2Y1L | pdb_00002y1l

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.218 (Depositor), 0.218 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

Caspase-8 in Complex with Darpin-8.4

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

To be published.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14790
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14790
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

Find similar proteins by: Sequence | 3D Structure

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

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C]	I [auth A], K [auth B], L [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth F] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth E] mmCIF format, chain O [auth F] mmCIF format, chain P [auth F]	J [auth B], M [auth C], N [auth E], O [auth F], P [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]

Biologically Interesting Molecules (External Reference)

1 Unique

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.218 (Depositor), 0.218 (DCC)
R-Value Work: 0.180 (Depositor), 0.182 (DCC)
R-Value Observed: 0.182 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-12-28

Deposition Author(s):

Revision History (Full details and data files)

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