8OUQ | pdb_00008ouq

Clr-11 from Rattus norvegicus

PDB DOI: https://doi.org/10.2210/pdb8OUQ/pdb

Classification: IMMUNE SYSTEM
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2023-04-24 Released: 2024-05-01
Deposition Author(s): Skalova, T., Blaha, J., Kalouskova, B., Skorepa, O., Vanek, O., Dohnalek, J.
Funding Organization(s): Czech Academy of Sciences, European Regional Development Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.235 (Depositor), 0.216 (DCC)
R-Value Work:
0.190 (Depositor), 0.200 (DCC)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Clr-11 from Rattus norvegicus

Skalova, T., Blaha, J., Kalouskova, B., Skorepa, O., Vanek, O., Dohnalek, J.

To be published.

Macromolecule Content

Total Structure Weight: 31.9 kDa
Atom Count: 2,410
Modeled Residue Count: 247
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 2 member D11	A [auth AAA], B [auth BBB]	133	Rattus norvegicus	Mutation(s): 1 Gene Names: Clec2d11, Clrb, Ocil
UniProt
Find proteins for Q0H8B9 (Rattus norvegicus) Explore Q0H8B9 Go to UniProtKB: Q0H8B9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0H8B9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth AAA] Focus chain B [auth BBB]	Go to GlyGen: Q0H8B9-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain C [auth AAA] SDF format, chain D [auth BBB] MOL2 format, chain C [auth AAA] MOL2 format, chain D [auth BBB] mmCIF format, chain C [auth AAA] mmCIF format, chain D [auth BBB]	C [auth AAA], D [auth BBB]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain C [auth AAA] Focus chain D [auth BBB] Interactions & Density Focus chain C [auth AAA] Focus chain D [auth BBB]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.235 (Depositor), 0.216 (DCC)
R-Value Work: 0.190 (Depositor), 0.200 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.863	α = 90
b = 69.346	β = 96.853
c = 62.473	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-05-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Czech Academy of Sciences	Czech Republic	86652036
European Regional Development Fund	European Union	CZ.02.1.01/0.0/0.0/15_003/0000447

Revision History (Full details and data files)

Version 1.0: 2024-05-01
Type: Initial release
Version 1.1: 2024-11-13
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.