5G6U

Crystal structure of langerin carbohydrate recognition domain with GlcNS6S

PDB DOI: https://doi.org/10.2210/pdb5G6U/pdb

Classification: CARBOHYDRATE BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-07-21 Released: 2018-02-21
Deposition Author(s): Porkolab, V., Chabrol, E., Varga, N., Ordanini, S., Sutkeviciute, I., Thepaut, M., Bernardi, A., Fieschi, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.180
R-Value Work: 0.152
R-Value Observed: 0.153

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 121.33 kDa
Atom Count: 4,932
Modelled Residue Count: 514
Deposited Residue Count: 1,044
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LANGERIN	A, B, C, D	261	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJ71 (Homo sapiens) Explore Q9UJ71 Go to UniProtKB: Q9UJ71
PHAROS: Q9UJ71 GTEx: ENSG00000116031
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UJ71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SGN Query on SGN Download Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain U [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain U [auth C]	CA [auth D], F [auth A], L [auth B], U [auth C]	2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose C₆ H₁₃ N O₁₁ S₂ DQTRACMFIGDHSN-UKFBFLRUSA-N		Interactions Focus chain CA [auth D] Focus chain F [auth A] Focus chain L [auth B] Focus chain U [auth C] Interactions & Density Focus chain CA [auth D] Focus chain F [auth A] Focus chain L [auth B] Focus chain U [auth C]
TRP Query on TRP Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B]	BA [auth D], E [auth A], K [auth B]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain K [auth B]
EU Query on EU Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	G [auth A] J [auth A] M [auth B] T [auth B] W [auth C] G [auth A], J [auth A], M [auth B], T [auth B], W [auth C], X [auth C]	EUROPIUM ION Eu MGVUQZZTJGLWJV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain T [auth B] Focus chain W [auth C] Focus chain X [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain DA [auth D] SDF format, chain H [auth A] SDF format, chain V [auth C] SDF format, chain N [auth B] MOL2 format, chain DA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B]	DA [auth D], H [auth A], N [auth B], V [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain DA [auth D] Focus chain H [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain DA [auth D] Focus chain H [auth A] Focus chain N [auth B] Focus chain V [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain EA [auth D] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth C] SDF format, chain FA [auth D] SDF format, chain GA [auth D] MOL2 format, chain AA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D]	AA [auth C] EA [auth D] FA [auth D] GA [auth D] I [auth A] AA [auth C], EA [auth D], FA [auth D], GA [auth D], I [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], Y [auth C], Z [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain I [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain Y [auth C] Focus chain Z [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
SGN	Binding MOAD: 5G6U	IC50: 220 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.180
R-Value Work: 0.152
R-Value Observed: 0.153
Space Group: P 4₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.483	α = 90
b = 79.483	β = 90
c = 90.71	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-02-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2018-02-21
Type: Initial release
Version 1.1: 2018-02-28
Changes: Derived calculations
Version 1.2: 2018-03-28
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2024-01-10
Changes: Data collection, Database references, Refinement description