1BJ1 Immune System date Jun 30, 1998
title Vascular Endothelial Growth Factor In Complex With A Neutral Antibody
authors Y.A.Muller, H.W.Christinger, A.M.De Vos
compound source
Molecule: Fab Fragment, Light Chain
Chain: L, J
Synonym: Fab-12
Engineered: Yes
Other_details: Humanized Version Of A Monoclonal Murine Ant Antibody;
Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Humanized Version Of A Monoclonal Murine Ant Antibody;

Molecule: Fab Fragment, Heavy Chain
Chain: H, K
Synonym: Fab-12
Engineered: Yes
Other_details: Humanized Version Of A Monoclonal Murine Ant Antibody;

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Humanized Version Of A Monoclonal Murine Ant Antibody;

Molecule: Vascular Endothelial Growth Factor A
Chain: V, W
Fragment: Receptor Binding Domain
Synonym: Vegf-A,Vascular Permeability Factor,Vpf
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vegfa, Vegf
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.196 R_Free 0.266
crystal
cell
length a length b length c angle alpha angle beta angle gamma
89.860 66.980 140.510 90.00 94.27 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand SO4 enzyme
related structures by homologous chain: 1C5D, 1CZ8, 1MJV, 1NGP
Gene
Ontology
ChainFunctionProcessComponent
W, V


Primary referenceVEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface., Muller YA, Chen Y, Christinger HW, Li B, Cunningham BC, Lowman HB, de Vos AM, Structure 1998 Sep 15;6(9):1153-67. PMID:9753694
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (181 Kb) [Save to disk]
  • Biological Unit Coordinates (1bj1.pdb1.gz) 175 Kb
  • LPC: Ligand-Protein Contacts for 1BJ1
  • CSU: Contacts of Structural Units for 1BJ1
  • Likely Quarternary Molecular Structure file(s) for 1BJ1
  • Structure Factors (523 Kb)
  • Retrieve 1BJ1 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1BJ1 from S2C, [Save to disk]
  • Re-refined 1bj1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1BJ1 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 1BJ1
  • 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
  • 3D motif for 1BJ1, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1bj1h1, region H:1-123 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1h2, region H:124-224 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1j1, region J:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1j2, region J:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1k1, region K:1-123 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1k2, region K:124-224 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1l1, region L:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1l2, region L:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1bj1v_, region V [Jmol] [rasmolscript] [script source]
        - Domain d1bj1w_, region W [Jmol] [rasmolscript] [script source]
  • 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: [1bj1_J] [1bj1_H] [1bj1_W] [1bj1_V] [1bj1] [1bj1_L] [1bj1_K]
  • SWISS-PROT database: [P15692]
  • Domain organization of [VEGFA_HUMAN] by SWISSPFAM
  • Domains found in 1BJ1: [IG_like] [IGv] [PDGF ] by SMART
  • Other resources with information on 1BJ1
  • Community annotation for 1BJ1 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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