2Y1L

Caspase-8 in Complex with DARPin-8.4

• PDB DOI: https://doi.org/10.2210/pdb2Y1L/pdb

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2010-12-08 Released: 2011-12-28 
• Deposition Author(s): Barandun, J., Schroeder, T., Mittl, P.R.E., Grutter, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Starting Models: experimental

Literature

Caspase-8 in Complex with Darpin-8.4

Schroeder, T., Barandun, J., Grutter, M.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A2B2C2D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A2B2C2 

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

Macromolecule Content

• Total Structure Weight: 98.12 kDa 
• Atom Count: 6,964 
• Modelled Residue Count: 795 
• Deposited Residue Count: 873 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-8 subunit p18	A, C	159	Homo sapiens	Mutation(s): 0  Gene Names: CASP8, MCH5
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens) Explore Q14790  Go to UniProtKB:  Q14790
PHAROS:  Q14790 GTEx:  ENSG00000064012

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-8	B, D	104	Homo sapiens	Mutation(s): 0  Gene Names: CASP8, MCH5 EC: 3.4.22.61
UniProt & NIH Common Fund Data Resources
Find proteins for Q14790 (Homo sapiens) Explore Q14790  Go to UniProtKB:  Q14790
PHAROS:  Q14790 GTEx:  ENSG00000064012

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN-8.4	E, F	169	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AC-IETD-CHO	G [auth H]	4	synthetic construct	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
N-(2-oxoethyl)-L-isoleucyl-L-alpha-glutamyl-N-[(1R)-2-carboxy-1-formylethyl]-L-threoninamide	H [auth I]	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	I [auth A], K [auth B], L [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	J [auth B], M [auth C], N [auth E], O [auth F], P [auth F]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 5
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000301	H [auth I]	N-(2-oxoethyl)-L-isoleucyl-L-alpha-glutamyl-N-[(1R)-2-carboxy-1-formylethyl]-L-threoninamide	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.218 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61	α = 90
b = 81.6	β = 90
c = 163.2	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-28 
Deposition Author(s): Barandun, J., Schroeder, T., Mittl, P.R.E., Grutter, M.G.

Revision History  

• Version 1.0: 2011-12-28
  Type: Initial release
  
• Version 1.1: 2012-04-11
  Changes: Other
• Version 1.2: 2012-10-03
  Changes: Derived calculations
• Version 1.3: 2014-03-12
  Changes: Source and taxonomy
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 2.0: 2024-08-07
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Source and taxonomy, Structure summary