5MVM

X-ray structure of the F14'A -N15'A double mutant of GLIC in complex with propofol

PDB DOI: https://doi.org/10.2210/pdb5MVM/pdb
Entry: 5MVM supersedes: 4HFC

Classification: TRANSPORT PROTEIN
Organism(s): Gloeobacter violaceus PCC 7421
Expression System: Escherichia coli
Mutation(s): Yes
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2017-01-16 Released: 2018-03-14
Deposition Author(s): Fourati, Z., Delarue, M.
Funding Organization(s): French National Research Agency

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.208
R-Value Work: 0.195
R-Value Observed: 0.196

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

X-ray structure of the F14'A -N15'A double mutant of GLIC in complex with propofol

Fourati, Z., Delarue, M.

To be published.

Macromolecule Content

Total Structure Weight: 195.02 kDa
Atom Count: 13,400
Modelled Residue Count: 1,555
Deposited Residue Count: 1,585
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proton-gated ion channel	A, B, C, D, E	317	Gloeobacter violaceus PCC 7421	Mutation(s): 2 Gene Names: glvI, glr4197 Membrane Entity: Yes
UniProt
Find proteins for Q7NDN8 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NDN8 Go to UniProtKB: Q7NDN8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NDN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLC Query on PLC Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain XA [auth E] SDF format, chain YA [auth E] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth E] MOL2 format, chain YA [auth E] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain OA [auth D] mmCIF format, chain PA [auth D] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth E] mmCIF format, chain YA [auth E]	DA [auth C] EA [auth C] FA [auth C] K [auth A] L [auth A] DA [auth C], EA [auth C], FA [auth C], K [auth A], L [auth A], M [auth A], NA [auth D], OA [auth D], PA [auth D], V [auth B], W [auth B], WA [auth E], X [auth B], XA [auth E], YA [auth E]	DIUNDECYL PHOSPHATIDYL CHOLINE C₃₂ H₆₅ N O₈ P IJFVSSZAOYLHEE-SSEXGKCCSA-O		Interactions Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YA [auth E] Interactions & Density Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain V [auth B] Focus chain W [auth B] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain YA [auth E]
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GA [auth C] SDF format, chain IA [auth D] SDF format, chain Q [auth B] SDF format, chain RA [auth E] SDF format, chain SA [auth E] MOL2 format, chain F [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain IA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain SA [auth E] mmCIF format, chain F [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain IA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain SA [auth E]	F [auth A] GA [auth C] IA [auth D] Q [auth B] RA [auth E] F [auth A], GA [auth C], IA [auth D], Q [auth B], RA [auth E], SA [auth E]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain F [auth A] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain Q [auth B] Focus chain RA [auth E] Focus chain SA [auth E] Interactions & Density Focus chain F [auth A] Focus chain GA [auth C] Focus chain IA [auth D] Focus chain Q [auth B] Focus chain RA [auth E] Focus chain SA [auth E]
PFL Query on PFL Download Ideal Coordinates CCD File SDF format, chain HA [auth C] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth E]	HA [auth C], O [auth A], P [auth A], Z [auth B], ZA [auth E]	2,6-BIS(1-METHYLETHYL)PHENOL C₁₂ H₁₈ O OLBCVFGFOZPWHH-UHFFFAOYSA-N		Interactions Focus chain HA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain HA [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain Z [auth B] Focus chain ZA [auth E]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain I [auth A] SDF format, chain JA [auth D] SDF format, chain LA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth B] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain Y [auth B] SDF format, chain G [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain LA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth B] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain G [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain LA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth B] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth E] mmCIF format, chain Y [auth B] mmCIF format, chain G [auth A]	AA [auth C] G [auth A] I [auth A] JA [auth D] LA [auth D] AA [auth C], G [auth A], I [auth A], JA [auth D], LA [auth D], QA [auth D], R [auth B], T [auth B], TA [auth E], Y [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth C] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain T [auth B] Focus chain TA [auth E] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain G [auth A] Focus chain I [auth A] Focus chain JA [auth D] Focus chain LA [auth D] Focus chain QA [auth D] Focus chain R [auth B] Focus chain T [auth B] Focus chain TA [auth E] Focus chain Y [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain H [auth A] SDF format, chain KA [auth D] SDF format, chain S [auth B] SDF format, chain UA [auth E] MOL2 format, chain BA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain S [auth B] MOL2 format, chain UA [auth E] mmCIF format, chain BA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain S [auth B] mmCIF format, chain UA [auth E]	BA [auth C], H [auth A], KA [auth D], S [auth B], UA [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain H [auth A] Focus chain KA [auth D] Focus chain S [auth B] Focus chain UA [auth E] Interactions & Density Focus chain BA [auth C] Focus chain H [auth A] Focus chain KA [auth D] Focus chain S [auth B] Focus chain UA [auth E]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth E] SDF format, chain CA [auth C] SDF format, chain J [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain U [auth B] SDF format, chain VA [auth E] MOL2 format, chain AB [auth E] MOL2 format, chain CA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] MOL2 format, chain VA [auth E] mmCIF format, chain AB [auth E] mmCIF format, chain CA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B] mmCIF format, chain VA [auth E]	AB [auth E] CA [auth C] J [auth A] MA [auth D] N [auth A] AB [auth E], CA [auth C], J [auth A], MA [auth D], N [auth A], U [auth B], VA [auth E]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth E] Focus chain CA [auth C] Focus chain J [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain U [auth B] Focus chain VA [auth E] Interactions & Density Focus chain AB [auth E] Focus chain CA [auth C] Focus chain J [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain U [auth B] Focus chain VA [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.10 Å
R-Value Free: 0.208
R-Value Work: 0.195
R-Value Observed: 0.196
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 181.76	α = 90
b = 132.51	β = 102.72
c = 160.52	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-14

Deposition Author(s):

Fourati, Z.

Delarue, M.

This entry supersedes: 4HFC

Funding Organization	Location	Grant Number
French National Research Agency	France	PENTAGATE

Revision History (Full details and data files)

Version 1.0: 2018-03-14
Type: Initial release
Version 1.1: 2019-10-16
Changes: Data collection
Version 1.2: 2024-02-07
Changes: Data collection, Database references, Refinement description