3HJD | pdb_00003hjd

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free:
0.203 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.186 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3HJD

This is version 1.5 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59665
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
IML Query on 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), 0.220 (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

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Entry History

Deposition Data

Released Date: 2009-10-13

Deposition Author(s):

Revision History (Full details and data files)

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

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.