1N8Y Transferase date Nov 21, 2002
title Crystal Structure Of The Extracellular Region Of Rat Her2
authors H.S.Cho, K.Mason, K.X.Ramyar, A.M.Stanley, S.B.Gabelli, D.W.Denn D.J.Leahy
compound source
Molecule: Protooncoprotein
Chain: C
Fragment: Extracellular Region (Residues 26-633)
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Norway Rat
Organism_taxid: 10116
Gene: Neu
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_strain: Cho(Lec1)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Psghv0
symmetry Space Group: P 21 21 2
R_factor 0.224 R_Free 0.282
crystal
cell
length a length b length c angle alpha angle beta angle gamma
130.870 116.400 55.370 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand NAG enzyme
related structures by homologous chain: 1N8Z
subcellular loc. Membrane localization by OPM: Eukaryotic plasma membrane
extracellular side
cytoplasmic side
Gene
Ontology
ChainFunctionProcessComponent
C


Primary referenceStructure of the extracellular region of HER2 alone and in complex with the Herceptin Fab., Cho HS, Mason K, Ramyar KX, Stanley AM, Gabelli SB, Denney DW Jr, Leahy DJ, Nature 2003 Feb 13;421(6924):756-60. PMID:12610629
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (101 Kb) [Save to disk]
  • Biological Unit Coordinates (1n8y.pdb1.gz) 95 Kb
  • LPC: Ligand-Protein Contacts for 1N8Y
  • CSU: Contacts of Structural Units for 1N8Y
  • Likely Quarternary Molecular Structure file(s) for 1N8Y
  • Structure Factors (490 Kb)
  • Retrieve 1N8Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N8Y from S2C, [Save to disk]
  • Re-refined 1n8y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1N8Y 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 1N8Y
  • 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 1N8Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n8yc1, region C:1-165 [Jmol] [rasmolscript] [script source]
        - Domain d1n8yc3, region C:166-322 [Jmol] [rasmolscript] [script source]
        - Domain d1n8yc2, region C:323-488 [Jmol] [rasmolscript] [script source]
        - Domain d1n8yc4, region C:489-608 [Jmol] [rasmolscript] [script source]
  • Fold representative 1n8y from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1n8y_C] [1n8y]
  • SWISS-PROT database: [P06494]
  • Domain organization of [ERBB2_RAT] by SWISSPFAM
  • Domain found in 1N8Y: [FU ] by SMART
  • Other resources with information on 1N8Y
  • Community annotation for 1N8Y 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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