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

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59665
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAB Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-05-29

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.