9FQB | pdb_00009fqb

crystal structure of ClY21-HNP1

• PDB DOI: https://doi.org/10.2210/pdb9FQB/pdb

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


• Deposited: 2024-06-14 Released: 2025-06-25 
• Deposition Author(s): Becker, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free: 
  0.122 (Depositor), 0.121 (DCC) 
• R-Value Work: 
  0.111 (Depositor), 0.111 (DCC) 
• R-Value Observed: 
  0.112 (Depositor) 

Starting Model: experimental

Literature

crystal structure of ClY21-HNP1

Becker, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 7.21 kDa 
• Atom Count: 609 
• Modeled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutrophil defensin 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth A], E [auth B], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
3CT	A, B	L-PEPTIDE LINKING	C9 H10 Cl N O3		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.09 Å
• R-Value Free:  0.122 (Depositor), 0.121 (DCC) 
• R-Value Work:  0.111 (Depositor), 0.111 (DCC) 
• R-Value Observed: 0.112 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.075	α = 90
b = 46.075	β = 90
c = 51.282	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-25 
Deposition Author(s): Becker, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-06-25
  Type: Initial release