4F44 | pdb_00004f44

Neurotrophin p75NTR intracellular domain

• PDB DOI: https://doi.org/10.2210/pdb4F44/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-05-10 Released: 2013-05-15 
• Deposition Author(s): Qu, Q., Jiang, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.280 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the allosteric activation mechanism of p75NTR

Qu, Q., Jiang, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.66 kDa 
• Atom Count: 1,377 
• Modeled Residue Count: 166 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tumor necrosis factor receptor superfamily member 16	A, B	94	Rattus norvegicus	Mutation(s): 0  Gene Names: Ngfr, NM_012610, Tnfrsf16
UniProt
Find proteins for P07174 (Rattus norvegicus) Explore P07174  Go to UniProtKB:  P07174

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MNB	C [auth A], D [auth B]	5-MERCAPTO-2-NITRO-BENZOIC ACID C7 H5 N O4 S GANZODCWZFAEGN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.280 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.372	α = 90
b = 53.372	β = 90
c = 73.486	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-15 
Deposition Author(s): Qu, Q., Jiang, T.

Revision History  

• Version 1.0: 2013-05-15
  Type: Initial release
  
• Version 1.1: 2013-05-22
  Changes: Refinement description
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary