4ZK9

The chemokine binding protein of orf virus complexed with CCL2

• PDB DOI: https://doi.org/10.2210/pdb4ZK9/pdb

• Classification: Viral Protein/cytokine
• Organism(s): Orf virus (strain NZ2), Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-04-30 Released: 2015-07-08 
• Deposition Author(s): Knapp, K.M., Nakatani, Y., Krause, K.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.281 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 41.21 kDa 
• Atom Count: 2,070 
• Modelled Residue Count: 277 
• Deposited Residue Count: 359 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chemokine binding protein	A	276	Orf virus (strain NZ2)	Mutation(s): 0
UniProt
Find proteins for Q2F862 (Orf virus) Explore Q2F862  Go to UniProtKB:  Q2F862

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-C motif chemokine 2	B	83	Homo sapiens	Mutation(s): 0  Gene Names: CCL2, MCP1, SCYA2
UniProt & NIH Common Fund Data Resources
Find proteins for P13500 (Homo sapiens) Explore P13500  Go to UniProtKB:  P13500
PHAROS:  P13500 GTEx:  ENSG00000108691

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.281 
• R-Value Work: 0.238 
• R-Value Observed: 0.241 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.802	α = 90
b = 78.802	β = 90
c = 185.613	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-08 
Deposition Author(s): Knapp, K.M., Nakatani, Y., Krause, K.L.

Revision History  

• Version 1.0: 2015-07-08
  Type: Initial release
  
• Version 1.1: 2015-07-15
  Changes: Database references
• Version 1.2: 2018-06-13
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary