5ZSI

Crystal structure of monkey TLR7 in complex with CL097

PDB DOI: https://doi.org/10.2210/pdb5ZSI/pdb

Classification: IMMUNE SYSTEM
Organism(s): Macaca mulatta
Expression System: Drosophila melanogaster
Mutation(s): Yes

Deposited: 2018-04-28 Released: 2019-01-30
Deposition Author(s): Zhang, Z., Ohto, U., Shimizu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.259
R-Value Work: 0.199
R-Value Observed: 0.202

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: 193.31 kDa
Atom Count: 12,927
Modelled Residue Count: 1,544
Deposited Residue Count: 1,646
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 7	A [auth B], B [auth A]	823	Macaca mulatta	Mutation(s): 4 Gene Names: TLR7
UniProt
Find proteins for B3Y653 (Macaca mulatta) Explore B3Y653 Go to UniProtKB: B3Y653
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3Y653
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C09 (Subject of Investigation/LOI) Query on C09 Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain R [auth A] MOL2 format, chain J [auth B] MOL2 format, chain R [auth A]	J [auth B], R [auth A]	2-(ethoxymethyl)-1H-imidazo[4,5-c]quinolin-4-amine C₁₃ H₁₄ N₄ O DEVCLHVFELRPIU-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain R [auth A] Interactions & Density Focus chain J [auth B] Focus chain R [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain N [auth A] SDF format, chain D [auth B] SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain M [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] MOL2 format, chain G [auth B] MOL2 format, chain N [auth A] MOL2 format, chain D [auth B] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain M [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A]	D [auth B] E [auth B] F [auth B] G [auth B] H [auth B] D [auth B], E [auth B], F [auth B], G [auth B], H [auth B], I [auth B], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Interactions & Density Focus chain D [auth B] Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain T [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain S [auth A] SDF format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A]	K [auth B], L [auth B], S [auth A], T [auth A], U [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain K [auth B] Focus chain L [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Interactions & Density Focus chain K [auth B] Focus chain L [auth B] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.259
R-Value Work: 0.199
R-Value Observed: 0.202
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.366	α = 90
b = 139.951	β = 90
c = 149.468	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Zhang, Z.

Ohto, U.

Shimizu, T.

Revision History (Full details and data files)

Version 1.0: 2019-01-30
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-03-13
Changes: Data collection, Database references, Structure summary