2PM5 | pdb_00002pm5

Human alpha-defensin 1 derivative (HNP1)

PDB DOI: https://doi.org/10.2210/pdb2PM5/pdb

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

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: 2.40 Å
R-Value Free:
0.218 (Depositor)
R-Value Work:
0.200 (Depositor), 0.190 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Human alpha-defensin 1 derivative (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: 6.83 kDa
Atom Count: 527
Modeled Residue Count: 60
Deposited Residue Count: 60
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, B	30	Homo sapiens	Mutation(s): 3 Gene Names: DEFA1, DEF1, DEFA2
UniProt & NIH Common Fund Data Resources
Find proteins for P59666 (Homo sapiens) Explore P59666 Go to UniProtKB: P59666
PHAROS: P59666 GTEx: ENSG00000239839
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59666
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ORN Query on ORN	A, B	L-PEPTIDE LINKING	C₅ H₁₂ N₂ O₂		ALA

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.218 (Depositor)
R-Value Work: 0.200 (Depositor), 0.190 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 4₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.409	α = 90
b = 57.409	β = 90
c = 96.967	γ = 90

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: Advisory, 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 U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.