9D97 | pdb_00009d97

KIR3DL - HLA complex

PDB DOI: https://doi.org/10.2210/pdb9D97/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli, synthetic construct, Homo sapiens
Mutation(s): No

Deposited: 2024-08-21 Released: 2025-09-03
Deposition Author(s): Zhu, S., Vivian, J., Petersen, J., Rossjohn, J.
Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.195 (Depositor), 0.196 (DCC)
R-Value Work:
0.164 (Depositor), 0.165 (DCC)
R-Value Observed:
0.165 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Literature

KIR3D recognition of a self-epitope

Zhu, S., Petersen, J., Rossjohn, J.

To be published.

Macromolecule Content

Total Structure Weight: 78.99 kDa
Atom Count: 5,961
Modeled Residue Count: 674
Deposited Residue Count: 686
Unique protein chains: 4

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B, HLA-DRB1
UniProt
Find proteins for E5FQ58 (Homo sapiens) Explore E5FQ58 Go to UniProtKB: E5FQ58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	E5FQ58
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	Homo sapiens	Mutation(s): 0 Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769 Go to UniProtKB: P61769
GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclin-A2	C	9	Homo sapiens	Mutation(s): 0 Gene Names: CCNA2, CCN1, CCNA
UniProt & NIH Common Fund Data Resources
Find proteins for P20248 (Homo sapiens) Explore P20248 Go to UniProtKB: P20248
GTEx: ENSG00000145386
Entity Groups
UniProt Group	P20248
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Killer cell immunoglobulin-like receptor 3DL1	D [auth G]	301	Homo sapiens	Mutation(s): 0 Gene Names: KIR3DL1, CD158E, NKAT3, NKB1
UniProt & NIH Common Fund Data Resources
Find proteins for P43629 (Homo sapiens) Explore P43629 Go to UniProtKB: P43629
GTEx: ENSG00000167633
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43629
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain D [auth G]	Go to GlyGen: P43629-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth G] SDF format, chain G SDF format, chain F [auth G] MOL2 format, chain E [auth G] MOL2 format, chain G MOL2 format, chain F [auth G] mmCIF format, chain E [auth G] mmCIF format, chain G mmCIF format, chain F [auth G]	E [auth G], F [auth G], G	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth G] Focus chain F [auth G] Focus chain G Interactions & Density Focus chain E [auth G] Focus chain F [auth G] Focus chain G

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.195 (Depositor), 0.196 (DCC)
R-Value Work: 0.164 (Depositor), 0.165 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.963	α = 94.96
b = 60.047	β = 95.5
c = 63.337	γ = 106.23

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	--

Revision History (Full details and data files)

Version 1.0: 2025-09-03
Type: Initial release
Version 1.1: 2025-11-12
Changes: Data collection
Version 2.0: 2026-07-29
Changes: Atomic model, Data collection, Database references, Structure summary