9C9D | pdb_00009c9d

Protein receptor

PDB DOI: https://doi.org/10.2210/pdb9C9D/pdb

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

Deposited: 2024-06-13 Released: 2025-08-27
Deposition Author(s): MacLachlan, B., Awad, W., Vivian, J., Rossjohn, J.
Funding Organization(s): Australian Research Council (ARC), National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.215 (Depositor), 0.213 (DCC)
R-Value Work:
0.190 (Depositor), 0.188 (DCC)
R-Value Observed:
0.191 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Protein complex

MacLachlan, B.

To be published.

Macromolecule Content

Total Structure Weight: 119.03 kDa
Atom Count: 8,189
Modeled Residue Count: 1,000
Deposited Residue Count: 1,032
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Major histocompatibility complex class I-related gene protein	A	271	Homo sapiens	Mutation(s): 0 Gene Names: MR1
UniProt & NIH Common Fund Data Resources
Find proteins for Q95460 (Homo sapiens) Explore Q95460 Go to UniProtKB: Q95460
PHAROS: Q95460 GTEx: ENSG00000153029
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q95460
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 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
PHAROS: P61769 GTEx: ENSG00000166710
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
T Cell Receptor Alpha Variable 1-2	C [auth D]	204	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta variable 6-1	D [auth E]	246	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukocyte immunoglobulin-like receptor subfamily B member 2	E [auth F]	211	Homo sapiens	Mutation(s): 0 Gene Names: LILRB2, ILT4, LIR2, MIR10
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N423 (Homo sapiens) Explore Q8N423 Go to UniProtKB: Q8N423
PHAROS: Q8N423 GTEx: ENSG00000131042
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N423
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
30W (Subject of Investigation/LOI) Query on 30W Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	N-(6-formyl-4-oxo-3,4-dihydropteridin-2-yl)acetamide C₉ H₇ N₅ O₃ DDBCPKAHJKOGKK-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain S [auth F] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth F] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain O [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain S [auth F]	H [auth A] I [auth A] M [auth D] N [auth D] O [auth D] H [auth A], I [auth A], M [auth D], N [auth D], O [auth D], Q [auth E], R [auth E], S [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth B] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth B] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth B]	G [auth A], J [auth A], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain P [auth E] MOL2 format, chain P [auth E] mmCIF format, chain P [auth E]	P [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain P [auth E] Interactions & Density Focus chain P [auth E]