8ZGD | pdb_00008zgd

The Crystal Structure of the NLRP1_LRR domain from Biortus.

PDB DOI: https://doi.org/10.2210/pdb8ZGD/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-05-09 Released: 2024-06-26
Deposition Author(s): Wang, F., Cheng, W., Yuan, Z., Qi, J., Pan, W.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.221 (Depositor), 0.230 (DCC)
R-Value Work:
0.176 (Depositor), 0.188 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZGD

This is version 1.0 of the entry. See complete history.

Literature

The Crystal Structure of the NLRP1_LRR domain from Biortus.

Wang, F., Cheng, W., Yuan, Z., Qi, J., Pan, W.

To be published.

Macromolecule Content

Total Structure Weight: 22.43 kDa
Atom Count: 1,762
Modeled Residue Count: 197
Deposited Residue Count: 200
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NACHT, LRR and PYD domains-containing protein 1, N-terminus	A	200	Homo sapiens	Mutation(s): 0 Gene Names: NLRP1, CARD7, DEFCAP, KIAA0926, NAC, NALP1 EC: 3.6.4 (UniProt), 3.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C000 (Homo sapiens) Explore Q9C000 Go to UniProtKB: Q9C000
PHAROS: Q9C000 GTEx: ENSG00000091592
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C000
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: 2.05 Å
R-Value Free: 0.221 (Depositor), 0.230 (DCC)
R-Value Work: 0.176 (Depositor), 0.188 (DCC)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.582	α = 90
b = 84.582	β = 90
c = 132.495	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2024-06-26
Type: Initial release

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.