7YTQ | pdb_00007ytq

Human langerin carbohydrate recognition domain in complex with an alpha-mannoside ligand

PDB DOI: https://doi.org/10.2210/pdb7YTQ/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens, unidentified
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-08-16 Released: 2022-09-07
Deposition Author(s): Wangkanont, K.
Funding Organization(s): Chulalongkorn University

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.213 (Depositor), 0.214 (DCC)
R-Value Work:
0.182 (Depositor), 0.183 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Human langerin carbohydrate recognition domain in complex with an alpha-mannoside ligand

Wangkanont, K.

To be published.

Macromolecule Content

Total Structure Weight: 74.16 kDa
Atom Count: 5,160
Modeled Residue Count: 526
Deposited Residue Count: 626
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CD207 molecule	A, B, C, D	156	Homo sapiens	Mutation(s): 0 Gene Names: CD207
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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UJ71
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-TRP	E	2	unidentified	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JMI (Subject of Investigation/LOI) Query on JMI Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain R [auth D] SDF format, chain N [auth C] SDF format, chain J [auth B] MOL2 format, chain G [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] MOL2 format, chain J [auth B] mmCIF format, chain G [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C] mmCIF format, chain J [auth B]	G [auth A], J [auth B], N [auth C], R [auth D]	~{N}-[2-[4-[(2~{R},3~{S},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxyphenyl]ethyl]ethanamide C₁₆ H₂₃ N O₇ JVYCDFJBIOIPDL-OWYFMNJBSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D]
TRP Query on TRP Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain P [auth D] MOL2 format, chain L [auth C] MOL2 format, chain P [auth D] mmCIF format, chain L [auth C] mmCIF format, chain P [auth D]	L [auth C], P [auth D]	TRYPTOPHAN C₁₁ H₁₂ N₂ O₂ QIVBCDIJIAJPQS-VIFPVBQESA-N		Interactions Focus chain L [auth C] Focus chain P [auth D] Interactions & Density Focus chain L [auth C] Focus chain P [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain Q [auth D] SDF format, chain M [auth C] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain M [auth C] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain M [auth C] mmCIF format, chain I [auth B]	F [auth A], I [auth B], M [auth C], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain M [auth C] Focus chain Q [auth D]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain K [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain K [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C] mmCIF format, chain S [auth D] mmCIF format, chain K [auth B]	H [auth A], K [auth B], O [auth C], S [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D]