3MJG

The structure of a platelet derived growth factor receptor complex

• PDB DOI: https://doi.org/10.2210/pdb3MJG/pdb

• Classification: Hormone/Transferase
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2010-04-12 Released: 2010-06-16 
• Deposition Author(s): Shim, A.H.R., He, X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 107.28 kDa 
• Atom Count: 7,254 
• Modelled Residue Count: 745 
• Deposited Residue Count: 922 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-derived growth factor subunit B	A, B	172	Homo sapiens	Mutation(s): 0  Gene Names: PDGF2, PDGFB, SIS
UniProt & NIH Common Fund Data Resources
Find proteins for P01127 (Homo sapiens) Explore P01127  Go to UniProtKB:  P01127
PHAROS:  P01127 GTEx:  ENSG00000100311

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-type platelet-derived growth factor receptor	C [auth X], D [auth Y]	289	Homo sapiens	Mutation(s): 0  Gene Names: PDGFRB EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P09619 (Homo sapiens) Explore P09619  Go to UniProtKB:  P09619
PHAROS:  P09619 GTEx:  ENSG00000113721

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth X], G [auth X], H [auth X], I [auth X], J [auth X], K [auth X], L [auth Y], M [auth Y], N [auth Y], O [auth Y], P [auth Y], Q [auth Y], R [auth Y]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NDG	E [auth X]	2-acetamido-2-deoxy-alpha-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-PVFLNQBWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.277 
• R-Value Work: 0.237 
• R-Value Observed: 0.237 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.47	α = 90
b = 116.82	β = 90
c = 134.15	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-16 
Deposition Author(s): Shim, A.H.R., He, X.

Revision History  

• Version 1.0: 2010-06-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary