6R2L

NYBR1-A2-SLSKILDTV

PDB DOI: https://doi.org/10.2210/pdb6R2L/pdb

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

Deposited: 2019-03-18 Released: 2020-02-26
Deposition Author(s): Rizkallah, P.J., Cole, D.K., Sami, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.265
R-Value Work: 0.214
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

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

Literature

NYBR1-A2-SLSKILDTV

Rizkallah, P.J., Cole, D.K., Sami, M.

To be published.

Macromolecule Content

Total Structure Weight: 95.89 kDa
Atom Count: 7,152
Modelled Residue Count: 826
Deposited Residue Count: 826
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A-2 alpha chain	A	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Explore P04439 Go to UniProtKB: P04439
PHAROS: P04439 GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04439
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

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-LEU-SER-LYS-ILE-LEU-ASP-THR-VAL	C	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXX3 (Homo sapiens) Explore Q9BXX3 Go to UniProtKB: Q9BXX3
PHAROS: Q9BXX3 GTEx: ENSG00000148513
Entity Groups
UniProt Group	Q9BXX3
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 alpha variable 22,Human nkt tcr alpha chain	D	194	Homo sapiens	Mutation(s): 0 Gene Names: TRAV22, B2M, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J277 (Homo sapiens) Explore A0A0B4J277 Go to UniProtKB: A0A0B4J277
PHAROS: A0A0B4J277 GTEx: ENSG00000211802
Find proteins for K7N5M3 (Homo sapiens) Explore K7N5M3 Go to UniProtKB: K7N5M3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	K7N5M3A0A0B4J277
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta variable 11-2,Human nkt tcr beta chain	E	247	Homo sapiens	Mutation(s): 0 Gene Names: TRBV11-2, TCRBV21S3A2N2T, B2M, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for A0A584 (Homo sapiens) Explore A0A584 Go to UniProtKB: A0A584
PHAROS: A0A584
Find proteins for K7N5M4 (Homo sapiens) Explore K7N5M4 Go to UniProtKB: K7N5M4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	K7N5M4A0A584
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain O [auth B] MOL2 format, chain O [auth B] mmCIF format, chain O [auth B]	O [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain O [auth B]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E]	K [auth A] L [auth A] M [auth A] N [auth A] P [auth B] K [auth A], L [auth A], M [auth A], N [auth A], P [auth B], Q [auth B], R [auth D], T [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth D] Focus chain T [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth E] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth E] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth E]	I [auth A], J [auth A], S [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A]