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), 0.198 (DCC)
R-Value Observed:
0.199 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6NRY

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
Modeled Residue Count: 245
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.198 (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

View more in-depth experimental data

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 is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.