3K3L

Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with apo Enterobactin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.260 

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
178Homo sapiensMutation(s): 1 
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
DBS
Query on DBS

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A
2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID
2,3,-DIHYDROXYBENZOYLSERINE
C10 H11 N O6
VDTYHTVHFIIEIL-LURJTMIESA-N
 Ligand Interaction
NA
Query on NA

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A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
DBH
Query on DBH

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

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C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MCK
Query on MCK

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Download CCD File 
C
N-[(2,3-dihydroxyphenyl)carbonyl]-O-[(2S)-2-{[(2,3-dihydroxyphenyl)carbonyl]amino}-3-(L-seryloxy)propanoyl]-L-serine
C23 H25 N3 O13
AVZOYWMPRGKOPV-IHRRRGAJSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.260 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.200α = 90.00
b = 114.200β = 90.00
c = 119.300γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
REFMACphasing
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-10-02 
  • Released Date: 2010-08-18 
  • Deposition Author(s): Clifton, M.C.

Revision History 

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2019-02-27
    Type: Data collection, Database references