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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.233 (Depositor), 0.217 (DCC)
R-Value Work:
0.191 (Depositor), 0.179 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of NaASP2 with Zn2+

Asojo, O.A.

To be published.

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

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	J9ULM6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.233 (Depositor), 0.217 (DCC)
R-Value Work: 0.191 (Depositor), 0.179 (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

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Entry History

Deposition Data

Released Date: 2014-06-04

Deposition Author(s):

Revision History (Full details and data files)

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

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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.