1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Townsley, L.E. Hinton, J.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 Univ. Arkansas,USA. (Thesis) Phd Thesis The Three-Dimensional Structure of Gramicidin Analogs in Micellar Environments Determined Using Two-Dimensional Nuclear Magnetic Resonance Spectroscopic Techniques 2000 10.2210/pdb1nrm/pdb pdb_00001nrm 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 SINGLE WAVELENGTH M x-ray 1 1.0 1882.294 GRAMICIDIN A 2 nat 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 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 Atomic model Data collection Database references Derived calculations 1 0 2003-02-04 1 1 2011-06-14 1 2 2011-07-13 1 3 2011-07-27 1 4 2012-12-12 2 0 2023-11-15 _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 THE GRAMICIDIN A 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 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 RCSB Y RCSB 2003-01-25 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 A 65MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED. 1 2D NOESY 4.0 AMBIENT 328 K THE STRUCTURE WAS MODELED USING 705 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS NUMBER OF CONSTRAINTS FOR THE DIMER. 100 STRUCTURES WERE GENERATED USING DSPACE, OF WHICH THE 10 WITH THE FEWEST VIOLATIONS FROM THE DISTANCE CONSTRAINTS WERE CHOSEN FOR THE AVERAGE STRUCTURE. THIS AVERAGE STRUCTURE WAS FURTHER REFINED BY CONSTRAINED MINIMIZATION WITH DISCOVER USING THE ALL-ATOM AMBER FORCE FIELD AND A DIELECTRIC CONSTANT OF 2.0 TO EMULATE THAT OF THE MICELLE INTERIOR. DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION minimized average structure 3.06MM GRAMICIDIN A ~20MM DODECYL PHOSPHOCHOLINE 90% PH 4.0 POTASSIUM BIPHTHALATE BUFFER, 10% D2O BIOSYM/MSI refinement DISCOVER 97.2 structure solution VNMR 3.2 structure solution FELIX 95.0 structure solution DSPACE 4.0 500 Varian VXRS 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 author_and_software_defined_assembly PISA 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 minimized average Gramicidin A in Dodecyl Phosphocholine Micelles (NMR) 1 N N 1 N N covale 1.340 both A FVA 1 A C FVA 1 1_555 A GLY 2 A N GLY 2 1_555 covale 1.339 both A ALA 3 A C ALA 3 1_555 A DLE 4 A N DLE 4 1_555 covale 1.337 both A DLE 4 A C DLE 4 1_555 A ALA 5 A N ALA 5 1_555 covale 1.339 both A ALA 5 A C ALA 5 1_555 A DVA 6 A N DVA 6 1_555 covale 1.341 both A DVA 6 A C DVA 6 1_555 A VAL 7 A N VAL 7 1_555 covale 1.342 both A VAL 7 A C VAL 7 1_555 A DVA 8 A N DVA 8 1_555 covale 1.339 both A DVA 8 A C DVA 8 1_555 A TRP 9 A N TRP 9 1_555 covale 1.341 both A TRP 9 A C TRP 9 1_555 A DLE 10 A N DLE 10 1_555 covale 1.340 both A DLE 10 A C DLE 10 1_555 A TRP 11 A N TRP 11 1_555 covale 1.341 both A TRP 11 A C TRP 11 1_555 A DLE 12 A N DLE 12 1_555 covale 1.341 both A DLE 12 A C DLE 12 1_555 A TRP 13 A N TRP 13 1_555 covale 1.343 both A TRP 13 A C TRP 13 1_555 A DLE 14 A N DLE 14 1_555 covale 1.340 both A DLE 14 A C DLE 14 1_555 A TRP 15 A N TRP 15 1_555 covale 1.340 both A TRP 15 A C TRP 15 1_555 A ETA 16 A N ETA 16 1_555 covale 1.341 both B FVA 1 B C FVA 1 1_555 B GLY 2 B N GLY 2 1_555 covale 1.340 both B ALA 3 B C ALA 3 1_555 B DLE 4 B N DLE 4 1_555 covale 1.337 both B DLE 4 B C DLE 4 1_555 B ALA 5 B N ALA 5 1_555 covale 1.340 both B ALA 5 B C ALA 5 1_555 B DVA 6 B N DVA 6 1_555 covale 1.340 both B DVA 6 B C DVA 6 1_555 B VAL 7 B N VAL 7 1_555 covale 1.340 both B VAL 7 B C VAL 7 1_555 B DVA 8 B N DVA 8 1_555 covale 1.338 both B DVA 8 B C DVA 8 1_555 B TRP 9 B N TRP 9 1_555 covale 1.341 both B TRP 9 B C TRP 9 1_555 B DLE 10 B N DLE 10 1_555 covale 1.340 both B DLE 10 B C DLE 10 1_555 B TRP 11 B N TRP 11 1_555 covale 1.341 both B TRP 11 B C TRP 11 1_555 B DLE 12 B N DLE 12 1_555 covale 1.342 both B DLE 12 B C DLE 12 1_555 B TRP 13 B N TRP 13 1_555 covale 1.343 both B TRP 13 B C TRP 13 1_555 B DLE 14 B N DLE 14 1_555 covale 1.340 both B DLE 14 B C DLE 14 1_555 B TRP 15 B N TRP 15 1_555 covale 1.339 both B TRP 15 B C TRP 15 1_555 B ETA 16 B N ETA 16 1_555 ANTIBIOTIC ANTIBIOTIC, GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, ANTIBIOTICS, MEMBRANE ION CHANNEL, LINEAR GRAMICIDIN, DPC MICELLES NOR00243 NOR 1 NOR00243 1 16 1NRM 1 16 NOR00243 A 1 1 16 1 16 1NRM 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