3TF6

Crystal structure of Neutrophil gelatinase-associated lipocalin (C87S mutant) in complex with Europium and the siderophore analog tren(cam)(1,2-hopo)2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Parsing the functional specificity of Siderocalin / Lipocalin 2 / NGAL for siderophores and related small-molecule ligands

Clifton, M.C.Rupert, P.B.Hoette, T.M.Raymond, K.N.Abergel, R.J.Strong, R.K.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Neutrophil gelatinase-associated lipocalinA, B, C179Homo sapiensMutation(s): 1 
Gene Names: LCN2HNLNGAL
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens)
Explore P80188 
Go to UniProtKB:  P80188
PHAROS:  P80188
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DBH (Subject of Investigation/LOI)
Query on DBH

Download Ideal Coordinates CCD File 
F [auth A], J [auth B], O [auth C]2,3-DIHYDROXY-BENZOIC ACID
C7 H6 O4
GLDQAMYCGOIJDV-UHFFFAOYSA-N
 Ligand Interaction
EU
Query on EU

Download Ideal Coordinates CCD File 
E [auth A], I [auth B], N [auth C]EUROPIUM ION
Eu
MGVUQZZTJGLWJV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A], K [auth B], P [auth C]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A], M [auth C], Q [auth C], R [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A], L [auth B], S [auth C], T [auth C], U [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
DBH PDBBind:  3TF6 Kd: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.09α = 90
b = 114.09β = 90
c = 118.19γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-09-07
    Type: Initial release
  • Version 1.1: 2013-10-09
    Changes: Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Database references