5LTL | pdb_00005ltl

Structure of human chemokine CCL16

• PDB DOI: https://doi.org/10.2210/pdb5LTL/pdb

• Classification: CYTOKINE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2016-09-07 Released: 2018-05-09 
• Deposition Author(s): Weiergraeber, O.H., Batra-Safferling, R., Haenel, K., Willbold, D.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Structure and dynamics of human chemokine CCL16

Weiergraeber, O.H., Petrovic, D., Kislat, A., Pattky, M., Fabig, J., Batra-Safferling, R., Haenel, K., Huhn, C., Strodel, B., Homey, B., Willbold, D.

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: 23.03 kDa 
• Atom Count: 1,238 
• Modelled Residue Count: 137 
• Deposited Residue Count: 200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-C motif chemokine 16	A, B	100	Homo sapiens	Mutation(s): 0  Gene Names: CCL16, ILINCK, NCC4, SCYA16
UniProt & NIH Common Fund Data Resources
Find proteins for O15467 (Homo sapiens) Explore O15467  Go to UniProtKB:  O15467
PHAROS:  O15467 GTEx:  ENSG00000275152

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.35	α = 90
b = 24.59	β = 93.12
c = 37.97	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-09 
Deposition Author(s): Weiergraeber, O.H., Batra-Safferling, R., Haenel, K., Willbold, D.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	--

Revision History  

• Version 1.0: 2018-05-09
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary