2IFG

Structure of the extracellular segment of human TRKA in complex with nerve growth factor

• PDB DOI: https://doi.org/10.2210/pdb2IFG/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2006-09-20 Released: 2007-02-13 
• Deposition Author(s): He, X., Garcia, K.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.331 
• R-Value Work: 0.297 
• R-Value Observed: 0.297 

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Macromolecule Content

• Total Structure Weight: 109.54 kDa 
• Atom Count: 7,483 
• Modelled Residue Count: 911 
• Deposited Residue Count: 934 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
High affinity nerve growth factor receptor	A, B	347	Homo sapiens	Mutation(s): 0  Gene Names: NTRK1, TRK EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04629 (Homo sapiens) Explore P04629  Go to UniProtKB:  P04629
PHAROS:  P04629 GTEx:  ENSG00000198400

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-nerve growth factor	C [auth E], D [auth F]	120	Homo sapiens	Mutation(s): 0  Gene Names: NGFB
UniProt & NIH Common Fund Data Resources
Find proteins for P01138 (Homo sapiens) Explore P01138  Go to UniProtKB:  P01138
PHAROS:  P01138 GTEx:  ENSG00000134259

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E [auth C], K	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07375KG GlyCosmos:  G07375KG GlyGen:  G07375KG

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth D], I, L, O	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G52260VY GlyCosmos:  G52260VY GlyGen:  G52260VY

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, J, M, N, P	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G35926TG GlyCosmos:  G35926TG GlyGen:  G35926TG

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
NGF	PDBBind:  2IFG	Kd: 0.9 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.40 Å
• R-Value Free: 0.331 
• R-Value Work: 0.297 
• R-Value Observed: 0.297 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.215	α = 90
b = 81.681	β = 104.15
c = 115.748	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-13 
Deposition Author(s): He, X., Garcia, K.C.

Revision History  

• Version 1.0: 2007-02-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  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, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary