6AWN

X-ray structure of the S439T human serotonin transporter complexed with paroxetine at the central site

PDB DOI: https://doi.org/10.2210/pdb6AWN/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens, Mus musculus
Expression System: Homo sapiens, Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2017-09-06 Released: 2017-10-25
Deposition Author(s): Coleman, J.A., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.62 Å
R-Value Free: 0.263
R-Value Work: 0.256
R-Value Observed: 0.256

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.8 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 112 kDa
Atom Count: 7,703
Modelled Residue Count: 976
Deposited Residue Count: 992
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent serotonin transporter	A	549	Homo sapiens	Mutation(s): 4 Gene Names: SLC6A4, HTT, SERT Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P31645 (Homo sapiens) Explore P31645 Go to UniProtKB: P31645
PHAROS: P31645 GTEx: ENSG00000108576
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31645
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
8B6 antibody FAB heavy chain	B	229	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A0F7R1P3 (Mus musculus) Explore A0A0F7R1P3 Go to UniProtKB: A0A0F7R1P3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F7R1P3
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
8B6 antibody FAB light chain	C	214	Mus musculus	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A0F7R5U8 (Mus musculus) Explore A0A0F7R5U8 Go to UniProtKB: A0A0F7R5U8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0F7R5U8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
8PR Query on 8PR Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	Paroxetine C₁₉ H₂₀ F N O₃ AHOUBRCZNHFOSL-YOEHRIQHSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A]	D [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Interactions & Density Focus chain D [auth A] Focus chain G [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A]	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
8PR	BindingDB: 6AWN	Ki: min: 0.02, max: 4.7 (nM) from 24 assay(s)
		Kd: min: 0.13, max: 0.15 (nM) from 2 assay(s)
		IC50: min: 0.2, max: 6.43 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.62 Å
R-Value Free: 0.263
R-Value Work: 0.256
R-Value Observed: 0.256
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.15	α = 90
b = 162.84	β = 90
c = 140.82	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-10-25

Deposition Author(s):

Coleman, J.A.

Gouaux, E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	5R37MH070039

Revision History (Full details and data files)

Version 1.0: 2017-10-25
Type: Initial release
Version 1.1: 2017-11-22
Changes: Database references
Version 1.2: 2017-12-06
Changes: Author supporting evidence
Version 1.3: 2018-01-31
Changes: Database references
Version 1.4: 2018-02-14
Changes: Database references
Version 1.5: 2018-02-21
Changes: Database references
Version 1.6: 2019-11-27
Changes: Author supporting evidence
Version 1.7: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.8: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary