3FXI

Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex

PDB DOI: https://doi.org/10.2210/pdb3FXI/pdb

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

Deposited: 2009-01-21 Released: 2009-03-03
Deposition Author(s): Park, B.S., Song, D.H., Kim, H.M., Lee, J.-O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.281
R-Value Work: 0.241

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: 180.25 kDa
Atom Count: 12,500
Modelled Residue Count: 1,482
Deposited Residue Count: 1,494
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toll-like receptor 4	A, B	605	Homo sapiens	Mutation(s): 0 Gene Names: TLR4
UniProt & NIH Common Fund Data Resources
Find proteins for O00206 (Homo sapiens) Explore O00206 Go to UniProtKB: O00206
PHAROS: O00206 GTEx: ENSG00000136869
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00206
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lymphocyte antigen 96	C, D	142	Homo sapiens	Mutation(s): 0 Gene Names: ESOP1, LY96, MD-2, MD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6Y9 (Homo sapiens) Explore Q9Y6Y9 Go to UniProtKB: Q9Y6Y9
PHAROS: Q9Y6Y9 GTEx: ENSG00000154589
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y6Y9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-alpha-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose	E	7		N/A	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G75876QI GlyCosmos: G75876QI

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

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
L-glycero-alpha-D-manno-heptopyranose-(1-7)-L-glycero-alpha-D-manno-heptopyranose-(1-3)-L-glycero-alpha-D-manno-heptopyranose-(1-5)-[3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-alpha-D-glucopyranose	H	7		N/A	Interactions Focus chain H Interactions & Density Focus chain H
Glycosylation Resources
GlyTouCan: G02042LC GlyCosmos: G02042LC

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FTT Query on FTT Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Y [auth B] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B]	AA [auth B] BA [auth B] K [auth A] L [auth A] M [auth A] AA [auth B], BA [auth B], K [auth A], L [auth A], M [auth A], N [auth A], Y [auth B], Z [auth B]	3-HYDROXY-TETRADECANOIC ACID C₁₄ H₂₈ O₃ ATRNZOYKSNPPBF-CYBMUJFWSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
MYR Query on MYR Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain P [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain P [auth A]	DA [auth B], P [auth A]	MYRISTIC ACID C₁₄ H₂₈ O₂ TUNFSRHWOTWDNC-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain P [auth A] Interactions & Density Focus chain DA [auth B] Focus chain P [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain IA [auth B] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain MA [auth C] SDF format, chain NA [auth D] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A]	IA [auth B] JA [auth B] KA [auth B] MA [auth C] NA [auth D] IA [auth B], JA [auth B], KA [auth B], MA [auth C], NA [auth D], U [auth A], V [auth A], W [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain IA [auth B] Focus chain JA [auth B] Focus chain KA [auth B] Focus chain MA [auth C] Focus chain NA [auth D] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A]
DAO Query on DAO Download Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain O [auth A] MOL2 format, chain CA [auth B] MOL2 format, chain O [auth A]	CA [auth B], O [auth A]	LAURIC ACID C₁₂ H₂₄ O₂ POULHZVOKOAJMA-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain O [auth A] Interactions & Density Focus chain CA [auth B] Focus chain O [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain HA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A]	EA [auth B] FA [auth B] GA [auth B] HA [auth B] Q [auth A] EA [auth B], FA [auth B], GA [auth B], HA [auth B], Q [auth A], R [auth A], S [auth A], T [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain LA [auth B] SDF format, chain X [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain X [auth A]	LA [auth B], X [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain LA [auth B] Focus chain X [auth A] Interactions & Density Focus chain LA [auth B] Focus chain X [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.281
R-Value Work: 0.241
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.16	α = 90
b = 103.5	β = 90
c = 251.81	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-03-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2012-06-20
Changes: Non-polymer description
Version 1.3: 2020-07-01
Changes: Advisory, Data collection, Derived calculations
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary

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Deposit Data

Help and Resources

3FXI

Crystal structure of the human TLR4-human MD-2-E.coli LPS Ra complex

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)