1N8Z Transferase date Nov 21, 2002
title Crystal Structure Of Extracellular Domain Of Human Her2 Complexed With Herceptin Fab
authors H.-S.Cho, K.Mason, K.X.Ramyar, A.M.Stanley, S.B.Gabelli, D.W.Denney Jr., D.J.Leahy
compound source
Molecule: Herceptin Fab (Antibody) - Light Chain
Chain: A
 Organism_scientific: Homo Sapiens
Organism_common: Human

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

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
Gene: Her2(Erbb2)
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
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
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, SO4enzyme Transferase E.C.2.7.1.112
note 1N8Z is a representative structure
related structures by homologous chain: 1B2W, 1FVD, 1FVE
similarity Belongs to the egf receptor family.[YLP]
subunit Heterodimer with each of the other erbb receptors (potential). Interacts with prkcabp (by similarity).
catalytic activ. Atp + a protein tyrosine = adp + protein tyrosine phosphate.
polymorphism There are fours alleles due to the variations in positions 654 and 655. Allele b1 (ile-654/ile-655) has a frequency of 0.782; allele b2 (ile-654/val-655) has a frequency of 0.206; allele b3 (val-654/val-655) has a frequency of 0.012.
post-translat. modifications Ligand-binding increases phosphorylation on tyrosine residues (by similarity).
subcellular loc. Type i membrane protein.
genes ERBB2, HER2, NEU, NGL (H. sapiens)
function Gp30 is a potential ligand for this receptor. Not activated by egf, tgf- alpha and amphiregulin. Essential component of a neuregulin-receptor complex, althought neuregulins do not interact with it alone.
Gene
Ontology 		chain C: GO:0004672, GO:0004713, GO:0004714, GO:0004716, GO:0004872, GO:0005006, GO:0005524, GO:0006468, GO:0007167, GO:0007169, GO:0008283, GO:0016020, GO:0016021, GO:0016740, GO:0043125
disease Sialidosis,type I
Sialidosis,type II
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] (183 Kb) [Save to disk]
  • Biological Unit Coordinates (1n8z.pdb1.gz) 160 Kb
  • LPC: Ligand-Protein Contacts for 1N8Z
  • CSU: Contacts of Structural Units for 1N8Z
  • Likely Quarternary Molecular Structure file(s) for 1N8Z
  • Structure Factors (r1n8zsf.ent.Z) 639 Kb
  • Retrieve 1N8Z in mmCIF format [Save to disk]
    • View 1N8Z in 3D
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On AstexViewer, from MSD-EBI (viewer documentation).
  • On RasMol (Install RasMol freeware) Here's help on how to use RasMol.
    • Visual 3D analysis of 1N8Z
  • STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure.
  • Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges.
  • GRASS (Graphical Representation and Analysis of Structure Server)
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Known point mutations with 2 PDB ids, from MutaProt at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 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)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1n8z_A] [1n8z_B] [1n8z_C]
  • SWISS-PROT database: [P04626]
  • Domain organization of [ERB2_HUMAN] by SWISSPFAM
  • Conserved protein region description, domain view and alignment from family YLP (PF02757) of Pfam.
  • Alignments of the sequence of 1N8Z with the sequences similar proteins can be viewed for classification [ERB2_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 [ERB2_HUMAN] at ProtoMap. Click on the Cluster number.
    • Other resources with information on 1N8Z
  • InterPro: IPR008266 , IPR006211 , IPR006212 , IPR000494 , IPR009030 , IPR004019 , IPR001245 , IPR000719
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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