7ODU | pdb_00007odu

Natural killer cell receptor NKR-P1B from Rattus norvegicus in complex with its cognate ligand Clr-11

PDB DOI: https://doi.org/10.2210/pdb7ODU/pdb

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

Deposited: 2021-04-30 Released: 2022-06-01
Deposition Author(s): Skalova, T., Blaha, J., Kalouskova, B., Skorepa, O., Vanek, O., Dohnalek, J.
Funding Organization(s): Czech Science Foundation, Ministry of Education, Youth and Sports of the Czech Republic

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.259 (Depositor), 0.230 (DCC)
R-Value Work:
0.208 (Depositor), 0.210 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Natural killer cell receptor NKR-P1B from Rattus norvegicus in complex with its cognate ligand Clr-11

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

To be published.

Macromolecule Content

Total Structure Weight: 49.88 kDa
Atom Count: 3,154
Modeled Residue Count: 372
Deposited Residue Count: 417
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-type lectin domain family 2 member D11	A, B	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0H8B9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B	Go to GlyGen: Q0H8B9-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell lectin-like receptor subfamily B member 1B allele A	C	151	Rattus norvegicus	Mutation(s): 0 Gene Names: Klrb1b, Nkrp1b
UniProt
Find proteins for A4KWA1 (Rattus norvegicus) Explore A4KWA1 Go to UniProtKB: A4KWA1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A4KWA1
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain C	Go to GlyGen: A4KWA1-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth C]	F [auth A], H [auth B], I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.259 (Depositor), 0.230 (DCC)
R-Value Work: 0.208 (Depositor), 0.210 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.593	α = 90
b = 111.593	β = 90
c = 110.107	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-06-01

Deposition Author(s):

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	18-10687S
Ministry of Education, Youth and Sports of the Czech Republic	Czech Republic	CZ.02.1.01/0.0/0.0/16_013/0001776