1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 RESIDUES LEU 4, VAL 6, VAL 8, LEU 10, LEU 12, AND LEU 14 IN EACH CHAIN EXHIBIT THE D CONFIGURATION OF THE AMINO ACID. Arseniev, A.S. Barsukov, I.L. Lomize, A.L. Orekhov, V.Y. Bystrov, V.F. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H13 N O2 131.173 D-LEUCINE D-peptide linking C5 H11 N O2 117.146 D-VALINE D-peptide linking C2 H7 N O 61.083 ETHANOLAMINE L-peptide COOH carboxy terminus C6 H11 N O3 145.156 n N-formyl-L-valine L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking N 1 N N N 2 S C N 3 N C N 4 N O N 5 N C N 6 N O N 7 N H N 8 N H N 9 N H N 10 N H N 11 N H N 12 N H N 13 N H N 14 N N N 15 R C N 16 N C N 17 N C N 18 N C N 19 N C N 20 N C N 21 N O N 22 N O N 23 N H N 24 N H N 25 N H N 26 N H N 27 N H N 28 N H N 29 N H N 30 N H N 31 N H N 32 N H N 33 N H N 34 N H N 35 N H N 36 N N N 37 R C N 38 N C N 39 N C N 40 N C N 41 N C N 42 N O N 43 N O N 44 N H N 45 N H N 46 N H N 47 N H N 48 N H N 49 N H N 50 N H N 51 N H N 52 N H N 53 N H N 54 N H N 55 N C N 56 N N N 57 N C N 58 N O N 59 N H N 60 N H N 61 N H N 62 N H N 63 N H N 64 N H N 65 N H N 66 N C N 67 N N N 68 N O N 69 S C N 70 N C N 71 N C N 72 N C N 73 N H N 74 N H N 75 N H N 76 N H N 77 N H N 78 N H N 79 N H N 80 N H N 81 N H N 82 N O N 83 N C N 84 N H N 85 N O N 86 N H N 87 N N N 88 N C N 89 N C N 90 N O N 91 N O N 92 N H N 93 N H N 94 N H N 95 N H N 96 N H N 97 N N N 98 S C N 99 N C N 100 N O N 101 N C Y 102 N C Y 103 N C Y 104 N C Y 105 N N Y 106 N C Y 107 N C Y 108 N C Y 109 N C Y 110 N C N 111 N O N 112 N H N 113 N H N 114 N H N 115 N H N 116 N H N 117 N H N 118 N H N 119 N H N 120 N H N 121 N H N 122 N H N 123 N H N 124 N N N 125 S C N 126 N C N 127 N O N 128 N C N 129 N C N 130 N C N 131 N O N 132 N H N 133 N H N 134 N H N 135 N H N 136 N H N 137 N H N 138 N H N 139 N H N 140 N H N 141 N H N 142 N H N 1 N sing N 2 N sing N 3 N sing N 4 N sing N 5 N sing N 6 N sing N 7 N doub N 8 N sing N 9 N sing N 10 N sing N 11 N sing N 12 N sing N 13 N sing N 14 N sing N 15 N sing N 16 N sing N 17 N sing N 18 N sing N 19 N sing N 20 N sing N 21 N sing N 22 N sing N 23 N sing N 24 N sing N 25 N sing N 26 N sing N 27 N sing N 28 N sing N 29 N sing N 30 N sing N 31 N doub N 32 N sing N 33 N sing N 34 N sing N 35 N sing N 36 N sing N 37 N sing N 38 N sing N 39 N sing N 40 N sing N 41 N sing N 42 N sing N 43 N sing N 44 N sing N 45 N sing N 46 N sing N 47 N sing N 48 N sing N 49 N doub N 50 N sing N 51 N sing N 52 N sing N 53 N sing N 54 N sing N 55 N sing N 56 N sing N 57 N sing N 58 N sing N 59 N sing N 60 N sing N 61 N sing N 62 N doub N 63 N sing N 64 N sing N 65 N sing N 66 N sing N 67 N sing N 68 N sing N 69 N sing N 70 N sing N 71 N sing N 72 N sing N 73 N sing N 74 N sing N 75 N sing N 76 N sing N 77 N sing N 78 N doub N 79 N sing N 80 N sing N 81 N sing N 82 N sing N 83 N sing N 84 N sing N 85 N sing N 86 N sing N 87 N sing N 88 N doub N 89 N sing N 90 N sing N 91 N sing N 92 N sing N 93 N sing N 94 N sing N 95 N sing N 96 N sing N 97 N doub N 98 N sing N 99 N sing N 100 N sing N 101 N sing Y 102 N doub Y 103 N sing Y 104 N sing N 105 N sing Y 106 N doub Y 107 N sing Y 108 N sing N 109 N sing Y 110 N sing Y 111 N doub N 112 N sing Y 113 N doub N 114 N sing Y 115 N sing N 116 N sing N 117 N sing N 118 N sing N 119 N sing N 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N doub N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N sing N 131 N sing N 132 N sing N 133 N sing N 134 N sing N 135 N sing N 136 N sing SU Biol.Membr.(Ussr) BIMEE9 2018 0233-4755 18 182 1376600 Refinement of the Spatial Structure of the Gramicidin a Ion Channel 1992 NE FEBS Lett. FEBLAL 0165 0014-5793 186 168 10.1016/0014-5793(85)80702-X 2408920 1H-NMR Study of Gramicidin a Transmembrane Ion Channel. Head-to-Head Right-Handed, Single-Stranded Helices. 1985 SU Biol.Membr.(Ussr) BIMEE9 2018 0233-4755 3 1077 Gramicidin a Transmembrane Ion-Channel. Three-Dimensional Structure Reconstruction Based on NMR Spectroscopy and Energy Refinement (Russian) 1986 SU Biol.Membr.(Ussr) BIMEE9 2018 0233-4755 3 437 Spatial Structure of Gramicidin a Transmembrane Ion Channel-NMR Analysis in Micelles (Russian) 1986 10.2210/pdb1grm/pdb pdb_00001grm 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1882.294 GRAMICIDIN A 2 man polymer VALYL GRAMICIDIN no yes (FVA)GA(DLE)A(DVA)V(DVA)W(DLE)W(DLE)W(DLE)W(ETA) VGALAVVVWLWLWLWX A,B polypeptide(L) n n n n n n n n n n n n n n n n sample 1393 BREVIBACILLUS BREVIS citation pdbx_database_status atom_site chem_comp_atom chem_comp_bond database_2 struct_conn repository Initial release Version format compliance Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Other Database references Other Atomic model Data collection Database references Derived calculations 1 0 1994-01-31 1 1 2011-06-14 1 2 2011-07-13 1 3 2011-07-27 1 4 2012-12-12 1 5 2017-12-20 2 0 2023-11-15 _citation.pdbx_database_id_DOI _pdbx_database_status.process_site _atom_site.auth_atom_id _atom_site.label_atom_id _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag CRYSTAL STRUCTURE OF GRAMICIDIN S COMPLEXED WITH ALKALINE PROTEINASE SAVINASE CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID CUBIC PHASE. CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE CRYSTAL STRUCTURE OF GRAMICIDIN A FROM BACILLUS BREVIS CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLRXED WITH POTASSIUM THIOCYANATE SOLUTION STRUCTURE OF GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A IN BENZENE/ACETONE 10:1 SOLID STATE NMR STRUCTURE OF GRAMICIDIN A IN HYDRATED DMPC BILAYERS, SOLUTION STRUCTURE OF GRAMICIDIN A IN METHANOL IN THE PRESENCE OF CACL SOLUTION STRUCTURE OF GRAMICIDIN A (W15G) IN SODIUM DODECYL SULFATE MICELLES SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES IN THE PRESENCE OF EXCESS NA+ SOLUTION STRUCTURE OF GRAMICIDIN A (V1F) IN SODIUM DODECYL SULFATE MICELLES SOLUTION STRUCTURE OF GRAMICIDIN B IN SODIUM DODECYL SULFATE MICELLES SOLUTION STRUCTURE OF GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN A IN A MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE, IN THE PRESENCE OF CSCL CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH KI IN METHANOL CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI CRYSTAL STRUCTURE OF GRAMICIDIN D IN N-PROPANOL CRYSTAL STRUCTURE OF GRAMICIDIN D IN METHANOL CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL Y BNL 1993-10-18 REL GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES) Antibiotic GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 0). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16). GRAMICIDIN A Polypeptide 5 FVA 1 n 1 FVA 1 A GLY 2 n 2 GLY 2 A ALA 3 n 3 ALA 3 A DLE 4 n 4 DLE 4 A ALA 5 n 5 ALA 5 A DVA 6 n 6 DVA 6 A VAL 7 n 7 VAL 7 A DVA 8 n 8 DVA 8 A TRP 9 n 9 TRP 9 A DLE 10 n 10 DLE 10 A TRP 11 n 11 TRP 11 A DLE 12 n 12 DLE 12 A TRP 13 n 13 TRP 13 A DLE 14 n 14 DLE 14 A TRP 15 n 15 TRP 15 A ETA 16 n 16 ETA 16 A FVA 1 n 1 FVA 1 B GLY 2 n 2 GLY 2 B ALA 3 n 3 ALA 3 B DLE 4 n 4 DLE 4 B ALA 5 n 5 ALA 5 B DVA 6 n 6 DVA 6 B VAL 7 n 7 VAL 7 B DVA 8 n 8 DVA 8 B TRP 9 n 9 TRP 9 B DLE 10 n 10 DLE 10 B TRP 11 n 11 TRP 11 B DLE 12 n 12 DLE 12 B TRP 13 n 13 TRP 13 B DLE 14 n 14 DLE 14 B TRP 15 n 15 TRP 15 B ETA 16 n 16 ETA 16 B software_defined_assembly PQS 2 dimeric 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 A N ALA 3 A N ALA 3 B O ALA 3 B O ALA 3 1 -5.54 0.90 133.90 128.36 A A A CG CD2 CE3 TRP TRP TRP 9 9 9 N 1 -5.54 0.90 133.90 128.36 A A A CG CD2 CE3 TRP TRP TRP 11 11 11 N 1 -5.59 0.90 133.90 128.31 A A A CG CD2 CE3 TRP TRP TRP 13 13 13 N 1 -5.58 0.90 133.90 128.32 A A A CG CD2 CE3 TRP TRP TRP 15 15 15 N 1 -5.57 0.90 133.90 128.33 B B B CG CD2 CE3 TRP TRP TRP 9 9 9 N 1 -5.51 0.90 133.90 128.39 B B B CG CD2 CE3 TRP TRP TRP 11 11 11 N 1 -5.60 0.90 133.90 128.30 B B B CG CD2 CE3 TRP TRP TRP 13 13 13 N 1 -5.50 0.90 133.90 128.40 B B B CG CD2 CE3 TRP TRP TRP 15 15 15 N 2 -5.54 0.90 133.90 128.36 A A A CG CD2 CE3 TRP TRP TRP 9 9 9 N 2 -5.55 0.90 133.90 128.35 A A A CG CD2 CE3 TRP TRP TRP 11 11 11 N 2 -5.58 0.90 133.90 128.32 A A A CG CD2 CE3 TRP TRP TRP 13 13 13 N 2 -5.57 0.90 133.90 128.33 A A A CG CD2 CE3 TRP TRP TRP 15 15 15 N 2 -5.54 0.90 133.90 128.36 B B B CG CD2 CE3 TRP TRP TRP 9 9 9 N 2 -5.49 0.90 133.90 128.41 B B B CG CD2 CE3 TRP TRP TRP 11 11 11 N 2 -5.57 0.90 133.90 128.33 B B B CG CD2 CE3 TRP TRP TRP 13 13 13 N 2 -5.55 0.90 133.90 128.35 B B B CG CD2 CE3 TRP TRP TRP 15 15 15 N 3 -5.58 0.90 133.90 128.32 A A A CG CD2 CE3 TRP TRP TRP 9 9 9 N 3 -5.56 0.90 133.90 128.34 A A A CG CD2 CE3 TRP TRP TRP 11 11 11 N 3 -5.50 0.90 133.90 128.40 A A A CG CD2 CE3 TRP TRP TRP 13 13 13 N 3 -5.56 0.90 133.90 128.34 A A A CG CD2 CE3 TRP TRP TRP 15 15 15 N 3 -5.60 0.90 133.90 128.30 B B B CG CD2 CE3 TRP TRP TRP 9 9 9 N 3 -5.60 0.90 133.90 128.30 B B B CG CD2 CE3 TRP TRP TRP 11 11 11 N 3 -5.51 0.90 133.90 128.39 B B B CG CD2 CE3 TRP TRP TRP 13 13 13 N 3 -5.49 0.90 133.90 128.41 B B B CG CD2 CE3 TRP TRP TRP 15 15 15 N 4 -5.53 0.90 133.90 128.37 A A A CG CD2 CE3 TRP TRP TRP 9 9 9 N 4 -5.53 0.90 133.90 128.37 A A A CG CD2 CE3 TRP TRP TRP 11 11 11 N 4 -5.55 0.90 133.90 128.35 A A A CG CD2 CE3 TRP TRP TRP 13 13 13 N 4 -5.52 0.90 133.90 128.38 A A A CG CD2 CE3 TRP TRP TRP 15 15 15 N 4 -5.54 0.90 133.90 128.36 B B B CG CD2 CE3 TRP TRP TRP 9 9 9 N 4 -5.54 0.90 133.90 128.36 B B B CG CD2 CE3 TRP TRP TRP 11 11 11 N 4 -5.47 0.90 133.90 128.43 B B B CG CD2 CE3 TRP TRP TRP 13 13 13 N 4 -5.49 0.90 133.90 128.41 B B B CG CD2 CE3 TRP TRP TRP 15 15 15 N 5 -5.52 0.90 133.90 128.38 A A A CG CD2 CE3 TRP TRP TRP 9 9 9 N 5 -5.55 0.90 133.90 128.35 A A A CG CD2 CE3 TRP TRP TRP 11 11 11 N 5 -5.50 0.90 133.90 128.40 A A A CG CD2 CE3 TRP TRP TRP 13 13 13 N 5 -5.53 0.90 133.90 128.37 A A A CG CD2 CE3 TRP TRP TRP 15 15 15 N 5 -5.52 0.90 133.90 128.38 B B B CG CD2 CE3 TRP TRP TRP 9 9 9 N 5 -5.55 0.90 133.90 128.35 B B B CG CD2 CE3 TRP TRP TRP 11 11 11 N 5 -5.50 0.90 133.90 128.40 B B B CG CD2 CE3 TRP TRP TRP 13 13 13 N 5 -5.53 0.90 133.90 128.37 B B B CG CD2 CE3 TRP TRP TRP 15 15 15 N 4 A DLE 10 155.35 -87.67 4 B DLE 10 155.35 -87.66 REFINEMENT OF THE SPATIAL STRUCTURE OF THE GRAMICIDIN A TRANSMEMBRANE ION-CHANNEL (RUSSIAN) 1 N N 1 N N covale 1.325 both A FVA 1 A C FVA 1 1_555 A GLY 2 A N GLY 2 1_555 covale 1.325 both A ALA 3 A C ALA 3 1_555 A DLE 4 A N DLE 4 1_555 covale 1.325 both A DLE 4 A C DLE 4 1_555 A ALA 5 A N ALA 5 1_555 covale 1.325 both A ALA 5 A C ALA 5 1_555 A DVA 6 A N DVA 6 1_555 covale 1.326 both A DVA 6 A C DVA 6 1_555 A VAL 7 A N VAL 7 1_555 covale 1.325 both A VAL 7 A C VAL 7 1_555 A DVA 8 A N DVA 8 1_555 covale 1.325 both A DVA 8 A C DVA 8 1_555 A TRP 9 A N TRP 9 1_555 covale 1.325 both A TRP 9 A C TRP 9 1_555 A DLE 10 A N DLE 10 1_555 covale 1.325 both A DLE 10 A C DLE 10 1_555 A TRP 11 A N TRP 11 1_555 covale 1.324 both A TRP 11 A C TRP 11 1_555 A DLE 12 A N DLE 12 1_555 covale 1.325 both A DLE 12 A C DLE 12 1_555 A TRP 13 A N TRP 13 1_555 covale 1.325 both A TRP 13 A C TRP 13 1_555 A DLE 14 A N DLE 14 1_555 covale 1.325 both A DLE 14 A C DLE 14 1_555 A TRP 15 A N TRP 15 1_555 covale 1.325 both A TRP 15 A C TRP 15 1_555 A ETA 16 A N ETA 16 1_555 covale 1.325 both B FVA 1 B C FVA 1 1_555 B GLY 2 B N GLY 2 1_555 covale 1.324 both B ALA 3 B C ALA 3 1_555 B DLE 4 B N DLE 4 1_555 covale 1.325 both B DLE 4 B C DLE 4 1_555 B ALA 5 B N ALA 5 1_555 covale 1.325 both B ALA 5 B C ALA 5 1_555 B DVA 6 B N DVA 6 1_555 covale 1.325 both B DVA 6 B C DVA 6 1_555 B VAL 7 B N VAL 7 1_555 covale 1.325 both B VAL 7 B C VAL 7 1_555 B DVA 8 B N DVA 8 1_555 covale 1.325 both B DVA 8 B C DVA 8 1_555 B TRP 9 B N TRP 9 1_555 covale 1.324 both B TRP 9 B C TRP 9 1_555 B DLE 10 B N DLE 10 1_555 covale 1.325 both B DLE 10 B C DLE 10 1_555 B TRP 11 B N TRP 11 1_555 covale 1.325 both B TRP 11 B C TRP 11 1_555 B DLE 12 B N DLE 12 1_555 covale 1.324 both B DLE 12 B C DLE 12 1_555 B TRP 13 B N TRP 13 1_555 covale 1.325 both B TRP 13 B C TRP 13 1_555 B DLE 14 B N DLE 14 1_555 covale 1.325 both B DLE 14 B C DLE 14 1_555 B TRP 15 B N TRP 15 1_555 covale 1.325 both B TRP 15 B C TRP 15 1_555 B ETA 16 B N ETA 16 1_555 ANTIBIOTIC ANTIBIOTIC, GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, MEMBRANE ION CHANNEL, LINEAR GRAMICIDIN NOR00243 NOR 1 NOR00243 1 16 1GRM 1 16 NOR00243 A 1 1 16 1 16 1GRM 1 16 NOR00243 B 1 1 16 2 anti-parallel A GLY 2 A GLY 2 A TRP 15 A TRP 15 B GLY 2 B GLY 2 B TRP 15 B TRP 15 BINDING SITE FOR CHAIN A OF GRAMICIDIN A Software 4 BINDING SITE FOR CHAIN B OF GRAMICIDIN A Software 4 B GLY 2 B GLY 2 4 1_555 B ALA 3 B ALA 3 4 1_555 B DLE 4 B DLE 4 4 1_555 B ALA 5 B ALA 5 4 1_555 A GLY 2 A GLY 2 4 1_555 A ALA 3 A ALA 3 4 1_555 A DLE 4 A DLE 4 4 1_555 A ALA 5 A ALA 5 4 1_555 1 P 1