HEADER SURFACTANT PROTEIN 21-FEB-24 8S4L TITLE NMR STRUCTURE OF ORFAMIDE A IN MICELLAR DPC SOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ORFAMIDE A; COMPND 3 CHAIN: A; COMPND 4 OTHER_DETAILS: 1) THE POLYPEPTIDE CHAIN OF ORFAMIDE A CONSISTS OF 10 COMPND 5 AMINO ACIDS. 2) THE N-TERMINAL AMINO ACID (DLE) IS ACYLATED WITH AN COMPND 6 (R)-3-HYDROXY-TETRADECANOIC ACID MOEITY (FTT) WHICH IS INDICATED AS COMPND 7 THE FIRST RESIDUE. 3) THE DEPSI (ESTER) BOND IS ESTABLISHED BETWEEN COMPND 8 THE VAL11 CARBOXYL AND 2TL4 SIDE-CHAIN OH GROUP. 4) THERE ARE 2 AMINO COMPND 9 ACIDS WITH UNUSUAL SIDE-CHAIN CONFIGURATIONS, D-ALLO-ILE5 (28J) AND COMPND 10 D-ALLO-THR4 (2TL4). SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS PROTEGENS; SOURCE 3 ORGANISM_TAXID: 220664 KEYWDS NON-RIBOSOMAL POLIPEPTIDE, CYCLIC LIPODEPSIPE, ANTIMICROBIAL PEPTIDE, KEYWDS 2 BIOSURFACTANT, SURFACTANT PROTEIN EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR B.KOVACS,N.GEUDENS,J.C.MARTINS REVDAT 2 14-JAN-26 8S4L 1 JRNL REVDAT 1 26-FEB-25 8S4L 0 JRNL AUTH B.KOVACS,D.PRASAD,V.DE ROO,M.VANHEEDE,P.MUANGKAEW,A.MADDER, JRNL AUTH 2 M.HOFTE,R.DE MOT,N.GEUDENS,J.C.MARTINS JRNL TITL HIGHER-LEVEL STRUCTURAL CLASSIFICATION OF PSEUDOMONAS CYCLIC JRNL TITL 2 LIPOPEPTIDES THROUGH THEIR BIOACTIVE CONFORMATION. JRNL REF ADV SCI 20365 2025 JRNL REFN ESSN 2198-3844 JRNL PMID 41391051 JRNL DOI 10.1002/ADVS.202520365 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE LOWEST ENERGY NMR STRUCTURE ISSUED REMARK 3 FROM CNS WAS REFINED USING UNRESTRAINED AMBER MOLECULAR DYNAMICS REMARK 3 SIMULATIONS (AGAINST THE FF14SB FORCE FIELD). HERE, WE MODELLED REMARK 3 THE INTERACTION OF A SINGLE PEPTIDE MOLECULE WITH AN EXPLICIT REMARK 3 DODECYLPHOSPHOCHOLINE (DPC) MICELLE. THE REPRESENTATIVE PEPTIDE REMARK 3 CONFORMATION OF THE TRAJECTORY (=REFINED STRUCTURE) WAS SELECTED REMARK 3 USING CLUSTER ANALYSIS. SOLVENT MODEL: TIP3P REMARK 4 REMARK 4 8S4L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-FEB-24. REMARK 100 THE DEPOSITION ID IS D_1292135425. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 26 (BUFFER ONLY) REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.9 MM ORFAMIDE A, 111.9 MM [U REMARK 210 -2H] DPC, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D 1H-1H TOCSY; 2D 1H REMARK 210 -1H COSY; 2D 1H-13C HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBERTOOLS, TOPSPIN, CCPNMR REMARK 210 ANALYSIS, CNS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 CYCLIC LIPOPEPTIDE WITH ANTIFUNGAL ACTIVITY REMARK 400 REMARK 400 THE ORFAMIDE A IS LIPOPEPTIDE, A MEMBER OF CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: ORFAMIDE A REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 COMPONENT_2: RESIDUE FTT REMARK 400 DESCRIPTION: Cyclic lipopeptide REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 2 LEU A 8 -38.84 -152.98 REMARK 500 4 LEU A 8 -28.02 -144.01 REMARK 500 7 LEU A 8 17.26 -145.54 REMARK 500 8 LEU A 8 -33.69 -142.35 REMARK 500 9 LEU A 7 33.40 -140.41 REMARK 500 9 LEU A 8 -28.19 -142.29 REMARK 500 11 LEU A 8 17.28 -145.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34905 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF ORFAMIDE A IN MICELLAR DPC SOLUTION DBREF 8S4L A 1 10 PDB 8S4L 8S4L 1 10 SEQRES 1 A 10 LEU DGL 2TL 28J DLE DSN LEU LEU DSN VAL HET DGL A 2 15 HET 2TL A 3 13 HET 28J A 4 19 HET DLE A 5 19 HET DSN A 6 11 HET DSN A 9 11 HET FTT A 101 43 HETNAM DGL D-GLUTAMIC ACID HETNAM 2TL D-ALLOTHREONINE HETNAM 28J D-ALLOISOLEUCINE HETNAM DLE D-LEUCINE HETNAM DSN D-SERINE HETNAM FTT 3-HYDROXY-TETRADECANOIC ACID HETSYN FTT 3-HYDROXY-MYRISTIC ACID FORMUL 1 DGL C5 H9 N O4 FORMUL 1 2TL C4 H9 N O3 FORMUL 1 28J C6 H13 N O2 FORMUL 1 DLE C6 H13 N O2 FORMUL 1 DSN 2(C3 H7 N O3) FORMUL 2 FTT C14 H28 O3 HELIX 1 AA1 LEU A 1 DSN A 6 1 6 LINK C LEU A 1 N DGL A 2 1555 1555 1.42 LINK N LEU A 1 C1 FTT A 101 1555 1555 1.35 LINK C DGL A 2 N 2TL A 3 1555 1555 1.38 LINK C 2TL A 3 N 28J A 4 1555 1555 1.35 LINK OG1 2TL A 3 C VAL A 10 1555 1555 1.34 LINK C 28J A 4 N DLE A 5 1555 1555 1.37 LINK C DLE A 5 N DSN A 6 1555 1555 1.41 LINK C DSN A 6 N LEU A 7 1555 1555 1.42 LINK C LEU A 8 N DSN A 9 1555 1555 1.39 LINK C DSN A 9 N VAL A 10 1555 1555 1.36 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL CONECT 1 163 CONECT 3 20 CONECT 20 3 21 29 CONECT 21 20 22 24 30 CONECT 22 21 23 35 CONECT 23 22 CONECT 24 21 25 31 32 CONECT 25 24 26 33 34 CONECT 26 25 27 28 CONECT 27 26 CONECT 28 26 CONECT 29 20 CONECT 30 21 CONECT 31 24 CONECT 32 24 CONECT 33 25 CONECT 34 25 CONECT 35 22 36 42 CONECT 36 35 37 40 43 CONECT 37 36 38 39 44 CONECT 38 37 148 CONECT 39 37 45 46 47 CONECT 40 36 41 48 CONECT 41 40 CONECT 42 35 CONECT 43 36 CONECT 44 37 CONECT 45 39 CONECT 46 39 CONECT 47 39 CONECT 48 40 49 56 CONECT 49 48 50 54 57 CONECT 50 49 51 52 58 CONECT 51 50 59 60 61 CONECT 52 50 53 62 63 CONECT 53 52 64 65 66 CONECT 54 49 55 67 CONECT 55 54 CONECT 56 48 CONECT 57 49 CONECT 58 50 CONECT 59 51 CONECT 60 51 CONECT 61 51 CONECT 62 52 CONECT 63 52 CONECT 64 53 CONECT 65 53 CONECT 66 53 CONECT 67 54 68 75 CONECT 68 67 69 73 76 CONECT 69 68 70 77 78 CONECT 70 69 71 72 79 CONECT 71 70 80 81 82 CONECT 72 70 83 84 85 CONECT 73 68 74 86 CONECT 74 73 CONECT 75 67 CONECT 76 68 CONECT 77 69 CONECT 78 69 CONECT 79 70 CONECT 80 71 CONECT 81 71 CONECT 82 71 CONECT 83 72 CONECT 84 72 CONECT 85 72 CONECT 86 73 87 92 CONECT 87 86 88 90 93 CONECT 88 87 89 97 CONECT 89 88 CONECT 90 87 91 94 95 CONECT 91 90 96 CONECT 92 86 CONECT 93 87 CONECT 94 90 CONECT 95 90 CONECT 96 91 CONECT 97 88 CONECT 118 135 CONECT 135 118 136 141 CONECT 136 135 137 139 142 CONECT 137 136 138 146 CONECT 138 137 CONECT 139 136 140 143 144 CONECT 140 139 145 CONECT 141 135 CONECT 142 136 CONECT 143 139 CONECT 144 139 CONECT 145 140 CONECT 146 137 CONECT 148 38 CONECT 163 1 164 177 CONECT 164 163 165 179 180 CONECT 165 164 166 178 181 CONECT 166 165 167 182 183 CONECT 167 166 168 184 185 CONECT 168 167 169 186 187 CONECT 169 168 170 188 189 CONECT 170 169 171 190 191 CONECT 171 170 172 192 193 CONECT 172 171 173 194 195 CONECT 173 172 174 196 197 CONECT 174 173 175 198 199 CONECT 175 174 176 200 201 CONECT 176 175 202 203 204 CONECT 177 163 CONECT 178 165 205 CONECT 179 164 CONECT 180 164 CONECT 181 165 CONECT 182 166 CONECT 183 166 CONECT 184 167 CONECT 185 167 CONECT 186 168 CONECT 187 168 CONECT 188 169 CONECT 189 169 CONECT 190 170 CONECT 191 170 CONECT 192 171 CONECT 193 171 CONECT 194 172 CONECT 195 172 CONECT 196 173 CONECT 197 173 CONECT 198 174 CONECT 199 174 CONECT 200 175 CONECT 201 175 CONECT 202 176 CONECT 203 176 CONECT 204 176 CONECT 205 178 MASTER 114 0 7 1 0 0 0 6 91 1 137 1 END