3HJ2 | pdb_00003hj2

Crystal structure of covalent dimer of HNP1

• PDB DOI: https://doi.org/10.2210/pdb3HJ2/pdb

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


• Deposited: 2009-05-20 Released: 2009-10-20 
• Deposition Author(s): Lubkowski, J., Pazgier, M., Lu, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.236 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.267 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

What Dictates the Multifaced Functions of the Human alpha-Defensin HNP1?

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

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

Macromolecule Content 

• Total Structure Weight: 7.34 kDa 
• Atom Count: 538 
• Modeled Residue Count: 66 
• Deposited Residue Count: 66 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN NEUTROPHIL PEPTIDE 1	A, B	33	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.236 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.267 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.07	α = 90
b = 49.37	β = 90
c = 24.99	γ = 90

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: 2009-10-20 
Deposition Author(s): Lubkowski, J., Pazgier, M., Lu, W.

Revision History  

• Version 1.0: 2009-10-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary