2YVI

Crystal structure of a death domain of human ankryn protein

• PDB DOI: https://doi.org/10.2210/pdb2YVI/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-04-12 Released: 2008-04-15 
• Deposition Author(s): Ihsanawati, Bessho, Y., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.217 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 

Literature

Crystal structure of a death domain of human ankryn protein

Ihsanawati, Bessho, Y., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 12.3 kDa 
• Atom Count: 804 
• Modelled Residue Count: 89 
• Deposited Residue Count: 111 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin-1	A	111	Homo sapiens	Mutation(s): 0  Gene Names: ANK1, ANK
UniProt & NIH Common Fund Data Resources
Find proteins for P16157 (Homo sapiens) Explore P16157  Go to UniProtKB:  P16157
PHAROS:  P16157 GTEx:  ENSG00000029534

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.217 
• R-Value Work: 0.198 
• R-Value Observed: 0.198 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.63	α = 90
b = 46.63	β = 90
c = 145.15	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-15 
Deposition Author(s): Ihsanawati, Bessho, Y., Chen, L., Liu, Z.J., Wang, B.C., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-04-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-02-01
  Changes: Structure summary
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations