Header list of 1t5n.pdb file
Complete list - 6 20 Bytes
HEADER ANTIBIOTIC 04-MAY-04 1T5N
TITLE STRUCTURAL TRANSITIONS AS DETERMINANTS OF CALCIUM-DEPENDENT ANTIBIOTIC
TITLE 2 DAPTOMYCIN
CAVEAT 1T5N THR A 5 C-BETA WRONG HAND IN ALL MODELS, THR A 5 C-ALPHA
CAVEAT 2 1T5N WRONG HAND IN ALL MODELS, LME A 13 C-BETA WRONG HAND IN ALL
CAVEAT 3 1T5N MODELS, KYN A 14 C-ALPHA WRONG HAND IN ALL MODELS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DAPTOMYCIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: A21978C, CUBICIN;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: STREPTOMYCES ROSEOSPORUS;
SOURCE 4 ORGANISM_TAXID: 67294
KEYWDS DAPTOMYCIN, CUBICIN, ANTIBIOTIC, LIPOPEPTIDE, CALCIUM-DEPENDENT
EXPDTA SOLUTION NMR
NUMMDL 17
AUTHOR D.JUNG,A.ROZEK,M.OKON,R.E.HANCOCK
REVDAT 5 06-NOV-19 1T5N 1 REMARK LINK
REVDAT 4 27-JUL-11 1T5N 1 ATOM CAVEAT REMARK
REVDAT 3 13-JUL-11 1T5N 1 VERSN
REVDAT 2 24-FEB-09 1T5N 1 VERSN
REVDAT 1 31-AUG-04 1T5N 0
JRNL AUTH D.JUNG,A.ROZEK,M.OKON,R.E.HANCOCK
JRNL TITL STRUCTURAL TRANSITIONS AS DETERMINANTS OF THE ACTION OF THE
JRNL TITL 2 CALCIUM-DEPENDENT ANTIBIOTIC DAPTOMYCIN.
JRNL REF CHEM.BIOL. V. 11 949 2004
JRNL REFN ISSN 1074-5521
JRNL PMID 15271353
JRNL DOI 10.1016/J.CHEMBIOL.2004.04.020
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DGII MODULE OF INSIGHT II VER. 97.2
REMARK 3 AUTHORS : ACCYLRYS INC.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 1T5N COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-04.
REMARK 100 THE DEPOSITION ID IS D_1000022342.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308.15
REMARK 210 PH : 6.7
REMARK 210 IONIC STRENGTH : 100MM KCL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2MM DAPTOMYCIN, 100MM KCL, 5MM
REMARK 210 CACL2, 0.2MM EDTA, 93% H2O, 7%
REMARK 210 D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY; INOVA
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : DGII MODULE OF INSIGHT II VER.
REMARK 210 97.2, NMRPIPE 1, NMRDRAW 5.0.4
REMARK 210 METHOD USED : NULL
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D
REMARK 210 HOMONUCLEAR TECHNIQUES.
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
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 DAPTOMYCIN IS A CYCLIC TRIDECAMER LIPOPETIDE.
REMARK 400 HERE, DAPTOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE
REMARK 400 SEQUENCE (SEQRES) AND ONE LIGAND (HET) DKA.
REMARK 400
REMARK 400 THE DAPTOMYCIN IS CYCLIC LIPOPEPTIDE, A MEMBER OF ANTIBIOTIC CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: DAPTOMYCIN
REMARK 400 CHAIN: A
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 COMPONENT_2: RESIDUE DKA
REMARK 400 DESCRIPTION: DAPTOMYCIN IS AN ACIDIC CYCLIC LIPOPEPTIDE. THE
REMARK 400 SCAFFOLD IS MADE OF TWO PARTS: (1) THREE RESIDUES N-
REMARK 400 TERM EXOCYCLIC PART (2) A DECAPEPTIDE LACTONE RING
REMARK 400 DERIVED FROM CYCLISATION OF THR3 SIDE CHAIN ONTO THE
REMARK 400 C-TER CARBOXYL GROUP THE N-DECANOYL FATTY ACID IS
REMARK 400 LINKED TO THE MAIN BODY OF THE MOLECULE VIA N-TERM
REMARK 400 ACYLATION.
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 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 1 DSN A 12 CB - CA - C ANGL. DEV. = 16.8 DEGREES
REMARK 500 2 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 2 DSN A 12 CB - CA - C ANGL. DEV. = 16.2 DEGREES
REMARK 500 3 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 3 DSN A 12 CB - CA - C ANGL. DEV. = 16.7 DEGREES
REMARK 500 4 TRP A 2 CB - CA - C ANGL. DEV. = 12.5 DEGREES
REMARK 500 4 DAL A 9 N - CA - CB ANGL. DEV. = 9.5 DEGREES
REMARK 500 4 DSN A 12 CB - CA - C ANGL. DEV. = 15.5 DEGREES
REMARK 500 5 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES
REMARK 500 5 DSN A 12 CB - CA - C ANGL. DEV. = 16.2 DEGREES
REMARK 500 6 DAL A 9 N - CA - CB ANGL. DEV. = 9.8 DEGREES
REMARK 500 6 DSN A 12 CB - CA - C ANGL. DEV. = 16.0 DEGREES
REMARK 500 7 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES
REMARK 500 7 DSN A 12 CB - CA - C ANGL. DEV. = 17.7 DEGREES
REMARK 500 8 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 8 DSN A 12 CB - CA - C ANGL. DEV. = 17.3 DEGREES
REMARK 500 9 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 9 DSN A 12 CB - CA - C ANGL. DEV. = 16.2 DEGREES
REMARK 500 10 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 10 DSN A 12 CB - CA - C ANGL. DEV. = 17.1 DEGREES
REMARK 500 11 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 11 DSN A 12 CB - CA - C ANGL. DEV. = 15.8 DEGREES
REMARK 500 12 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES
REMARK 500 12 DSN A 12 CB - CA - C ANGL. DEV. = 15.5 DEGREES
REMARK 500 13 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES
REMARK 500 13 DSN A 12 CB - CA - C ANGL. DEV. = 17.0 DEGREES
REMARK 500 14 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 14 DSN A 12 CB - CA - C ANGL. DEV. = 17.7 DEGREES
REMARK 500 15 DAL A 9 N - CA - CB ANGL. DEV. = 9.6 DEGREES
REMARK 500 15 DSN A 12 CB - CA - C ANGL. DEV. = 15.8 DEGREES
REMARK 500 16 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 16 DSN A 12 CB - CA - C ANGL. DEV. = 16.6 DEGREES
REMARK 500 17 DAL A 9 N - CA - CB ANGL. DEV. = 9.7 DEGREES
REMARK 500 17 DSN A 12 CB - CA - C ANGL. DEV. = 16.5 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 DSG A 3 -34.83 148.43
REMARK 500 1 ASP A 4 -112.55 -77.94
REMARK 500 1 THR A 5 96.67 117.85
REMARK 500 1 ORN A 7 106.20 -14.39
REMARK 500 1 ASP A 8 -159.43 -132.77
REMARK 500 1 DSN A 12 -172.56 54.44
REMARK 500 1 LME A 13 -172.51 -68.50
REMARK 500 2 DSG A 3 155.19 -68.20
REMARK 500 2 THR A 5 89.87 84.61
REMARK 500 2 ORN A 7 113.59 6.12
REMARK 500 2 ASP A 8 166.03 93.50
REMARK 500 3 THR A 5 82.26 91.23
REMARK 500 3 ORN A 7 -93.20 15.99
REMARK 500 3 LME A 13 -173.23 62.28
REMARK 500 4 DSG A 3 81.67 -10.65
REMARK 500 4 THR A 5 68.73 89.02
REMARK 500 4 ORN A 7 -137.64 16.35
REMARK 500 4 ASP A 10 -71.38 -56.79
REMARK 500 5 DSG A 3 172.13 -103.23
REMARK 500 5 THR A 5 99.27 122.95
REMARK 500 5 ORN A 7 121.64 -1.57
REMARK 500 5 ASP A 8 -163.14 92.89
REMARK 500 6 DSG A 3 86.81 95.87
REMARK 500 6 THR A 5 86.91 97.66
REMARK 500 6 ORN A 7 94.15 -58.72
REMARK 500 6 DSN A 12 81.22 138.08
REMARK 500 7 DSG A 3 -102.70 -102.08
REMARK 500 7 THR A 5 97.49 123.93
REMARK 500 7 ASP A 8 167.40 95.85
REMARK 500 7 DSN A 12 121.43 121.37
REMARK 500 8 THR A 5 98.14 116.54
REMARK 500 8 ORN A 7 126.96 -4.57
REMARK 500 8 ASP A 8 124.58 100.66
REMARK 500 9 DSG A 3 100.09 104.72
REMARK 500 9 THR A 5 64.45 76.30
REMARK 500 9 ORN A 7 -89.70 -61.21
REMARK 500 9 DAL A 9 -123.00 -179.75
REMARK 500 9 DSN A 12 93.12 147.56
REMARK 500 9 LME A 13 161.89 85.50
REMARK 500 10 DSG A 3 167.23 -123.90
REMARK 500 10 THR A 5 98.13 97.75
REMARK 500 10 ORN A 7 -78.32 -23.01
REMARK 500 10 ASP A 10 -21.98 -173.56
REMARK 500 10 DSN A 12 111.06 117.02
REMARK 500 11 DSG A 3 177.95 -98.09
REMARK 500 11 THR A 5 95.24 84.43
REMARK 500 12 THR A 5 74.83 130.15
REMARK 500 12 ASP A 8 -158.20 -93.31
REMARK 500 13 DSG A 3 60.50 -123.67
REMARK 500 13 THR A 5 102.73 136.00
REMARK 500
REMARK 500 THIS ENTRY HAS 68 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 DSN A 12 LME A 13 2 -149.93
REMARK 500 TRP A 2 DSG A 3 4 143.88
REMARK 500 DSN A 12 LME A 13 4 -147.82
REMARK 500 TRP A 2 DSG A 3 5 -144.00
REMARK 500 DSN A 12 LME A 13 6 -30.20
REMARK 500 DSN A 12 LME A 13 8 -31.19
REMARK 500 DSN A 12 LME A 13 9 147.64
REMARK 500 DSN A 12 LME A 13 10 30.59
REMARK 500 TRP A 2 DSG A 3 11 -147.98
REMARK 500 DSN A 12 LME A 13 12 -148.93
REMARK 500 DSN A 12 LME A 13 13 32.51
REMARK 500 DSN A 12 LME A 13 14 -30.34
REMARK 500 DSN A 12 LME A 13 16 148.07
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1XT7 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE ANTIBIOTIC DAPTOMYCIN
REMARK 900 RELATED ID: 1T5M RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE CALCIUM-DEPENDENT ANTIBIOTIC DAPTOMYCIN
DBREF 1T5N A 2 14 NOR NOR00001 NOR00001 2 14
SEQRES 1 A 13 TRP DSG ASP THR GLY ORN ASP DAL ASP GLY DSN LME KYN
HET DSG A 3 14
HET ORN A 7 19
HET DAL A 9 10
HET DSN A 12 11
HET LME A 13 18
HET KYN A 14 24
HET DKA A 1 30
HETNAM DSG D-ASPARAGINE
HETNAM ORN L-ORNITHINE
HETNAM DAL D-ALANINE
HETNAM DSN D-SERINE
HETNAM LME (2S,3R)-2-AZANYL-3-METHYL-PENTANEDIOIC ACID
HETNAM KYN (2S)-2-AMINO-4-(2-AMINOPHENYL)-4-OXOBUTANOIC ACID
HETNAM DKA DECANOIC ACID
HETSYN LME (3R)-3-METHYL-L-GLUTAMIC ACID
HETSYN KYN L-KYNURENINE
FORMUL 1 DSG C4 H8 N2 O3
FORMUL 1 ORN C5 H12 N2 O2
FORMUL 1 DAL C3 H7 N O2
FORMUL 1 DSN C3 H7 N O3
FORMUL 1 LME C6 H11 N O4
FORMUL 1 KYN C10 H12 N2 O3
FORMUL 2 DKA C10 H20 O2
LINK C1 DKA A 1 N TRP A 2 1555 1555 1.35
LINK C TRP A 2 N DSG A 3 1555 1555 1.35
LINK C DSG A 3 N ASP A 4 1555 1555 1.35
LINK OG1 THR A 5 C KYN A 14 1555 1555 1.39
LINK C GLY A 6 N ORN A 7 1555 1555 1.35
LINK C ORN A 7 N ASP A 8 1555 1555 1.35
LINK C ASP A 8 N DAL A 9 1555 1555 1.35
LINK C DAL A 9 N ASP A 10 1555 1555 1.35
LINK C GLY A 11 N DSN A 12 1555 1555 1.35
LINK C DSN A 12 N LME A 13 1555 1555 1.35
LINK C LME A 13 N KYN A 14 1555 1555 1.35
CISPEP 1 ORN A 7 ASP A 8 1 21.71
CISPEP 2 DSN A 12 LME A 13 1 -28.55
CISPEP 3 GLY A 11 DSN A 12 2 -24.71
CISPEP 4 GLY A 11 DSN A 12 3 -23.70
CISPEP 5 DSN A 12 LME A 13 3 -29.37
CISPEP 6 GLY A 11 DSN A 12 6 23.75
CISPEP 7 DSG A 3 ASP A 4 7 -29.17
CISPEP 8 DSN A 12 LME A 13 7 -26.38
CISPEP 9 DSG A 3 ASP A 4 8 -21.35
CISPEP 10 ORN A 7 ASP A 8 12 25.02
CISPEP 11 GLY A 11 DSN A 12 16 28.61
CISPEP 12 DSN A 12 LME A 13 17 15.53
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