1L6M

Neutrophil Gelatinase-associated Lipocalin is a Novel Bacteriostatic Agent that Interferes with Siderophore-mediated Iron Acquisition

Structural Biology Knowledgebase: 1L6M SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.232

Literature

Macromolecules
Sequence Display for 1L6M

Classification: TRANSPORT PROTEIN

Total Structure Weight: 64052.14

Macromolecule Entities
Molecule Chains Length Organism Details
Neutrophil gelatinase-associated lipocalin A, B, C 180 Homo sapiens Mutation: C87S
Gene Name(s): LCN2 Gene View HNL NGAL
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DBS
Query on DBS

A, B, C 2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY- PROPIONIC ACID
2,3,-DIHYDROXYBENZOYLSERINE (Synonym)
C10 H11 N O6
VDTYHTVHFIIEIL-LURJTMIESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DBH
Query on DBH

A, B, C 2,3-DIHYDROXY-BENZOIC ACID
C7 H6 O4
GLDQAMYCGOIJDV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, C SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FE
Query on FE

A, B, C FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DBH N/A in BindingDB
Kd: 7.9 nM  BindingMOAD
Kd: 7.9 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.232
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 115.08 α = 90.00
b = 115.08 β = 90.00
c = 115.22 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-03-11
  • Released Date: 2003-03-11
  • Deposition author(s): Goetz, D.H., Borregaard, N., Bluhm, M.E., Raymond, K.N., Strong, R.K.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4