3I0A

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.255 

wwPDB Validation 3D Report Full Report


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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutrophil gelatinase-associated lipocalin
A, B, C
198Homo sapiensMutation(s): 2 
Gene Names: LCN2 (HNL, NGAL)
Find proteins for P80188 (Homo sapiens)
Go to Gene View: LCN2
Go to UniProtKB:  P80188
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MCJ
Query on MCJ

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Download CCD File 
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
Query on 2DS

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Download CCD File 
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
SO4
Query on SO4

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Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
3ET
Query on 3ET

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Download CCD File 
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
Query on DBH

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Download CCD File 
B
2,3-DIHYDROXY-BENZOIC ACID
C7 H6 O4
GLDQAMYCGOIJDV-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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Download CCD File 
A, B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.255 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.253α = 90.00
b = 114.253β = 90.00
c = 117.950γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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