4EDX Immune System date Mar 27, 2012
title Nerve Growth Factor In Complex With Fab From Mouse Mab 911
authors C.Eigenbrot, M.Ultsch
compound source
Molecule: Beta-Nerve Growth Factor
Chain: W, V
Synonym: Beta-Ngf
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ngf, Ngfb
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Light Chain Of Fab Of Murine Anti-Ngf
Chain: A, L
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Heavy Chain Of Fab Of Murine Anti-Ngf
Chain: B, H
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_taxid: 10090
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.208 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
57.748 69.931 83.736 104.34 94.13 110.42
method X-Ray Diffractionresolution 2.50 Å
Gene
Ontology
ChainFunctionProcessComponent
W, V


Primary referenceGeneration of a high-fidelity antibody against nerve growth factor using library scanning mutagenesis and validation with structures of the initial and optimized Fab-antigen complexes., La Porte SL, Eigenbrot C, Ultsch M, Ho WH, Foletti D, Forgie A, Lindquist KC, Shelton DL, Pons J, MAbs. 2014 Jul-Aug;6(4):1059-68. PMID:24830649
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (353 Kb) [Save to disk]
  • Biological Unit Coordinates (4edx.pdb1.gz) 346 Kb
  • CSU: Contacts of Structural Units for 4EDX
  • Structure Factors (491 Kb)
  • Retrieve 4EDX in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4EDX from S2C, [Save to disk]
  • Re-refined 4edx structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4EDX 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 4EDX
  • 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 4EDX, from MSDmotif at EBI
  • Fold representative 4edx from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4edx] [4edx_L] [4edx_B] [4edx_A] [4edx_H] [4edx_W] [4edx_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4EDX: [IG_like] [IGv] [NGF ] by SMART
  • Other resources with information on 4EDX
  • Community annotation for 4EDX at PDBWiki (http://pdbwiki.org)

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