1IVO Transferase Signaling Protein date Mar 28, 2002
title Crystal Structure Of The Complex Of Human Epidermal Growth F Receptor Extracellular Domains.
authors H.Ogiso, R.Ishitani, O.Nureki, S.Fukai, M.Yamanaka, J.H.Kim, K.Sai M.Shirouzu, S.Yokoyama, Riken Structural Genomicsproteomics Initiative (Rsgi)
compound source
Molecule: Epidermal Growth Factor Receptor
Chain: A, B
Fragment: Extracellular Domains I, II, II And Iv
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_strain: Lec8
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdna-Segfr

Molecule: Epidermal Growth Factor
Chain: C, D
Fragment: Residues 1-53
Synonym: Egf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 31 2 1
R_factor 0.255 R_Free 0.326
length a length b length c angle alpha angle beta angle gamma
220.164 220.164 113.121 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.30 Å
ligand NAG enzyme Transferase E.C. BRENDA
note 1IVO (Molecule of the Month:pdb126)
A, B

Primary referenceCrystal structure of the complex of human epidermal growth factor and receptor extracellular domains., Ogiso H, Ishitani R, Nureki O, Fukai S, Yamanaka M, Kim JH, Saito K, Sakamoto A, Inoue M, Shirouzu M, Yokoyama S, Cell 2002 Sep 20;110(6):775-87. PMID:12297050
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (192 Kb) [Save to disk]
  • Biological Unit Coordinates (1ivo.pdb1.gz) 184 Kb
  • LPC: Ligand-Protein Contacts for 1IVO
  • CSU: Contacts of Structural Units for 1IVO
  • Likely Quarternary Molecular Structure file(s) for 1IVO
  • Retrieve 1IVO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1IVO from S2C, [Save to disk]
  • View 1IVO 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 1IVO
  • 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 1IVO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ivoa3, region A:163-311 [Jmol] [rasmolscript] [script source]
        - Domain d1ivoa1, region A:2-162 [Jmol] [rasmolscript] [script source]
        - Domain d1ivoa2, region A:312-480 [Jmol] [rasmolscript] [script source]
        - Domain d1ivoa4, region A:481-512 [Jmol] [rasmolscript] [script source]
        - Domain d1ivob3, region B:163-311 [Jmol] [rasmolscript] [script source]
        - Domain d1ivob1, region B:3-162 [Jmol] [rasmolscript] [script source]
        - Domain d1ivob2, region B:312-480 [Jmol] [rasmolscript] [script source]
        - Domain d1ivob4, region B:481-512 [Jmol] [rasmolscript] [script source]
        - Domain d1ivoc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ivod_, region D [Jmol] [rasmolscript] [script source]
  • Fold representative 1ivo 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: [1ivo_C] [1ivo_A] [1ivo] [1ivo_D] [1ivo_B]
  • SWISS-PROT database: [P00533] [P01133]
  • Domain organization of [EGFR_HUMAN] [EGF_HUMAN] by SWISSPFAM
  • Domains found in 1IVO: [EGF] [FU ] by SMART
  • Other resources with information on 1IVO
  • Community annotation for 1IVO 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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