5F1C

Crystal structure of an invertebrate P2X receptor from the Gulf Coast tick in the presence of ATP and Zn2+ ion at 2.9 Angstroms

PDB DOI: https://doi.org/10.2210/pdb5F1C/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Amblyomma maculatum
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTMMemProtMDmpstruc

Deposited: 2015-11-30 Released: 2016-03-16
Deposition Author(s): Kasuya, G., Hattori, M., Ishitani, R., Nureki, O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.289
R-Value Work: 0.255
R-Value Observed: 0.256

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 124.03 kDa
Atom Count: 8,095
Modelled Residue Count: 1,042
Deposited Residue Count: 1,074
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B, C	358	Amblyomma maculatum	Mutation(s): 2 Membrane Entity: Yes
UniProt
Find proteins for G3MM57 (Amblyomma maculatum) Explore G3MM57 Go to UniProtKB: G3MM57
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3MM57
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain T [auth C] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain T [auth C]	L [auth A], S [auth B], T [auth C]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth C] Interactions & Density Focus chain L [auth A] Focus chain S [auth B] Focus chain T [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain U [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain U [auth C]	D [auth A], E [auth A], M [auth B], N [auth B], U [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain U [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C]	F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], V [auth C], W [auth C], X [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.289
R-Value Work: 0.255
R-Value Observed: 0.256
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.458	α = 90
b = 139.9	β = 90
c = 202.015	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-03-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-03-16
Type: Initial release
Version 1.1: 2020-02-19
Changes: Data collection, Derived calculations
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary