubtype antigen and a protein G domain., Derrick JP, Maiden MC, Feavers IM, J Mol Biol 1999 Oct 15;293(1):81-91. PMID:10512717
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (91 Kb) [Save to disk]
  • Biological Unit Coordinates (1qkz.pdb1.gz) 86 Kb
  • CSU: Contacts of Structural Units for 1QKZ
  • Likely Quarternary Molecular Structure file(s) for 1QKZ
  • Retrieve 1QKZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1QKZ from S2C, [Save to disk]
  • View 1QKZ 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 1QKZ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1QKZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1qkza_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1qkzh1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1qkzh2, region H:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1qkzl1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1qkzl2, 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: [1qkz_A] [1qkz_P] [1qkz_L] [1qkz_H] [1qkz]
  • SWISS-PROT database: [P57041] [P19909]
  • Domain organization of [OMPA_NEIMA] [SPG2_STRSG] by SWISSPFAM
  • Domains found in 1QKZ: [IG_like] [IGv ] by SMART
  • Other resources with information on 1QKZ
  • Community annotation for 1QKZ 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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