2PM1

Derivative of human alpha-defensin 1 (HNP1)

• PDB DOI: https://doi.org/10.2210/pdb2PM1/pdb

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPM


• Deposited: 2007-04-20 Released: 2007-05-29 
• Deposition Author(s): Lubkowski, J., Pazgier, M., Lu, W.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.151 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

Derivative of human alpha-defensin 1 (HNP1)

Lubkowski, J., Lu, W., Zou, G., de Leeuw, E., Li, C., Pazgier, M., Zeng, P., Lu, W.Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 3.28 kDa 
• Atom Count: 279 
• Modelled Residue Count: 30 
• Deposited Residue Count: 30 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)	A	30	Homo sapiens	Mutation(s): 3  Gene Names: DEFA1, DEF1, DEFA2 Membrane Entity: Yes
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
DAB	A	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.201 
• R-Value Work: 0.151 
• R-Value Observed: 0.154 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.811	α = 90
b = 38.811	β = 90
c = 31.56	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Lubkowski, J., Pazgier, M., Lu, W.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-30
  Changes: Data collection, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary