6BJ2

TCR589 in complex with HIV(Pol448-456)/HLA-B35

PDB DOI: https://doi.org/10.2210/pdb6BJ2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Human immunodeficiency virus 1
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2017-11-03 Released: 2018-07-25
Deposition Author(s): Jude, K.M., Sibener, L.V., Garcia, K.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.276
R-Value Work: 0.245
R-Value Observed: 0.247

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 96.02 kDa
Atom Count: 6,445
Modelled Residue Count: 824
Deposited Residue Count: 831
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR 589 alpha chain	A [auth D]	206	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6IRV4 (Homo sapiens) Explore Q6IRV4 Go to UniProtKB: Q6IRV4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6IRV4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR 589 beta chain	B [auth E]	241	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for K7N5M4 (Homo sapiens) Explore K7N5M4 Go to UniProtKB: K7N5M4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	K7N5M4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, B-35 alpha chain	C [auth A]	276	Homo sapiens	Mutation(s): 0 Gene Names: HLA-B, HLAB
UniProt & NIH Common Fund Data Resources
Find proteins for P01889 (Homo sapiens) Explore P01889 Go to UniProtKB: P01889
PHAROS: P01889 GTEx: ENSG00000234745
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01889
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D [auth B]	99	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV Pol B35 peptide	E [auth C]	9	Human immunodeficiency virus 1	Mutation(s): 0
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585 Go to UniProtKB: P04585
Entity Groups
UniProt Group	P04585
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
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 H [auth E] MOL2 format, chain H [auth E]	H [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth E] Interactions & Density Focus chain H [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain J [auth A] SDF format, chain I [auth E] MOL2 format, chain G [auth D] MOL2 format, chain J [auth A] MOL2 format, chain I [auth E]	G [auth D], I [auth E], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth D] Focus chain I [auth E] Focus chain J [auth A] Interactions & Density Focus chain G [auth D] Focus chain I [auth E] Focus chain J [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A [auth D]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.276
R-Value Work: 0.245
R-Value Observed: 0.247
Space Group: C 1 2 1
Diffraction Data: https://doi.org/10.15785/SBGRID/518

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.48	α = 90
b = 59.28	β = 110.77
c = 123.57	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-07-25

Deposition Author(s):

Jude, K.M.

Sibener, L.V.

Garcia, K.C.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI103867

Revision History (Full details and data files)

Version 1.0: 2018-07-25
Type: Initial release
Version 1.1: 2018-08-08
Changes: Data collection, Database references
Version 1.2: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 2.0: 2019-12-11
Changes: Author supporting evidence, Polymer sequence
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary