1DFV

CRYSTAL STRUCTURE OF HUMAN NEUTROPHIL GELATINASE ASSOCIATED LIPOCALIN MONOMER

• PDB DOI: https://doi.org/10.2210/pdb1DFV/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: unidentified baculovirus
• Mutation(s): No 


• Deposited: 1999-11-22 Released: 2000-03-06 
• Deposition Author(s): Goetz, D.H., Willie, S.T., Armen, R.S., Bratt, T., Borregaard, N., Strong, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.293 
• R-Value Work: 0.281 
• R-Value Observed: 0.281 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.96 kDa 
• Atom Count: 3,011 
• Modelled Residue Count: 347 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN NEUTROPHIL GELATINASE	A, B	177	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P80188 (Homo sapiens) Explore P80188  Go to UniProtKB:  P80188
PHAROS:  P80188 GTEx:  ENSG00000148346

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4	D [auth A], E [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.293 
• R-Value Work: 0.281 
• R-Value Observed: 0.281 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.021	α = 90
b = 115.021	β = 90
c = 117.638	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-03-06 
Deposition Author(s): Goetz, D.H., Willie, S.T., Armen, R.S., Bratt, T., Borregaard, N., Strong, R.K.

Revision History  

• Version 1.0: 2000-03-06
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary