4LY5 | pdb_00004ly5

Crystal structure of NaASP2 with Zn2+

• PDB DOI: https://doi.org/10.2210/pdb4LY5/pdb

• Classification: ANTIBIOTIC
• Organism(s): Necator americanus
• Mutation(s): No 


• Deposited: 2013-07-30 Released: 2014-06-04 
• Deposition Author(s): Asojo, O.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of NaASP2 with Zn2+

Asojo, O.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.28 kDa 
• Atom Count: 1,531 
• Modeled Residue Count: 190 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ancylostoma secreted protein 2	A	196	Necator americanus	Mutation(s): 0  Gene Names: ASP2
UniProt
Find proteins for J9ULM6 (Necator americanus) Explore J9ULM6  Go to UniProtKB:  J9ULM6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.233 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.1	α = 90
b = 51.86	β = 113.88
c = 43.58	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Asojo, O.A.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary