1SGF

CRYSTAL STRUCTURE OF 7S NGF: A COMPLEX OF NERVE GROWTH FACTOR WITH FOUR BINDING PROTEINS (SERINE PROTEINASES)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history. 


Literature

Structure of mouse 7S NGF: a complex of nerve growth factor with four binding proteins.

Bax, B., Blundell, T.L., Murray-Rust, J., McDonald, N.Q.

(1997) Structure 5: 1275-1285

  • DOI: 10.1016/s0969-2126(97)00280-3
  • Primary Citation of Related Structures:  
    1SGF

  • PubMed Abstract: 

    • Nerve growth factor (NGF) is a neurotrophic factor that promotes the differentiation and survival of certain populations of neurons in the central and peripheral nervous systems. 7S NGF is an alpha 2 beta 2 gamma 2 complex in which the beta-NGF dimer (the active neurotrophin) is associated with two alpha-NGF and two gamma-NGF subunits, which belong to the glandular kallikrein family of serine proteinases ...

    Nerve growth factor (NGF) is a neurotrophic factor that promotes the differentiation and survival of certain populations of neurons in the central and peripheral nervous systems. 7S NGF is an alpha 2 beta 2 gamma 2 complex in which the beta-NGF dimer (the active neurotrophin) is associated with two alpha-NGF and two gamma-NGF subunits, which belong to the glandular kallikrein family of serine proteinases. The gamma-NGF subunit is an active serine proteinase capable of processing the precursor form of beta-NGF, whereas alpha-NGF is an inactive serine proteinase. The structure of 7S NGF could be used as a starting point to design inhibitors that prevent NGF binding to its receptors, as a potential treatment of neurodegenerative diseases.

    Related Citations: 
    • Crystallization and Characterization of the High Molecular Weight Form of Nerve Growth Factor (7 S Ngf)
      Mcdonald, N.Q., Blundell, T.L.
      (1991) J Mol Biol 219: 595
    Organizational Affiliation: 

    Department of Crystallography, Birkbeck College, London, UK. b.bax@cryst.bbk.ac.uk



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NERVE GROWTH FACTORA,
D [auth X]		240Mus musculusMutation(s): 0 
Gene Names: Klk1b4, Klk-4, Klk4, Ngfa
EC: 3.4.21.35
UniProt
Find proteins for P00757 (Mus musculus)
Explore P00757 
Go to UniProtKB:  P00757
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00757
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NERVE GROWTH FACTORB,
E [auth Y]		118Mus musculusMutation(s): 0 
Gene Names: Ngf, Ngfb
EC: 3.4.21.35
UniProt
Find proteins for P01139 (Mus musculus)
Explore P01139 
Go to UniProtKB:  P01139
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01139
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
NERVE GROWTH FACTORC [auth G],
F [auth Z]		237Mus musculusMutation(s): 0 
Gene Names: Klk1b3, Klk-3, Klk3, Ngfg
EC: 3.4.21.35
UniProt
Find proteins for P00756 (Mus musculus)
Explore P00756 
Go to UniProtKB:  P00756
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00756
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth C],
H [auth D]		2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
I [auth A],
K [auth X]		2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
J [auth A],
L [auth X]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.68α = 90
b = 96.59β = 90
c = 147γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
TFFCmodel building
X-PLORmodel building
X-PLORrefinement
CCP4data scaling
ROTAVATAdata scaling
TFFCphasing
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary