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- PDB-6bkl: Influenza A M2 transmembrane domain bound to rimantadine -

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Basic information

Entry
Database: PDB / ID: 6bkl
TitleInfluenza A M2 transmembrane domain bound to rimantadine
ComponentsMatrix protein 2
KeywordsMEMBRANE PROTEIN / influenza M2 / proton channel / rimantadine
Function / homology
Function and homology information


suppression by virus of host autophagy / proton transmembrane transporter activity / : / protein complex oligomerization / monoatomic ion channel activity / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Influenza virus matrix protein 2 / Influenza Matrix protein (M2)
Similarity search - Domain/homology
Chem-EU7 / RIMANTADINE / Matrix protein 2 / Matrix protein 2
Similarity search - Component
Biological speciesInfluenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.995 Å
AuthorsThomaston, J.L. / DeGrado, W.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM056423 United States
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Inhibitors of the M2 Proton Channel Engage and Disrupt Transmembrane Networks of Hydrogen-Bonded Waters.
Authors: Thomaston, J.L. / Polizzi, N.F. / Konstantinidi, A. / Wang, J. / Kolocouris, A. / DeGrado, W.F.
History
DepositionNov 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Matrix protein 2
B: Matrix protein 2
C: Matrix protein 2
D: Matrix protein 2
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,75212
Polymers22,0358
Non-polymers7174
Water57632
1
A: Matrix protein 2
B: Matrix protein 2
C: Matrix protein 2
D: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3766
Polymers11,0174
Non-polymers3592
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-46 kcal/mol
Surface area5490 Å2
MethodPISA
2
E: Matrix protein 2
F: Matrix protein 2
G: Matrix protein 2
H: Matrix protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3766
Polymers11,0174
Non-polymers3592
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-44 kcal/mol
Surface area5520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.460, 47.840, 48.530
Angle α, β, γ (deg.)90.00, 96.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Matrix protein 2


Mass: 2754.340 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Influenza A virus / References: UniProt: Q20MD5, UniProt: Q9Q0L9*PLUS
#2: Chemical ChemComp-EU7 / (1S)-1-[(3R,5R,7R)-tricyclo[3.3.1.1~3,7~]decan-1-yl]ethan-1-amine / S-RIMANTADINE


Mass: 179.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N
#3: Chemical ChemComp-RIM / RIMANTADINE / 1-(1-ADAMANTYL)ETHANAMINE / Rimantadine


Mass: 179.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H21N / Comment: antivirus*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.2 M MgCl2, 0.1 M sodium acetate / acetic acid pH 4.5, 20% w/v PEG 8000, monoolein, rimantadine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 1.995→48.193 Å / Num. obs: 10589 / % possible obs: 93.3 % / Redundancy: 4.8 % / CC1/2: 0.994 / Rmerge(I) obs: 0.114 / Net I/σ(I): 7.1
Reflection shellResolution: 1.995→2.05 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 754 / CC1/2: 0.959 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LBW

3lbw


Resolution: 1.995→48.193 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2439 1052 9.98 %
Rwork0.1863 --
obs0.1919 10543 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.995→48.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 52 32 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071536
X-RAY DIFFRACTIONf_angle_d0.7352120
X-RAY DIFFRACTIONf_dihedral_angle_d10.977508
X-RAY DIFFRACTIONf_chiral_restr0.431302
X-RAY DIFFRACTIONf_plane_restr0.006226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.995-2.08580.27241260.19751142X-RAY DIFFRACTION90
2.0858-2.19580.28341320.1721178X-RAY DIFFRACTION92
2.1958-2.33340.23851300.17621163X-RAY DIFFRACTION91
2.3334-2.51350.30981310.18381200X-RAY DIFFRACTION92
2.5135-2.76640.2271330.17261186X-RAY DIFFRACTION93
2.7664-3.16670.23111340.17981206X-RAY DIFFRACTION94
3.1667-3.98940.25291330.18831208X-RAY DIFFRACTION93
3.9894-48.20670.21851330.19831208X-RAY DIFFRACTION92

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