9G11

sugar/H+ symporter STP6 in inward occluded conformation with glucose bound

PDB DOI: https://doi.org/10.2210/pdb9G11/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Arabidopsis thaliana
Expression System: Saccharomyces cerevisiae
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMD

Deposited: 2024-07-09 Released: 2024-08-14
Deposition Author(s): Andersen, C.G., Bavnhoej, L., Pedersen, B.P.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 ?
R-Value Free: 0.252
R-Value Work: 0.227
R-Value Observed: 0.230

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Comparative biochemical analysis of the plant sugar transporters STP6 and STP10

Andersen, C.G., Bavnhoej, L., Driller, J.H., Brag, S., Pedersen, B.P.

To be published.

Macromolecule Content

Total Structure Weight: 57.59 kDa
Atom Count: 3,824
Modelled Residue Count: 476
Deposited Residue Count: 507
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sugar transport protein 6	A	507	Arabidopsis thaliana	Mutation(s): 0 Gene Names: STP6, At3g05960, F2O10.8 Membrane Entity: Yes
UniProt
Find proteins for Q9SFG0 (Arabidopsis thaliana) Explore Q9SFG0 Go to UniProtKB: Q9SFG0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9SFG0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]
BGC (Subject of Investigation/LOI) Query on BGC 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]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 ?
R-Value Free: 0.252
R-Value Work: 0.227
R-Value Observed: 0.230
Space Group: P 3₂ 2 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 122.221	α = 90
b = 122.221	β = 90
c = 139.091	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-08-14

Deposition Author(s):

Andersen, C.G.

Bavnhoej, L.

Pedersen, B.P.

Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	637372

Revision History (Full details and data files)

Version 1.0: 2024-08-14
Type: Initial release
Version 1.1: 2024-10-30
Changes: Advisory, Database references, Derived calculations, Structure summary

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Help and Resources

9G11

sugar/H+ symporter STP6 in inward occluded conformation with glucose bound

Comparative biochemical analysis of the plant sugar transporters STP6 and STP10

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)