1N8Z Transferase date Nov 21, 2002
title Crystal Structure Of Extracellular Domain Of Human Her2 Comp Herceptin Fab
authors H.S.Cho, K.Mason, K.X.Ramyar, A.M.Stanley, S.B.Gabelli, D.W.Denn D.J.Leahy
compound source
Molecule: Herceptin Fab (Antibody) - Light Chain
Chain: A
Engineered: Yes
Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mousehuman
Organism_taxid: 10090, 9606

Molecule: Herceptin Fab (Antibody) - Heavy Chain
Chain: B
Engineered: Yes

Organism_scientific: Mus Musculus, Homo Sapiens
Organism_common: Mousehuman
Organism_taxid: 10090, 9606

Molecule: Receptor Protein-Tyrosine Kinase Erbb-2
Chain: C
Fragment: Extracellular Domain
Synonym: Tyrosine Kinase-Type Cell Surface Receptor Her2
Ec: 2.7.1.112
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Her2(Erbb2)
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 21
R_factor 0.222 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.170 109.770 175.140 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.52 Å
ligand NAG, SO4 enzyme Transferase E.C.2.7.1.112 BRENDA
note 1N8Z (Molecule of the Month:pdb126)
related structures by homologous chain: 1JHK, 1N8Y, 1U8N, 1V7M
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] (166 Kb) [Save to disk]
  • Biological Unit Coordinates (1n8z.pdb1.gz) 159 Kb
  • LPC: Ligand-Protein Contacts for 1N8Z
  • CSU: Contacts of Structural Units for 1N8Z
  • Likely Quarternary Molecular Structure file(s) for 1N8Z
  • Structure Factors (625 Kb)
  • Retrieve 1N8Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N8Z from S2C, [Save to disk]
  • Re-refined 1n8z structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1N8Z 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 1N8Z
  • 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 1N8Z, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n8za1, region A:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1n8za2, region A:108-214 [Jmol] [rasmolscript] [script source]
        - Domain d1n8zb1, region B:1-120 [Jmol] [rasmolscript] [script source]
        - Domain d1n8zb2, region B:121-220 [Jmol] [rasmolscript] [script source]
        - Domain d1n8zc1, region C:1-165 [Jmol] [rasmolscript] [script source]
        - Domain d1n8zc3, region C:166-322 [Jmol] [rasmolscript] [script source]
        - Domain d1n8zc2, region C:323-488 [Jmol] [rasmolscript] [script source]
        - Domain d1n8zc4, region C:489-607 [Jmol] [rasmolscript] [script source]
  • Fold representative 1n8z 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: [1n8z_B] [1n8z_C] [1n8z_A] [1n8z]
  • SWISS-PROT database: [P04626]
  • Domain organization of [ERBB2_HUMAN] by SWISSPFAM
  • Domains found in 1N8Z: [FU] [IG_like] [IGv ] by SMART
  • Alignments of the sequence of 1N8Z with the sequences similar proteins can be viewed for 1N8Z's classification [ERBB2_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [ERBB2_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1N8Z
  • Community annotation for 1N8Z 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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