1IC5 Protein Binding Hydrolase date Mar 30, 2001
title Crystal Structure Of Hyhel-10 Fv Mutant(Hd99a)-Hen Lysozyme Complex
authors M.Shiroishi, A.Yokota, K.Tsumoto, H.Kondo, Y.Nishimiya, K.Horii, M.Matsushima, K.Ogasahara, K.Yutani, I.Kumagai
compound source
Molecule: Lysozyme Binding Ig Kappa Chain
Chain: L
Engineered: Yes
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Igg1 Fab Chain H
Chain: H
Fragment: Residues 1-114
Engineered: Yes
Mutation: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Lysozyme C
Chain: Y
Ec: 3.2.1.17

Organism_scientific: Gallus Gallus
Organism_common: Chicken
Organism_taxid: 9031
symmetry Space Group: P 41 21 2
R_factor 0.165 R_Free 0.252
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.001 57.001 238.086 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand
enzyme Hydrolase E.C.3.2.1.17 BRENDA
related structures by homologous chain: 1DN0, 1KCU, 1XEK, 2LZ2
Gene
Ontology
ChainFunctionProcessComponent
H


L


Y


Primary referenceStructural evidence for entropic contribution of salt bridge formation to a protein antigen-antibody interaction: the case of hen lysozyme-HyHEL-10 Fv complex., Shiroishi M, Yokota A, Tsumoto K, Kondo H, Nishimiya Y, Horii K, Matsushima M, Ogasahara K, Yutani K, Kumagai I, J Biol Chem 2001 Jun 22;276(25):23042-50. PMID:11297547
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (62 Kb) [Save to disk]
  • Biological Unit Coordinates (1ic5.pdb1.gz) 58 Kb
  • CSU: Contacts of Structural Units for 1IC5
  • Likely Quarternary Molecular Structure file(s) for 1IC5
  • Retrieve 1IC5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IC5 from S2C, [Save to disk]
  • View 1IC5 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 1IC5
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1IC5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ic5h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1ic5l_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1ic5y_, region Y [Jmol] [rasmolscript] [script source]
  • Fold representative 1ic5 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: [1ic5] [1ic5_L] [1ic5_H] [1ic5_Y]
  • SWISS-PROT database: [P01823] [P01642] [P00698]
  • Domain organization of [HVM47_MOUSE] [KV5A9_MOUSE] [LYSC_CHICK] by SWISSPFAM
  • Domains found in 1IC5: [IGv] [LYZ1 ] by SMART
  • Other resources with information on 1IC5
  • Community annotation for 1IC5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Domain movements in 1IC5 from the Database of Macromolecular Movements.
  • Images from IMB Jena Image Library of Biological Macromolecules.

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