0.067083 0.000000 0.002378 0.000000 0.038441 0.000000 0.000000 0.000000 0.031357 0.00000 0.00000 0.00000 Burkhart, B.M. Langs, D.A. Smith, G.D. Courseille, C. Precigoux, G. Hospital, M. Pangborn, W.A. Duax, W.L. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 2 90.00 92.03 90.00 14.907 26.014 31.911 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 C H4 O 32.042 METHANOL non-polymer C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE 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 C N 98 N O N 99 N H N 100 N H N 101 N H N 102 N H N 103 N N N 104 S C N 105 N C N 106 N O N 107 N C Y 108 N C Y 109 N C Y 110 N C Y 111 N N Y 112 N C Y 113 N C Y 114 N C Y 115 N C Y 116 N C N 117 N O 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 H N 125 N H N 126 N H N 127 N H N 128 N H N 129 N H N 130 N N N 131 S C N 132 N C N 133 N O N 134 N C Y 135 N C Y 136 N C Y 137 N C Y 138 N C Y 139 N C Y 140 N C N 141 N O N 142 N O N 143 N H N 144 N H N 145 N H N 146 N H N 147 N H N 148 N H N 149 N H N 150 N H N 151 N H N 152 N H N 153 N H N 154 N N N 155 S C N 156 N C N 157 N O N 158 N C N 159 N C N 160 N C N 161 N O N 162 N H N 163 N H N 164 N H N 165 N H N 166 N H N 167 N H N 168 N H N 169 N H N 170 N H N 171 N H N 172 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 sing N 98 N sing N 99 N sing N 100 N sing N 101 N sing N 102 N doub N 103 N sing N 104 N sing N 105 N sing N 106 N sing Y 107 N doub Y 108 N sing Y 109 N sing N 110 N sing Y 111 N doub Y 112 N sing Y 113 N sing N 114 N sing Y 115 N sing Y 116 N doub N 117 N sing Y 118 N doub N 119 N sing Y 120 N sing N 121 N sing N 122 N sing N 123 N sing N 124 N sing N 125 N sing N 126 N sing N 127 N sing N 128 N sing N 129 N sing N 130 N doub N 131 N sing N 132 N sing N 133 N sing N 134 N sing Y 135 N doub Y 136 N sing Y 137 N sing N 138 N sing Y 139 N doub N 140 N sing Y 141 N doub N 142 N sing Y 143 N sing N 144 N sing N 145 N sing N 146 N sing N 147 N sing N 148 N sing N 149 N sing N 150 N sing N 151 N sing N 152 N sing N 153 N sing N 154 N doub N 155 N sing N 156 N sing N 157 N sing N 158 N sing N 159 N sing N 160 N sing N 161 N sing N 162 N sing N 163 N sing N 164 N sing N 165 N sing US Biophys.J. BIOJAU 0030 0006-3495 75 2135 10.1016/S0006-3495(98)77656-8 9788907 Heterodimer Formation and Crystal Nucleation of Gramicidin D 1998 US Proc.Natl.Acad.Sci.USA PNASA6 0040 0027-8424 88 5345 10.1073/PNAS.88.12.5345 1711230 Monoclinic Uncomplexed Double-Stranded, Antiparallel, Left-Handed Beta 5.6-Helix (Increases Decreases Beta 5.6) Structure of Gramicidin A: Alternate Patterns of Helical Association and Deformation 1991 10.2210/pdb1alx/pdb pdb_00001alx 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 120 1 COLLIMATOR DIFFRACTOMETER 1990-01 ENRAF-NONIUS FAST GRAPHITE(002) M x-ray 1 1.5418 1.0 1.5418 ROTATING ANODE RIGAKU RUH2R 1859.258 GRAMICIDIN A 1 nat polymer 1882.294 GRAMICIDIN A 1 nat polymer 32.042 METHANOL 20 syn non-polymer VALYL GRAMICIDIN VALYL GRAMICIDIN no yes (FVA)GA(DLE)A(DVA)V(DVA)W(DLE)Y(DLE)W(DLE)W(ETA) VGALAVVVWLYLWLWX A polypeptide(L) no yes (FVA)GA(DLE)A(DVA)V(DVA)W(DLE)W(DLE)W(DLE)W(ETA) VGALAVVVWLWLWLWX B polypeptide(L) n n n n n n n n n n y y n n n n n n n n n n n n n n n n n n n n n sample 1393 BREVIBACILLUS BREVIS sample 1393 BREVIBACILLUS BREVIS 1 1.65 25.57 7.0 CRYSTALLIZED BY BATCH METHODS FROM A SATURATED SOLUTION OF GRAMICIDIN D IN METHANOL., PH 7.0, BATCH METHOD diffrn_detector pdbx_database_status database_2 pdbx_initial_refinement_model struct_conn struct_ref_seq_dif atom_site atom_site_anisotrop chem_comp_atom chem_comp_bond struct_conn repository Initial release Version format compliance Version format compliance Atomic model Database references Derived calculations Non-polymer description Structure summary Other Derived calculations Data collection Other Database references Derived calculations Refinement description Atomic model Data collection Derived calculations 1 0 1998-03-04 1 1 2011-06-14 1 2 2011-07-13 1 3 2011-07-27 1 4 2012-12-12 1 5 2013-02-06 1 6 2018-04-18 1 7 2023-08-02 2 0 2023-11-15 _diffrn_detector.detector _pdbx_database_status.process_site _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details _atom_site.auth_atom_id _atom_site.label_atom_id _atom_site_anisotrop.pdbx_auth_atom_id _atom_site_anisotrop.pdbx_label_atom_id _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 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 ETHANOL Y BNL 1997-06-05 REL REL MOH METHANOL 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 D IS REPRESENTED BY THE SEQUENCE (SEQRES) 1GMA PDB ENTRY 1GMA PDB experimental model Antibiotic GRAMICIDIN D IS A HEXADECAMERIC HELICAL PEPTIDE WITH ALTERNATING D,L CHARACTERISTICS. THE N-TERM IS FORMYLATED (RESIDUE 1). THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16). GRAMICIDIN D Polypeptide MOH 501 3 MOH MOH 501 A MOH 502 3 MOH MOH 502 A MOH 505 3 MOH MOH 505 A MOH 506 3 MOH MOH 506 A MOH 508 3 MOH MOH 508 A MOH 515 3 MOH MOH 515 A MOH 516 3 MOH MOH 516 A MOH 518 3 MOH MOH 518 A MOH 519 3 MOH MOH 519 A MOH 503 3 MOH MOH 503 B MOH 504 3 MOH MOH 504 B MOH 507 3 MOH MOH 507 B MOH 509 3 MOH MOH 509 B MOH 510 3 MOH MOH 510 B MOH 511 3 MOH MOH 511 B MOH 512 3 MOH MOH 512 B MOH 513 3 MOH MOH 513 B MOH 514 3 MOH MOH 514 B MOH 517 3 MOH MOH 517 B MOH 520 3 MOH MOH 520 B 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 TYR 11 y 11 TYR 11 A TRP 11 y 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 0.102 0.102 0.100 0.100 0.168 0.168 376 376 5.000 5.000 7726 author_defined_assembly 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 TRP 13 A N TRP 13 B O ALA 3 B O ALA 3 1 A A HE1 H1 TRP MOH 9 515 1.31 A 1 A B HO O MOH MOH 515 504 1.52 B 1 B A HE1 HO TRP MOH 11 519 1.26 A 1_555 2_654 1 A TRP 13 -167.58 99.32 1 A TRP 15 -153.59 89.49 1 B TRP 11 -166.98 98.04 1 B TRP 15 -157.95 75.92 1 B TRP 15 -157.95 83.62 1 B TRP 15 -157.95 84.70 0.168 0.102 0.100 1.20 100.00 3422 376 7726 5704 5.000 99.9 5% OF REFLECTIONS IN THIN RESOLUTION SHELLS. 1 FREE R-VALUE 0.000 MOLECULAR REPLACEMENT PDB ENTRY 1GMA MODIFIED ENGH AND HUBER FOR ETHANOLAMINE BASED ON SERINE ENGH AND HUBER MOEWS & KRETSINGER (G = 0.12792 U = 0.82322) 5 367.54 315.41 1.20 100.00 0 324 40 0 284 0.014 0.031 0.326 0.167 0.119 0.006 0.033 0.045 1.250 100.000 1ALX 7726 -3.000 1 85.4100 1.000 99.9 1.20 1.24 35.530 1 1.00 99.0 model building SHELXL-97 refinement SHELXL-97 data reduction ENRAF-NONIUS phasing SHELXL-97 GRAMICIDIN D FROM BACILLUS BREVIS (METHANOL SOLVATE) 1 N N 2 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N 3 N N covale 1.295 both A FVA 1 A C FVA 1 1_555 A GLY 2 A N GLY 2 1_555 covale 1.316 both A ALA 3 A C ALA 3 1_555 A DLE 4 A N DLE 4 1_555 covale 1.318 both A DLE 4 A C DLE 4 1_555 A ALA 5 A N ALA 5 1_555 covale 1.322 both A ALA 5 A C ALA 5 1_555 A DVA 6 A N DVA 6 1_555 covale 1.303 both A DVA 6 A C DVA 6 1_555 A VAL 7 A N VAL 7 1_555 covale 1.316 both A VAL 7 A C VAL 7 1_555 A DVA 8 A N DVA 8 1_555 covale 1.346 both A DVA 8 A C DVA 8 1_555 A TRP 9 A N TRP 9 1_555 covale 1.327 both A TRP 9 A C TRP 9 1_555 A DLE 10 A N DLE 10 1_555 covale 1.345 both B A DLE 10 A C DLE 10 1_555 A TRP 11 A N TRP 11 1_555 covale 1.345 both A A DLE 10 A C DLE 10 1_555 A TYR 11 A N TYR 11 1_555 covale 1.358 both A A TYR 11 A C TYR 11 1_555 A DLE 12 A N DLE 12 1_555 covale 1.358 both B A TRP 11 A C TRP 11 1_555 A DLE 12 A N DLE 12 1_555 covale 1.280 both A DLE 12 A C DLE 12 1_555 A TRP 13 A N TRP 13 1_555 covale 1.335 both A TRP 13 A C TRP 13 1_555 A DLE 14 A N DLE 14 1_555 covale 1.317 both A DLE 14 A C DLE 14 1_555 A TRP 15 A N TRP 15 1_555 covale 1.311 both A A TRP 15 A C TRP 15 1_555 A ETA 16 A N ETA 16 1_555 covale 1.320 both C A TRP 15 A C TRP 15 1_555 A ETA 16 A N ETA 16 1_555 covale 1.317 both B A TRP 15 A C TRP 15 1_555 A ETA 16 A N ETA 16 1_555 covale 1.323 both B FVA 1 B C FVA 1 1_555 B GLY 2 B N GLY 2 1_555 covale 1.314 both B ALA 3 B C ALA 3 1_555 B DLE 4 B N DLE 4 1_555 covale 1.339 both B DLE 4 B C DLE 4 1_555 B ALA 5 B N ALA 5 1_555 covale 1.318 both B ALA 5 B C ALA 5 1_555 B DVA 6 B N DVA 6 1_555 covale 1.326 both B DVA 6 B C DVA 6 1_555 B VAL 7 B N VAL 7 1_555 covale 1.327 both B VAL 7 B C VAL 7 1_555 B DVA 8 B N DVA 8 1_555 covale 1.318 both B DVA 8 B C DVA 8 1_555 B TRP 9 B N TRP 9 1_555 covale 1.333 both B TRP 9 B C TRP 9 1_555 B DLE 10 B N DLE 10 1_555 covale 1.354 both B DLE 10 B C DLE 10 1_555 B TRP 11 B N TRP 11 1_555 covale 1.321 both B TRP 11 B C TRP 11 1_555 B DLE 12 B N DLE 12 1_555 covale 1.307 both B DLE 12 B C DLE 12 1_555 B TRP 13 B N TRP 13 1_555 covale 1.317 both B TRP 13 B C TRP 13 1_555 B DLE 14 B N DLE 14 1_555 covale 1.317 both B DLE 14 B C DLE 14 1_555 B TRP 15 B N TRP 15 1_555 covale 1.332 both B B TRP 15 B C TRP 15 1_555 B ETA 16 B N ETA 16 1_555 covale 1.341 both C B TRP 15 B C TRP 15 1_555 B ETA 16 B N ETA 16 1_555 covale 1.340 both A B TRP 15 B C TRP 15 1_555 B ETA 16 B N ETA 16 1_555 ANTIBIOTIC ANTIBIOTIC, GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, ABTIBIOTIC, MEMBRANE ION CHANNEL, LINEAR GRAMICIDIN given 0.968610 0.175300 -0.176240 0.178140 -0.984010 0.000300 -0.173370 -0.031690 -0.984350 -0.39000 -1.54000 -6.71000 NOR00243 NOR 1 NOR00243 NOR00243 NOR 2 NOR00243 1 16 1ALX 1 16 NOR00243 A 1 1 16 1 16 1ALX 1 16 NOR00243 B 2 1 16 1 TRP microheterogeneity TYR 11 1ALX A NOR00243 NOR 11 11 2 anti-parallel A GLY 2 A GLY 2 A DLE 14 A DLE 14 B GLY 2 B GLY 2 B DLE 14 B DLE 14 BINDING SITE FOR CHAIN A OF GRAMICIDIN A Software 19 BINDING SITE FOR CHAIN B OF GRAMICIDIN A Software 21 B GLY 2 B GLY 2 19 1_554 B GLY 2 B GLY 2 19 1_555 B ALA 3 B ALA 3 19 1_555 B DLE 4 B DLE 4 19 1_555 B ALA 5 B ALA 5 19 1_555 B DVA 6 B DVA 6 19 1_555 B VAL 7 B VAL 7 19 1_555 B DVA 8 B DVA 8 19 1_555 B TRP 9 B TRP 9 19 1_555 B DLE 10 B DLE 10 19 1_455 B DLE 10 B DLE 10 19 1_555 B TRP 11 B TRP 11 19 1_555 B DLE 12 B DLE 12 19 1_555 B TRP 13 B TRP 13 19 1_655 B TRP 13 B TRP 13 19 1_555 B DLE 14 B DLE 14 19 1_555 B TRP 15 B TRP 15 19 1_555 B ETA 16 B ETA 16 19 1_556 B ETA 16 B ETA 16 19 1_555 A GLY 2 A GLY 2 21 1_556 A GLY 2 A GLY 2 21 1_555 A ALA 3 A ALA 3 21 1_556 A ALA 3 A ALA 3 21 1_555 A DLE 4 A DLE 4 21 1_556 A DLE 4 A DLE 4 21 1_555 A ALA 5 A ALA 5 21 1_455 A ALA 5 A ALA 5 21 1_555 A DVA 6 A DVA 6 21 1_555 A VAL 7 A VAL 7 21 1_555 A VAL 7 A VAL 7 21 1_655 A DVA 8 A DVA 8 21 1_555 A TRP 9 A TRP 9 21 1_555 A DLE 10 A DLE 10 21 1_555 A TYR 11 A TYR 11 21 1_555 A DLE 12 A DLE 12 21 1_555 A TRP 13 A TRP 13 21 1_555 A DLE 14 A DLE 14 21 1_555 A TRP 15 A TRP 15 21 1_555 A ETA 16 A ETA 16 21 1_554 A ETA 16 A ETA 16 21 1_555 4 P 1 21 1