5GY2

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5

PDB DOI: https://doi.org/10.2210/pdb5GY2/pdb

Classification: IMMUNE SYSTEM
Organism(s): Danio rerio, Eptatretus burgeri, Bacillus spizizenii str. W23
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): Yes

Deposited: 2016-09-21 Released: 2017-02-15
Deposition Author(s): Song, W.S., Yoon, S.I.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.236
R-Value Work: 0.195
R-Value Observed: 0.197

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: 143.41 kDa
Atom Count: 10,156
Modelled Residue Count: 1,221
Deposited Residue Count: 1,276
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tlr5b protein,Variable lymphocyte receptor B	A, C [auth B]	455	Danio rerio, Eptatretus burgeri This entity is chimeric	Mutation(s): 6 Gene Names: tlr5b, VLRB
UniProt
Find proteins for Q4G1L2 (Eptatretus burgeri) Explore Q4G1L2 Go to UniProtKB: Q4G1L2
Find proteins for B3DIN1 (Danio rerio) Explore B3DIN1 Go to UniProtKB: B3DIN1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	B3DIN1Q4G1L2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Flagellin	B [auth C], D	183	Bacillus spizizenii str. W23	Mutation(s): 0 Gene Names: hag, BSUW23_17335
UniProt
Find proteins for E0U497 (Bacillus spizizenii (strain ATCC 23059 / NRRL B-14472 / W23)) Explore E0U497 Go to UniProtKB: E0U497
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E0U497
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, F	2		N-Glycosylation	Interactions Focus chain E Focus chain F Interactions & Density Focus chain E 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 G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B]	G [auth A] H [auth A] I [auth A] K [auth B] L [auth B] G [auth A], H [auth A], I [auth A], K [auth B], L [auth B], M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain N [auth B] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B]	J [auth A], N [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain N [auth B] Interactions & Density Focus chain J [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.236
R-Value Work: 0.195
R-Value Observed: 0.197
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.146	α = 90
b = 54.281	β = 98.62
c = 165.98	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-02-15

Deposition Author(s):

Song, W.S.

Yoon, S.I.

Revision History (Full details and data files)

Version 1.0: 2017-02-15
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

5GY2

Crystal structure of a complex between Bacillus subtilis flagellin and zebrafish Toll-like receptor 5

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2