4TWK

Crystal structure of human two pore domain potassium ion channel TREK1 (K2P2.1)

PDB DOI: https://doi.org/10.2210/pdb4TWK/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2014-06-30 Released: 2014-08-06
Deposition Author(s): Pike, A.C.W., Dong, Y.Y., Tessitore, A., Goubin, S., Strain-Damerell, C., Mukhopadhyay, S., Kupinska, K., Wang, D., Chalk, R., Berridge, G., Grieben, M., Shrestha, L., Ang, J.H., Mackenzie, A., Quigley, A., Bushell, S.R., Shintre, C.A., Faust, B., Chu, A., Dong, L., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Burgess-Brown, N.A., Carpenter, E.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.258
R-Value Work: 0.231
R-Value Observed: 0.232

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of human two pore domain potassium ion channel TREK1 (K2P2.1)

Pike, A.C.W., Dong, Y.Y., Tessitore, A., Goubin, S., Strain-Damerell, C., Mukhopadhyay, S., Kupinska, K., Wang, D., Chalk, R., Berridge, G., Grieben, M., Shrestha, L., Ang, J.H., Mackenzie, A., Quigley, A., Bushell, S.R., Shintre, C.A., Faust, B., Chu, A., Dong, L., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Burgess-Brown, N.A., Carpenter, E.P.

To be published.

Macromolecule Content

Total Structure Weight: 65.67 kDa
Atom Count: 3,941
Modelled Residue Count: 496
Deposited Residue Count: 566
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Potassium channel subfamily K member 2	A, B	283	Homo sapiens	Mutation(s): 0 Gene Names: KCNK2, TREK, TREK1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O95069 (Homo sapiens) Explore O95069 Go to UniProtKB: O95069
PHAROS: O95069 GTEx: ENSG00000082482
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95069
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: O95069-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
37X Query on 37X Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B]	E [auth A], F [auth A], G [auth A], H [auth A], L [auth B]	Octyl Glucose Neopentyl Glycol C₂₇ H₅₂ O₁₂ TYXCLOLHZMMLEK-RNDJEAJNSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain K [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	C [auth A], D [auth A], J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain J [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.258
R-Value Work: 0.231
R-Value Observed: 0.232
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.47	α = 90
b = 105.975	β = 90
c = 128.27	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.3: 2024-10-16
Changes: Structure summary