5WKV

Structure of an acid sensing ion channel in a resting state with calcium

PDB DOI: https://doi.org/10.2210/pdb5WKV/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Gallus gallus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2017-07-25 Released: 2018-03-14
Deposition Author(s): Yoder, N., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.297
R-Value Work: 0.287
R-Value Observed: 0.287

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 152.77 kDa
Atom Count: 9,383
Modelled Residue Count: 1,249
Deposited Residue Count: 1,317
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid-sensing ion channel 1	A, B [auth C], C [auth B]	439	Gallus gallus	Mutation(s): 0 Gene Names: ASIC1, ACCN2 Membrane Entity: Yes
UniProt
Find proteins for Q1XA76 (Gallus gallus) Explore Q1XA76 Go to UniProtKB: Q1XA76
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q1XA76
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E	2		N-Glycosylation	Interactions Focus chain D Focus chain E Interactions & Density Focus chain D Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth B]	F [auth A], G [auth A], K [auth C], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain N [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth C] Focus chain N [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain P [auth B] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B]	I [auth A] J [auth A] L [auth C] M [auth C] P [auth B] I [auth A], J [auth A], L [auth C], M [auth C], P [auth B], Q [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth B] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain P [auth B] Focus chain Q [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B]	H [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain H [auth A] Focus chain O [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.297
R-Value Work: 0.287
R-Value Observed: 0.287
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.18	α = 90
b = 133.7	β = 90
c = 157.65	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Yoder, N.

Gouaux, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	5T32DK007680
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	5F31NS096782
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	5R01NS038631

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2018-03-21
Changes: Database references
Version 1.2: 2018-03-28
Changes: Data collection, Database references
Version 1.3: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 1.4: 2019-12-18
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary