4E9M | pdb_00004e9m

NOD1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric unit

PDB DOI: https://doi.org/10.2210/pdb4E9M/pdb

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

Deposited: 2012-03-21 Released: 2012-04-04
Deposition Author(s): Berry, E.A., Huang, L.S., Walker-Kopp, N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.275 (Depositor), 0.271 (DCC)
R-Value Work:
0.245 (Depositor), 0.244 (DCC)
R-Value Observed:
0.245 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of nod1 card domain with three disulfide-clinched, domain-swapped dimers in the asymmetric unit

Berry, E.A., Huang, L.S., Walker-Kopp, N.

To be published.

Macromolecule Content

Total Structure Weight: 100.32 kDa
Atom Count: 4,641
Modeled Residue Count: 559
Deposited Residue Count: 864
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide-binding oligomerization domain-containing protein 1	A, B, C, D, E A, B, C, D, E, F	144	Homo sapiens	Mutation(s): 0 Gene Names: CARD4, NOD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y239 (Homo sapiens) Explore Q9Y239 Go to UniProtKB: Q9Y239
PHAROS: Q9Y239 GTEx: ENSG00000106100
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y239
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.275 (Depositor), 0.271 (DCC)
R-Value Work: 0.245 (Depositor), 0.244 (DCC)
R-Value Observed: 0.245 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.846	α = 90
b = 85.335	β = 90
c = 113.682	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-04-04

Deposition Author(s):

Walker-Kopp, N.

Revision History (Full details and data files)

Version 1.0: 2012-04-04
Type: Initial release
Version 1.1: 2013-02-06
Changes: Other
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-27
Changes: Structure summary

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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.