5GS0

Crystal structure of the complex of TLR3 and bi-specific diabody

PDB DOI: https://doi.org/10.2210/pdb5GS0/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Mus musculus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2016-08-13 Released: 2016-10-12
Deposition Author(s): Kim, J.H., Song, D.H., Youn, S.J., Kim, J.W., Cho, G., Lee, H., Lee, J.O.
Funding Organization(s): Ministry of Science, ICT and Future Planning, Ministry of Health & Welfare

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.27 Å
R-Value Free: 0.248
R-Value Work: 0.192
R-Value Observed: 0.195

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: 262.27 kDa
Atom Count: 18,219
Modelled Residue Count: 2,226
Deposited Residue Count: 2,266
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 3	A, D [auth B]	671	Homo sapiens	Mutation(s): 0 Gene Names: TLR3
UniProt & NIH Common Fund Data Resources
Find proteins for O15455 (Homo sapiens) Explore O15455 Go to UniProtKB: O15455
PHAROS: O15455 GTEx: ENSG00000164342
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O15455
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain (anti-TLR3)	B [auth C], E	107	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain (anti-TLR3)	C [auth D], F	127	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
heavy chain (anti-Lid)	G [auth X], I [auth H]	121	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
light chain (anti-Lid)	H [auth Y], J [auth L]	107	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain WA [auth B] SDF format, chain X [auth A] SDF format, chain Y [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A]	AA [auth A] BA [auth A] FA [auth B] GA [auth B] HA [auth B] AA [auth A], BA [auth A], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], V [auth A], VA [auth B], W [auth A], WA [auth B], X [auth A], Y [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain X [auth A] Focus chain Y [auth A]
MAN Query on MAN Download Ideal Coordinates CCD File SDF format, chain DA [auth A] SDF format, chain EA [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain EA [auth B]	DA [auth A], EA [auth B]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain DA [auth A] Focus chain EA [auth B] Interactions & Density Focus chain DA [auth A] Focus chain EA [auth B]
BMA Query on BMA Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain UA [auth B] SDF format, chain XA [auth B] SDF format, chain Z [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain Z [auth A]	CA [auth A], UA [auth B], XA [auth B], Z [auth A]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain CA [auth A] Focus chain UA [auth B] Focus chain XA [auth B] Focus chain Z [auth A] Interactions & Density Focus chain CA [auth A] Focus chain UA [auth B] Focus chain XA [auth B] Focus chain Z [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.27 Å
R-Value Free: 0.248
R-Value Work: 0.192
R-Value Observed: 0.195
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.519	α = 90
b = 141.329	β = 106.88
c = 150.831	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2016-10-12

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science, ICT and Future Planning	Korea, Republic Of	NRF-2014R1A2A1A10050436
Ministry of Health & Welfare	Korea, Republic Of	HI15C1886

Revision History (Full details and data files)

Version 1.0: 2016-10-12
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-03-20
Changes: Source and taxonomy