3FXI

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

Structural Biology Knowledgebase: 3FXI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.241

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3FXI

Classification: IMMUNE SYSTEM

Total Structure Weight: 180252.63

Macromolecule Entities
Molecule Chains Length Organism Details
Toll-like receptor 4 A, B 605 Homo sapiens Fragment: extracellular domain, residues 27-631
Gene Name(s): TLR4 Gene View
Lymphocyte antigen 96 C, D 142 Homo sapiens Gene Name(s): LY96 Gene View ESOP1 MD2

Small Molecules
Ligands 10 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FTT
Query on FTT

A, B 3-HYDROXY-TETRADECANOIC ACID
3-HYDROXY-MYRISTIC ACID (Synonym)
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
KDO
Query on KDO

A, B 3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MYR
Query on MYR

A, B MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B, C, D N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GMH
Query on GMH

A, B L-GLYCERO-D-MANNO-HEPTOPYRANOSE
C7 H14 O7
BGWQRWREUZVRGI-QQABCQGCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DAO
Query on DAO

A, B LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PA1
Query on PA1

A, B 2-amino-2-deoxy-alpha-D-glucopyranose
C6 H13 N O5
MSWZFWKMSRAUBD-UKFBFLRUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GCS
Query on GCS

B D-GLUCOSAMINE
2-AMINO-2-DEOXY-D-GLUCOSE (Synonym)
C6 H13 N O5
MSWZFWKMSRAUBD-QZABAPFNSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.241
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 91.16 α = 90.00
b = 103.50 β = 90.00
c = 251.81 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

  • 2012-06-20
    Type: Non-polymer description | Details: update PA1
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update