6NRY | pdb_00006nry

Crystal structure of human caspase-4

PDB DOI: https://doi.org/10.2210/pdb6NRY/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2019-01-24 Released: 2020-07-29
Deposition Author(s): Yang, J., Liu, Z., Shi, W., Xiao, T.S.
Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.237 (Depositor), 0.240 (DCC)
R-Value Work:
0.195 (Depositor), 0.190 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of human caspase-4

Yang, J., Liu, Z., Xiao, T.S.

To be published.

Macromolecule Content

Total Structure Weight: 32.92 kDa
Atom Count: 2,067
Modelled Residue Count: 245
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caspase-4	A	288	Homo sapiens	Mutation(s): 1 Gene Names: CASP4, ICH2 EC: 3.4.22.57
UniProt & NIH Common Fund Data Resources
Find proteins for P49662 (Homo sapiens) Explore P49662 Go to UniProtKB: P49662
PHAROS: P49662 GTEx: ENSG00000196954
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49662
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.237 (Depositor), 0.240 (DCC)
R-Value Work: 0.195 (Depositor), 0.190 (DCC)
R-Value Observed: 0.199 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.687	α = 90
b = 163.383	β = 90
c = 103.661	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2020-07-29

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	GM127609

Revision History (Full details and data files)

Version 1.0: 2020-07-29
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.