3HJD

X-ray structure of monomeric variant of HNP1

• PDB DOI: https://doi.org/10.2210/pdb3HJD/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2009-05-21 Released: 2009-10-13 
• Deposition Author(s): Lubkowski, J., Pazgier, M., Lu, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.203 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

What Dictates the Multifaced Functions of the Human alpha-Defensin HNP?

Wei, G., de Leeuw, E., Pazgier, M., Rajabi, M., Li, J., Zou, G., Ericksen, B., Wu, Z., Yuan, W., Szmacinski, H., Lu, W.-Y., Lubkowski, J., Lehrer, R.L., Lu, W.

To be published.

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 and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 6.93 kDa 
• Atom Count: 553 
• Modelled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human neutrophil peptide 1	A, B	30	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P59665 (Homo sapiens) Explore P59665  Go to UniProtKB:  P59665
PHAROS:  P59665 GTEx:  ENSG00000240247 ENSG00000206047

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IML	A, B	L-PEPTIDE LINKING	C7 H15 N O2		ILE

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.203 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.85	α = 90
b = 69.85	β = 90
c = 46.33	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Lubkowski, J., Pazgier, M., Lu, W.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-09-07
  Changes: Advisory
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Derived calculations, Structure summary