5L2K

Crystal structure of GEM42 TCR-CD1b-GMM complex

PDB DOI: https://doi.org/10.2210/pdb5L2K/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-08-02 Released: 2016-11-16
Deposition Author(s): Gras, S., Shahine, A., Le Nours, J., Rossjohn, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.239
R-Value Work: 0.218
R-Value Observed: 0.219

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 97.84 kDa
Atom Count: 6,497
Modelled Residue Count: 801
Deposited Residue Count: 845
Unique protein chains: 4

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell surface glycoprotein CD1b	A	300	Homo sapiens	Mutation(s): 1 Gene Names: CD1B
UniProt & NIH Common Fund Data Resources
Find proteins for P29016 (Homo sapiens) Explore P29016 Go to UniProtKB: P29016
PHAROS: P29016 GTEx: ENSG00000158485
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29016
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	98	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:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GEM42 TCR alpha chain	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

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GEM42 TCR beta chain	D [auth E]	243	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
70E Query on 70E Download Ideal Coordinates CCD File SDF format, chain U [auth E] MOL2 format, chain U [auth E]	U [auth E]	6-O-[(2R,3R)-3-hydroxy-2-tetradecyldocosanoyl]-alpha-L-idopyranose C₄₂ H₈₂ O₈ YOCZDGRJDQLKHW-GWLFWXKWSA-N		Interactions Focus chain U [auth E] Interactions & Density Focus chain U [auth E]
6UL Query on 6UL Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A]	O [auth A]	TETRACOSYL PALMITATE C₄₀ H₈₀ O₂ KKTAIMZGSAQXRE-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A]	E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A]
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain R [auth D] MOL2 format, chain R [auth D]	R [auth D]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain R [auth D] Interactions & Density Focus chain R [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain Q [auth D] SDF format, chain S [auth E] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E]	H [auth A], I [auth A], J [auth A], Q [auth D], S [auth E]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth D] Focus chain S [auth E] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain Q [auth D] Focus chain S [auth E]
CL Query on CL 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 P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B]	K [auth A], L [auth A], M [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain P [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain T [auth E] MOL2 format, chain N [auth A] MOL2 format, chain T [auth E]	N [auth A], T [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain T [auth E] Interactions & Density Focus chain N [auth A] Focus chain T [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.239
R-Value Work: 0.218
R-Value Observed: 0.219
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.998	α = 90
b = 174.998	β = 90
c = 170.869	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
SCALA	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-11-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-11-16
Type: Initial release
Version 1.1: 2016-12-07
Changes: Other
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 1.3: 2023-10-04
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

5L2K

Crystal structure of GEM42 TCR-CD1b-GMM complex

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Entity Groups

Sequence Annotations

Expand

Entity ID: 4

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)