1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Cady, S.D. Schmidt-Rohr, K. Wang, J. Soto, C.S. DeGrado, W.F. Hong, M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C10 H17 N 151.249 (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine Amantadine non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK Nature NATUAS 0006 0028-0836 463 689 692 10.1038/nature08722 20130653 Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers 2010 UK J.Mol.Biol. JMOBAK 0070 0022-2836 385 1127 1141 10.1016/j.jmb.2008.11.022 19061899 Structure of amantadine-bound M2 transmembrane peptide of influenza A in lipid bilayers from magic-angle-spinning solid-state NMR: the role of Ser31 in amantadine binding. 2009 US Biophys.J. BIOJAU 0030 0006-3495 92 4335 4343 10.1529/biophysj.106.090183 17384070 Backbone structure of the amantadine-blocked trans-membrane domain M2 proton channel from Influenza A virus. 2007 10.2210/pdb2kqt/pdb pdb_00002kqt 1 1 1.0 2730.295 M2 protein residues 22-46 4 syn polymer 151.249 (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine 1 syn non-polymer no no SSDPLVVAASIIGILHLILWILDRL SSDPLVVAASIIGILHLILWILDRL A,B,C,D polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n database_2 pdbx_database_status pdbx_nmr_software pdbx_nmr_spectrometer database_2 pdbx_database_status repository Initial release Version format compliance Other Data collection Database references Other Database references Other 1 0 2010-02-09 1 1 2011-07-13 1 2 2011-10-26 1 3 2020-02-26 1 4 2023-06-14 _pdbx_database_status.status_code_cs _pdbx_nmr_software.name _pdbx_nmr_spectrometer.model _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.status_code_nmr_data Magic-Angle-Spinning Solid-State NMR Structure of Influenza A M2 Transmembrane Domain Structure of the Amantadine-Blocked Influenza A M2 Proton Channel Trans-membrane Domain by Solid-state NMR spectroscopy Proton Channel M2 from Influenza A in complex with inhibitor rimantadine The Crystal structure of Transmembrane domain of M2 protein and Amantadine complex The closed state structure of M2 protein H+ channel by solid state NMR spectroscopy High resolution Crystal structure of Transmembrane domain of M2 protein THIS ENTRY 2KQT REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA 2H95 and 2KAD BMRB Y RCSB 2009-11-18 REL REL REL REL 308 (3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine Solid-phase synthesis sample 8 structures with the least restraint violations 24 17 2D 13C-13C Spin Diffusion 2D 13C-13C Spin Diffusion 2D 13C-13C Spin Diffusion 2D 13C-15N HETCOR 2D 13C-15N HETCOR 2D 13C-15N HETCOR 1D 2H-13C REDOR, single 13C pulse 1D 2H-13C REDOR, single 13C pulse 1D 2H-13C REDOR, single 13C pulse 1D 2H-13C REDOR, single 13C pulse 1D 2H-13C REDOR, single 2H pulse 1D 2H-13C REDOR, single 2H pulse 1D 2H-13C REDOR, single 2H pulse 2H Static Quadrupolar Echo 2H Static Quadrupolar Echo 2H Static Quadrupolar Echo 5.8 mg/mL [U-99% 13C; U-99% 15N] at S31, I32 and D44 21.6 mg/mL 10 mM 10 mM 1 mM .1 mM .42 mg/mL [U-2H] 5.0 mg/mL [U-99% 13C; U-99% 15N] at S31, I32 and D44 10.4 mg/mL 10 mM 10 mM 1 mM 0.1 mM 0.09 mg/mL [U-2H] 5.2 mg/mL [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 19.9 mg/mL 10 mM 10 mM 1 mM .1 mM 0.38 mg/mL [U-2H] 7 mg/mL [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 27 mg/mL 10 mM 10 mM 1 mM .1 mM 2.0 mg/mL [U-2H] 7 mg/mL [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 27 mg/mL 10 mM 10 mM 1 mM .1 mM 0.5 mg/mL [U-2H] 7.5 ambient 243 K The temperature was initially set to 1,000,000K and decreased by 10% every 100 steps until a temperature of 25 K was reached. The constants (CI-CIV) were obtained through a trial-and-error process. Some side chain rotamers were changed to maximize agreement with the radial distances., An ensemble of models was obtained by selecting the top scoring model after one round of Monte Carlo/Simulated Annealing minimization and refining again with the inverse kinematics algorithm. The distance potential constant CIII was set to 50 kcal/mol-radians^2. Since the radial distance provided excellent restraints between the drug and M2, we were able to position the amantidine molecule near with S31 without the need for further minimization. THE POSITION OF THE AMANTADINE LIGAND (PDB CODE 308) IS IDENTICAL IN ALL OF THE MINIMIZED STRUCTURE SINCE IT IS THE AVERAGE LIGAND POSITION RELATIVE TO THE BACKBONE. WE HAVE MEASURED A 13C-2H DIPOLAR COUPLING FROM SEVERAL PEPTIDE BACKBONE AND SIDECHAIN CARBONS TO THE DEUTERONS ON THE 308 LIGAND. WE SIMULATED THE THE RADIUS OF THE M2 CHANNEL PORE FOR THE SITES WHERE WE OBSERVED 13C-2H DIPOLAR COUPLING, AND FOUND PORE RADII FOR THESE SITES THAT CORRESPONDED WITH THE MEASURED 13C-2H DIPOLAR COUPLING AT THAT SITE. THUS, IN THE FINAL STRUCTURE MINIMIZATION, WE USED THE PORE RADII AS A CONSTRAINT RATHER THAN PEPTIDE-DRUG DISTANCES SINCE THE LIGAND IS ROTATING IN THE CHANNEL. simulated annealing, Monte Carlo 1 fewest violations 5.8 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 21.6 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, .42 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration 10mM pH 7.5 phosphate buffer, 50% hydration 5.0 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 10.4 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.09 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration 10mM pH 7.5 phosphate buffer, 50% hydration 5.2 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 19.9 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.38 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration 10mM pH 7.5 phosphate buffer, 50% hydration 7 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 27 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 2.0 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration 10mM pH 7.5 phosphate buffer, 50% hydration 7 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 27 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO, 1 mM EDTA, 0.1 mM NaN3, 0.5 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration 10mM pH 7.5 phosphate buffer, 50% hydration Bruker Biospin collection TopSpin 1.3 Bruker Biospin chemical shift assignment TopSpin 1.3 Bruker Biospin processing TopSpin 1.3 Bruker Biospin data analysis TopSpin 1.3 Bruker Biospin peak picking TopSpin 1.3 Schwieters, Kuszewski, Tjandra and Clore refinement X-PLOR_NIH, IN-HOUSE METHOD Bruker Biospin collection XwinNMR Bruker Biospin chemical shift assignment XwinNMR 400 Bruker AVANCE Bruker Avance 600 Bruker AVANCE Bruker Avance 308 1 2 308 308 1 C SER 22 n 1 SER 22 A SER 23 n 2 SER 23 A ASP 24 n 3 ASP 24 A PRO 25 n 4 PRO 25 A LEU 26 n 5 LEU 26 A VAL 27 n 6 VAL 27 A VAL 28 n 7 VAL 28 A ALA 29 n 8 ALA 29 A ALA 30 n 9 ALA 30 A SER 31 n 10 SER 31 A ILE 32 n 11 ILE 32 A ILE 33 n 12 ILE 33 A GLY 34 n 13 GLY 34 A ILE 35 n 14 ILE 35 A LEU 36 n 15 LEU 36 A HIS 37 n 16 HIS 37 A LEU 38 n 17 LEU 38 A ILE 39 n 18 ILE 39 A LEU 40 n 19 LEU 40 A TRP 41 n 20 TRP 41 A ILE 42 n 21 ILE 42 A LEU 43 n 22 LEU 43 A ASP 44 n 23 ASP 44 A ARG 45 n 24 ARG 45 A LEU 46 n 25 LEU 46 A SER 22 n 1 SER 22 B SER 23 n 2 SER 23 B ASP 24 n 3 ASP 24 B PRO 25 n 4 PRO 25 B LEU 26 n 5 LEU 26 B VAL 27 n 6 VAL 27 B VAL 28 n 7 VAL 28 B ALA 29 n 8 ALA 29 B ALA 30 n 9 ALA 30 B SER 31 n 10 SER 31 B ILE 32 n 11 ILE 32 B ILE 33 n 12 ILE 33 B GLY 34 n 13 GLY 34 B ILE 35 n 14 ILE 35 B LEU 36 n 15 LEU 36 B HIS 37 n 16 HIS 37 B LEU 38 n 17 LEU 38 B ILE 39 n 18 ILE 39 B LEU 40 n 19 LEU 40 B TRP 41 n 20 TRP 41 B ILE 42 n 21 ILE 42 B LEU 43 n 22 LEU 43 B ASP 44 n 23 ASP 44 B ARG 45 n 24 ARG 45 B LEU 46 n 25 LEU 46 B SER 22 n 1 SER 22 C SER 23 n 2 SER 23 C ASP 24 n 3 ASP 24 C PRO 25 n 4 PRO 25 C LEU 26 n 5 LEU 26 C VAL 27 n 6 VAL 27 C VAL 28 n 7 VAL 28 C ALA 29 n 8 ALA 29 C ALA 30 n 9 ALA 30 C SER 31 n 10 SER 31 C ILE 32 n 11 ILE 32 C ILE 33 n 12 ILE 33 C GLY 34 n 13 GLY 34 C ILE 35 n 14 ILE 35 C LEU 36 n 15 LEU 36 C HIS 37 n 16 HIS 37 C LEU 38 n 17 LEU 38 C ILE 39 n 18 ILE 39 C LEU 40 n 19 LEU 40 C TRP 41 n 20 TRP 41 C ILE 42 n 21 ILE 42 C LEU 43 n 22 LEU 43 C ASP 44 n 23 ASP 44 C ARG 45 n 24 ARG 45 C LEU 46 n 25 LEU 46 C SER 22 n 1 SER 22 D SER 23 n 2 SER 23 D ASP 24 n 3 ASP 24 D PRO 25 n 4 PRO 25 D LEU 26 n 5 LEU 26 D VAL 27 n 6 VAL 27 D VAL 28 n 7 VAL 28 D ALA 29 n 8 ALA 29 D ALA 30 n 9 ALA 30 D SER 31 n 10 SER 31 D ILE 32 n 11 ILE 32 D ILE 33 n 12 ILE 33 D GLY 34 n 13 GLY 34 D ILE 35 n 14 ILE 35 D LEU 36 n 15 LEU 36 D HIS 37 n 16 HIS 37 D LEU 38 n 17 LEU 38 D ILE 39 n 18 ILE 39 D LEU 40 n 19 LEU 40 D TRP 41 n 20 TRP 41 D ILE 42 n 21 ILE 42 D LEU 43 n 22 LEU 43 D ASP 44 n 23 ASP 44 D ARG 45 n 24 ARG 45 D LEU 46 n 25 LEU 46 D author_defined_assembly 4 tetrameric 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A GLY 34 -15.25 1 B GLY 34 -15.25 1 C GLY 34 -15.25 1 D GLY 34 -15.25 2 A GLY 34 -15.32 2 B GLY 34 -15.32 2 C GLY 34 -15.32 2 D GLY 34 -15.32 3 A GLY 34 -15.22 3 B GLY 34 -15.22 3 C GLY 34 -15.22 3 D GLY 34 -15.22 4 A GLY 34 -15.25 4 B GLY 34 -15.25 4 C GLY 34 -15.25 4 D GLY 34 -15.25 5 A GLY 34 -15.24 5 B GLY 34 -15.24 5 C GLY 34 -15.24 5 D GLY 34 -15.24 6 A GLY 34 -15.24 6 B GLY 34 -15.24 6 C GLY 34 -15.24 6 D GLY 34 -15.24 7 A GLY 34 -15.23 7 B GLY 34 -15.23 7 C GLY 34 -15.23 7 D GLY 34 -15.23 8 A GLY 34 -15.25 8 B GLY 34 -15.25 8 C GLY 34 -15.25 8 D GLY 34 -15.25 9 A GLY 34 -15.27 9 B GLY 34 -15.27 9 C GLY 34 -15.27 9 D GLY 34 -15.27 10 A GLY 34 -15.23 10 B GLY 34 -15.23 10 C GLY 34 -15.23 10 D GLY 34 -15.23 11 A GLY 34 -15.27 11 B GLY 34 -15.27 11 C GLY 34 -15.27 11 D GLY 34 -15.27 12 A GLY 34 -15.28 12 B GLY 34 -15.28 12 C GLY 34 -15.28 12 D GLY 34 -15.28 13 A GLY 34 -15.24 13 B GLY 34 -15.24 13 C GLY 34 -15.24 13 D GLY 34 -15.24 14 A GLY 34 -15.28 14 B GLY 34 -15.28 14 C GLY 34 -15.28 14 D GLY 34 -15.28 15 A GLY 34 -15.30 15 B GLY 34 -15.30 15 C GLY 34 -15.30 15 D GLY 34 -15.30 16 A GLY 34 -15.31 16 B GLY 34 -15.31 16 C GLY 34 -15.31 16 D GLY 34 -15.31 17 A GLY 34 -15.25 17 B GLY 34 -15.25 17 C GLY 34 -15.25 17 D GLY 34 -15.25 1 A SER 23 -123.82 -167.72 1 B SER 23 -123.82 -167.72 1 C SER 23 -123.82 -167.72 1 D SER 23 -123.82 -167.72 2 A SER 23 -122.24 -167.89 2 B SER 23 -122.24 -167.89 2 C SER 23 -122.24 -167.89 2 D SER 23 -122.24 -167.89 3 A SER 23 -121.93 -166.76 3 B SER 23 -121.93 -166.76 3 C SER 23 -121.93 -166.76 3 D SER 23 -121.93 -166.76 4 A SER 23 -121.59 -167.19 4 B SER 23 -121.59 -167.19 4 C SER 23 -121.59 -167.19 4 D SER 23 -121.59 -167.19 5 A SER 23 -121.03 -166.86 5 B SER 23 -121.03 -166.86 5 C SER 23 -121.03 -166.86 5 D SER 23 -121.03 -166.86 6 A SER 23 -121.08 -167.07 6 B SER 23 -121.08 -167.07 6 C SER 23 -121.08 -167.07 6 D SER 23 -121.08 -167.07 7 A SER 23 -121.66 -167.36 7 B SER 23 -121.66 -167.36 7 C SER 23 -121.66 -167.36 7 D SER 23 -121.66 -167.36 8 A SER 23 -122.81 -167.85 8 B SER 23 -122.81 -167.85 8 C SER 23 -122.81 -167.85 8 D SER 23 -122.81 -167.85 9 A SER 23 -122.37 -167.42 9 B SER 23 -122.37 -167.42 9 C SER 23 -122.37 -167.42 9 D SER 23 -122.37 -167.42 10 A SER 23 -123.11 -166.78 10 B SER 23 -123.11 -166.78 10 C SER 23 -123.11 -166.78 10 D SER 23 -123.11 -166.78 11 A SER 23 -122.89 -166.50 11 B SER 23 -122.89 -166.50 11 C SER 23 -122.89 -166.50 11 D SER 23 -122.89 -166.50 12 A SER 23 -124.50 -165.70 12 B SER 23 -124.50 -165.70 12 C SER 23 -124.50 -165.70 12 D SER 23 -124.50 -165.70 13 A SER 23 -124.12 -165.71 13 B SER 23 -124.12 -165.71 13 C SER 23 -124.12 -165.71 13 D SER 23 -124.12 -165.71 14 A SER 23 -124.33 -165.77 14 B SER 23 -124.33 -165.77 14 C SER 23 -124.33 -165.77 14 D SER 23 -124.33 -165.77 15 A SER 23 -123.57 -166.13 15 B SER 23 -123.57 -166.13 15 C SER 23 -123.57 -166.13 15 D SER 23 -123.57 -166.13 16 A SER 23 -123.17 -166.53 16 B SER 23 -123.17 -166.53 16 C SER 23 -123.17 -166.53 16 D SER 23 -123.17 -166.53 17 A SER 23 -122.63 -166.47 17 B SER 23 -122.63 -166.47 17 C SER 23 -122.63 -166.47 17 D SER 23 -122.63 -166.47 fewest violations, model 1 Solid-state NMR structure of the M2 transmembrane peptide of the influenza A virus in DMPC lipid bilayers bound to deuterated amantadine 1 N N 1 N N 1 N N 1 N N 2 N N A ASP 24 A ASP 3 HELX_P A LEU 46 A LEU 25 1 1 23 B ASP 24 B ASP 3 HELX_P B LEU 46 B LEU 25 1 2 23 C ASP 24 C ASP 3 HELX_P C LEU 46 C LEU 25 1 3 23 D ASP 24 D ASP 3 HELX_P D LEU 46 D LEU 25 1 4 23 TRANSPORT PROTEIN influenza, transmembrane, amantadine, REDOR, TRANSPORT PROTEIN Q9YP62_9INFA UNP 1 22 Q9YP62 SSDPLVVAASIIGILHLILWILDRL 22 46 2KQT 22 46 Q9YP62 A 1 1 25 22 46 2KQT 22 46 Q9YP62 B 1 1 25 22 46 2KQT 22 46 Q9YP62 C 1 1 25 22 46 2KQT 22 46 Q9YP62 D 1 1 25 1 P 1