3T1D

The mutant structure of human Siderocalin W79A, R81A, Y106F bound to Enterobactin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.4 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): 3 
Gene Names: LCN2 (HNL, NGAL)
Find proteins for P80188 (Homo sapiens)
Go to Gene View: LCN2
Go to UniProtKB:  P80188
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DBS
Query on DBS

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Download CCD File 
B, C
2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID
2,3,-DIHYDROXYBENZOYLSERINE
C10 H11 N O6
VDTYHTVHFIIEIL-LURJTMIESA-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
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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

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Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
TD1
Query on TD1

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Download CCD File 
A
O-[(2S)-2-amino-3-hydroxypropanoyl]-N-(2,3-dihydroxybenzoyl)-L-serine
C13 H16 N2 O8
NNOZTAPXJBUXBD-YUMQZZPRSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 114.749α = 90.00
b = 114.749β = 90.00
c = 119.065γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PDB_EXTRACTdata extraction
HKL-2000data scaling
REFMACphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-08-17
    Type: Initial release
  • Version 1.1: 2013-10-09
    Type: Database references
  • Version 1.2: 2017-11-08
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Database references
  • Version 1.4: 2019-02-27
    Type: Data collection, Database references