4QFJ | pdb_00004qfj

The crystal structure of rat angiogenin-heparin complex

• PDB DOI: https://doi.org/10.2210/pdb4QFJ/pdb

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


• Deposited: 2014-05-21 Released: 2014-08-27 
• Deposition Author(s): Yeo, K.J., Hwang, E., Min, K.M., Hwang, K.Y., Jeon, Y.H., Chang, S.I., Cheong, H.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.266 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of rat angiogenin-heparin complex

Yeo, K.J., Hwang, E., Min, K.M., Hwang, K.Y., Jeon, Y.H., Chang, S.I., Cheong, H.K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 30.09 kDa 
• Atom Count: 1,938 
• Modeled Residue Count: 227 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Angiogenin	A, B	126	Rattus norvegicus	Mutation(s): 0  Gene Names: Ang, Ang1
UniProt
Find proteins for Q5WRG2 (Rattus norvegicus) Explore Q5WRG2  Go to UniProtKB:  Q5WRG2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	C	6		N/A
Glycosylation Resources
GlyTouCan:  G30141AL GlyCosmos:  G30141AL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACY	E [auth A], G [auth B]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.266 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.415	α = 90
b = 42.42	β = 90
c = 154.312	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Yeo, K.J., Hwang, E., Min, K.M., Hwang, K.Y., Jeon, Y.H., Chang, S.I., Cheong, H.K.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2020-10-14
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
• Version 3.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 3.2: 2024-10-30
  Changes: Structure summary