3I0A

Crystal structure of Siderocalin (NGAL, Lipocalin 2) K134A mutant complexed with Ferric Enterobactin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 

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, C198Homo sapiensMutation(s): 2 
Gene Names: HNLLCN2NGAL
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 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MCJ (Subject of Investigation/LOI)
Query on MCJ

Download Ideal Coordinates CCD File 
N [auth C]N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-({N-[(2,3-dihydroxyphenyl)carbonyl]-L-seryl}oxy)propanoyl]-D-serine
C30 H29 N3 O16
NTWRWGRCGVKQNS-KSZLIROESA-N
 Ligand Interaction
2DS (Subject of Investigation/LOI)
Query on 2DS

Download Ideal Coordinates CCD File 
G [auth A]N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2R)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-hydroxypropanoyl]-L-serine
C20 H20 N2 O11
KLXJDVFEFZPIMN-NEPJUHHUSA-N
 Ligand Interaction
3ET (Subject of Investigation/LOI)
Query on 3ET

Download Ideal Coordinates CCD File 
F [auth A]O-[(2R)-2-amino-3-(D-seryloxy)propanoyl]-N-[(2,3-dihydroxyphenyl)carbonyl]-L-serine
C16 H21 N3 O10
ZXSIADNPWRCRTI-BBBLOLIVSA-N
 Ligand Interaction
DBH (Subject of Investigation/LOI)
Query on DBH

Download Ideal Coordinates CCD File 
I [auth B]2,3-DIHYDROXY-BENZOIC ACID
C7 H6 O4
GLDQAMYCGOIJDV-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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

Download Ideal Coordinates CCD File 
L [auth C], M [auth C]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download Ideal Coordinates CCD File 
E [auth A], H [auth B], K [auth C]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.257 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.253α = 90
b = 114.253β = 90
c = 117.95γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

  • Deposited Date: 2009-06-24 
  • Released Date: 2010-06-09 
  • Deposition Author(s): Clifton, M.C.

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-02-27
    Changes: Data collection, Database references