Header list of 2dde.pdb file
Complete list - 6 20 Bytes
HEADER ANTIBIOTIC 27-JAN-06 2DDE TITLE STRUCTURE OF CINNAMYCIN COMPLEXED WITH LYSOPHOSPHATIDYLETHANOLAMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LANTIBIOTIC CINNAMYCIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LANTHIOPEPTIN, LANTIBIOTIC RO 09- 0198 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES GRISEOVERTICILLATUS; SOURCE 3 ORGANISM_TAXID: 68215 KEYWDS ANTIBIOTIC, IMMUNOPOTENTIATOR, ANTIMICROBIAL, ANTITUMOR, LIPID KEYWDS 2 BINDING, PHOSPHATIDYLETHANOLAMINE, LANTHIONINE, THIOESTER EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.HOSODA,M.OHYA,T.KOHNO,T.MAEDA,S.ENDO,K.WAKAMATSU REVDAT 5 06-NOV-19 2DDE 1 JRNL REMARK LINK REVDAT 4 27-JUL-11 2DDE 1 ATOM CAVEAT REMARK REVDAT 3 13-JUL-11 2DDE 1 VERSN REVDAT 2 24-FEB-09 2DDE 1 VERSN REVDAT 1 21-FEB-06 2DDE 0 JRNL AUTH K.HOSODA,M.OHYA,T.KOHNO,T.MAEDA,S.ENDO,K.WAKAMATSU JRNL TITL STRUCTURE DETERMINATION OF AN IMMUNOPOTENTIATOR PEPTIDE, JRNL TITL 2 CINNAMYCIN, COMPLEXED WITH LYSOPHOSPHATIDYLETHANOLAMINE BY JRNL TITL 3 1H-NMR1. JRNL REF J.BIOCHEM. V. 119 226 1996 JRNL REFN ISSN 0021-924X JRNL PMID 8882709 JRNL DOI 10.1093/OXFORDJOURNALS.JBCHEM.A021226 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DDE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000025283. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 10MM CINNAMYCIN-C12-LYSOPE; DMSO REMARK 210 -D6 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; PE-COSY; 2D NOESY; REMARK 210 ROESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, DADAS90 2.1, X-PLOR 3.1 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 CINNAMYCIN IS A GLOBULAR TYPE B LANTIBIOTIC. THE LANTIBIOTICS REMARK 400 ARE CHARACTERIZED BY THIOESTER AMINO ACIDS LANTHIONINE REMARK 400 AND/OR METHYLLANTHIONINE. REMARK 400 HERE, CINNAMYCIN IS REPRESENTED BY THE SEQUENCE (SEQRES) REMARK 400 REMARK 400 THE CINNAMYCIN IS POLYPEPTIDE, A MEMBER OF LANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: CINNAMYCIN REMARK 400 CHAIN: A REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: CINNAMYCIN IS A TETRACYCLIC PEPTIDE. POST REMARK 400 TRANSLATIONAL MATURATION OF LANTIBIOTICS INVOLVES REMARK 400 THE ENZYMIC CONVERSION OF THR AND SER INTO REMARK 400 DEHYDRATED AMINO ACIDS AND THE FORMATION OF REMARK 400 THIOETHER BONDS WITH CYSTEINE. THE 14-19 BETA- REMARK 400 METHYLLANTHIONINE THIOETHER BOND IS OXIDIZED TO A REMARK 400 SULFOXIDE. THE THIOETHER BONDS WITH CYSTEINE RESULT REMARK 400 IN THREE RING STRUCTURES, CROSSLINK BETWEEN SER AND REMARK 400 LYS RESULT IN THE FOURTH RING. THIS IS FOLLOWED BY REMARK 400 MEMBRANE TRANSLOCATION AND CLEAVAGE OF THE MODIFIED REMARK 400 PRECURSOR. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HB2 SER A 6 NZ LYS A 19 1.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 CYS A 1 CA - CB - SG ANGL. DEV. = 16.4 DEGREES REMARK 500 1 CYS A 5 CA - CB - SG ANGL. DEV. = 44.9 DEGREES REMARK 500 2 CYS A 5 CA - CB - SG ANGL. DEV. = 38.3 DEGREES REMARK 500 3 CYS A 1 CA - CB - SG ANGL. DEV. = 54.1 DEGREES REMARK 500 3 CYS A 5 CA - CB - SG ANGL. DEV. = 41.4 DEGREES REMARK 500 4 CYS A 1 CA - CB - SG ANGL. DEV. = 8.7 DEGREES REMARK 500 4 CYS A 5 CA - CB - SG ANGL. DEV. = 9.4 DEGREES REMARK 500 5 CYS A 1 CA - CB - SG ANGL. DEV. = 27.3 DEGREES REMARK 500 5 CYS A 5 CA - CB - SG ANGL. DEV. = 25.4 DEGREES REMARK 500 6 CYS A 1 CA - CB - SG ANGL. DEV. = 57.8 DEGREES REMARK 500 6 CYS A 5 CA - CB - SG ANGL. DEV. = 28.7 DEGREES REMARK 500 7 CYS A 1 CA - CB - SG ANGL. DEV. = 16.9 DEGREES REMARK 500 7 CYS A 5 CA - CB - SG ANGL. DEV. = 25.3 DEGREES REMARK 500 8 CYS A 1 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 8 CYS A 5 CA - CB - SG ANGL. DEV. = 16.0 DEGREES REMARK 500 9 CYS A 1 CA - CB - SG ANGL. DEV. = 32.5 DEGREES REMARK 500 9 CYS A 5 CA - CB - SG ANGL. DEV. = 11.1 DEGREES REMARK 500 10 CYS A 1 CA - CB - SG ANGL. DEV. = 29.0 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 1 DAL A 4 26.92 -147.47 REMARK 500 1 CYS A 5 103.11 60.77 REMARK 500 1 PHE A 10 -74.97 -120.24 REMARK 500 1 DBB A 11 32.65 144.60 REMARK 500 1 CYS A 14 79.29 78.49 REMARK 500 2 ARG A 2 -162.82 52.04 REMARK 500 2 DAL A 4 16.52 -147.63 REMARK 500 2 CYS A 5 91.50 50.72 REMARK 500 2 PHE A 10 -80.87 -100.14 REMARK 500 2 CYS A 14 82.85 56.62 REMARK 500 2 BH2 A 15 20.71 -140.23 REMARK 500 2 ASN A 17 73.62 -101.40 REMARK 500 2 DBB A 18 40.02 131.64 REMARK 500 3 GLN A 3 40.05 -107.58 REMARK 500 3 DAL A 4 46.57 -146.20 REMARK 500 3 CYS A 5 99.83 67.66 REMARK 500 3 PHE A 10 -80.56 -101.46 REMARK 500 3 CYS A 14 74.16 73.24 REMARK 500 4 DAL A 4 -170.03 -147.47 REMARK 500 4 PHE A 10 -83.64 -100.00 REMARK 500 4 DBB A 11 31.03 139.30 REMARK 500 4 PHE A 12 12.45 -140.52 REMARK 500 5 DAL A 4 49.23 -147.03 REMARK 500 5 CYS A 5 84.48 75.03 REMARK 500 5 PHE A 10 -72.65 -109.00 REMARK 500 5 CYS A 14 79.36 77.73 REMARK 500 5 DBB A 18 73.05 122.16 REMARK 500 6 DAL A 4 33.99 -146.83 REMARK 500 6 CYS A 5 111.82 75.08 REMARK 500 6 CYS A 14 71.72 53.38 REMARK 500 6 DBB A 18 -69.25 108.26 REMARK 500 7 DAL A 4 63.89 -92.61 REMARK 500 7 CYS A 5 73.24 79.33 REMARK 500 7 PHE A 10 -86.64 -106.64 REMARK 500 7 CYS A 14 125.91 72.77 REMARK 500 7 DBB A 18 56.22 133.45 REMARK 500 8 GLN A 3 60.09 -119.83 REMARK 500 8 DAL A 4 27.98 -146.33 REMARK 500 8 CYS A 5 91.74 73.88 REMARK 500 8 DBB A 18 99.46 154.43 REMARK 500 9 DAL A 4 38.31 -146.46 REMARK 500 9 CYS A 5 111.10 75.65 REMARK 500 9 PHE A 10 -55.58 -134.80 REMARK 500 10 ARG A 2 -167.27 57.36 REMARK 500 10 DAL A 4 176.68 -147.04 REMARK 500 10 PHE A 10 -90.43 -106.05 REMARK 500 10 CYS A 14 147.73 60.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 2 0.28 SIDE CHAIN REMARK 500 2 ARG A 2 0.12 SIDE CHAIN REMARK 500 3 ARG A 2 0.30 SIDE CHAIN REMARK 500 4 ARG A 2 0.19 SIDE CHAIN REMARK 500 5 ARG A 2 0.23 SIDE CHAIN REMARK 500 6 ARG A 2 0.22 SIDE CHAIN REMARK 500 8 ARG A 2 0.19 SIDE CHAIN REMARK 500 9 ARG A 2 0.31 SIDE CHAIN REMARK 500 10 ARG A 2 0.30 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LSP A 100 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN A OF LANTIBIOTIC REMARK 800 CINNAMYCIN REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AJ1 RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE LANTIBIOTIC ACTAGARDINE REMARK 900 RELATED ID: 1MQX RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN IN MEOH/H2O REMARK 900 MIXTURE REMARK 900 RELATED ID: 1MQY RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN IN DPC MICELLES REMARK 900 RELATED ID: 1MQZ RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF TYPE B LANTIBIOTICS MERSACIDIN BOUND TO LIPID REMARK 900 II IN DPC MICELLES REMARK 900 RELATED ID: 1QOW RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE TUPE B LANTIBIOTIC MERSACIDIN REMARK 900 RELATED ID: 1W9N RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE LANTIBIOTIC EPILANCIN 15X REMARK 900 RELATED ID: 1WCO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF NISIN AND LIPID II COMPLEX REMARK 900 RELATED ID: 2KTN RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LCH-ALPHA PEPTIDE FROM TWO-COMPONENT REMARK 900 LANTIBIOTIC SYSTEM LICHENICIDIN VK21 A1 REMARK 900 RELATED ID: 2KTO RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF LCH-BETA PEPTIDE FROM TWO-COMPONENT REMARK 900 LANTIBIOTIC LICHENICIDIN VK21 A2 DBREF 2DDE A 1 19 UNP P29827 CINA_STRGV 60 78 SEQRES 1 A 19 CYS ARG GLN DAL CYS SER PHE GLY PRO PHE DBB PHE VAL SEQRES 2 A 19 CYS BH2 GLY ASN DBB LYS MODRES 2DDE DAL A 4 SER POST-TRANSLATIONAL MODIFICATION MODRES 2DDE DBB A 11 THR POST-TRANSLATIONAL MODIFICATION MODRES 2DDE BH2 A 15 ASP POST-TRANSLATIONAL MODIFICATION MODRES 2DDE DBB A 18 THR POST-TRANSLATIONAL MODIFICATION HET DAL A 4 9 HET DBB A 11 12 HET BH2 A 15 13 HET DBB A 18 12 HET LSP A 100 31 HETNAM DAL D-ALANINE HETNAM DBB D-ALPHA-AMINOBUTYRIC ACID HETNAM BH2 (3R)-3-HYDROXY-L-ASPARTIC ACID HETNAM LSP (7S)-4,7-DIHYDROXY-10-OXO-3,5,9-TRIOXA-4- HETNAM 2 LSP PHOSPHAUNDECAN-1-AMINIUM 4-OXIDE HETSYN LSP 1-ACETYL-2-LYSO-SN-GLYCERO-3-PHOSPHOETHANOLAMINE FORMUL 1 DAL C3 H7 N O2 FORMUL 1 DBB 2(C4 H9 N O2) FORMUL 1 BH2 C4 H7 N O5 FORMUL 2 LSP C7 H17 N O7 P 1+ LINK SG CYS A 1 CB DBB A 18 1555 1555 1.81 LINK C GLN A 3 N DAL A 4 1555 1555 1.31 LINK CB DAL A 4 SG CYS A 14 1555 1555 1.81 LINK C DAL A 4 N CYS A 5 1555 1555 1.31 LINK SG CYS A 5 CB DBB A 11 1555 1555 1.81 LINK CB SER A 6 NZ LYS A 19 1555 1555 1.49 LINK C PHE A 10 N DBB A 11 1555 1555 1.31 LINK C DBB A 11 N PHE A 12 1555 1555 1.31 LINK C CYS A 14 N BH2 A 15 1555 1555 1.31 LINK C BH2 A 15 N GLY A 16 1555 1555 1.31 LINK C ASN A 17 N DBB A 18 1555 1555 1.31 LINK C DBB A 18 N LYS A 19 1555 1555 1.30 SITE 1 AC1 5 CYS A 5 GLY A 8 PRO A 9 VAL A 13 SITE 2 AC1 5 BH2 A 15 SITE 1 AC2 1 LSP A 100 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
Complete list - 6 20 Bytes