Header list of 1tkq.pdb file
Complete list - 25 201 Bytes
HEADER ANTIBIOTIC 09-JUN-04 1TKQ
TITLE SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN IN A MEMBRANE-
TITLE 2 ISOELECTRICAL SOLVENTS MIXTURE IN THE PRESENCE OF CSCL
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: MINI-GRAMICIDIN A;
COMPND 3 CHAIN: A;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: GRAMICIDIN A;
COMPND 7 CHAIN: B;
COMPND 8 SYNONYM: VALYL GRAMICIDIN;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS;
SOURCE 4 ORGANISM_TAXID: 1393;
SOURCE 5 MOL_ID: 2;
SOURCE 6 SYNTHETIC: YES;
SOURCE 7 ORGANISM_SCIENTIFIC: BREVIBACILLUS BREVIS;
SOURCE 8 ORGANISM_TAXID: 1393
KEYWDS GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, ANTIBIOTIC, MEMBRANE ION
KEYWDS 2 CHANNEL, LINEAR GRAMICIDIN
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR X.XIE,L.AL-MOMANI,D.BOCKELMANN,C.GRIESINGER,U.KOERT
REVDAT 6 25-SEP-19 1TKQ 1 REMARK LINK ATOM
REVDAT 5 27-JUL-11 1TKQ 1 ATOM HET HETATM LINK
REVDAT 5 2 1 REMARK
REVDAT 4 13-JUL-11 1TKQ 1 VERSN
REVDAT 3 24-FEB-09 1TKQ 1 VERSN
REVDAT 2 12-APR-05 1TKQ 1 JRNL
REVDAT 1 13-JUL-04 1TKQ 0
JRNL AUTH X.XIE,L.AL-MOMANI,P.REISS,C.GRIESINGER,U.KOERT
JRNL TITL AN ASYMMETRIC ION CHANNEL DERIVED FROM GRAMICIDIN A.
JRNL TITL 2 SYNTHESIS, FUNCTION AND NMR STRUCTURE.
JRNL REF FEBS J. V. 272 975 2005
JRNL REFN ISSN 1742-464X
JRNL PMID 15691331
JRNL DOI 10.1111/J.1742-4658.2004.04531.X
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH R.R.KETCHEM,W.HU,T.A.CROSS
REMARK 1 TITL HIGH-RESOLUTION CONFORMATION OF GRAMICIDIN A IN A LIPID
REMARK 1 TITL 2 BILAYER BY SOLID-STATE NMR
REMARK 1 REF SCIENCE V. 261 1457 1993
REMARK 1 REFN ISSN 0036-8075
REMARK 1 PMID 7690158
REMARK 1 DOI 10.1126/SCIENCE.7690158
REMARK 1 REFERENCE 2
REMARK 1 AUTH Y.CHEN,A.TUCKER,B.A.WALLACE
REMARK 1 TITL SOLUTION STRUCTURE OF A PARALLEL LEFT-HANDED DOUBLE-HELICAL
REMARK 1 TITL 2 GRAMICIDIN-A DETERMINED BY 2D 1H NMR
REMARK 1 REF J.MOL.BIOL. V. 264 757 1996
REMARK 1 REFN ISSN 0022-2836
REMARK 1 PMID 8980684
REMARK 1 DOI 10.1006/JMBI.1996.0675
REMARK 1 REFERENCE 3
REMARK 1 AUTH H.-D.ARNDT,D.BOCKELMANN,A.KNOLL,S.LAMBERTH,C.GRIESINGER,
REMARK 1 AUTH 2 U.KOERT
REMARK 1 TITL CATION CONTROL IN FUNCTIONAL HELICAL PROGRAMMING: STRUCTURES
REMARK 1 TITL 2 OF A D,L-PEPTIDE ION CHANNEL
REMARK 1 REF ANGEW.CHEM.INT.ED.ENGL. V. 41 4062 2002
REMARK 1 REFN ISSN 1433-7851
REMARK 1 PMID 12412082
REMARK 1 DOI 10.1002/1521-3773(20021104)41:21<4062::AID-ANIE4062>3.0.CO;2
REMARK 1 DOI 2 -U
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SYBYL/DYANA 6.8
REMARK 3 AUTHORS : GUENTERT
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 160 NOE-
REMARK 3 DERIVED DISTANCE CONSTRAINTS, 39 DIHEDRAL ANGLE RESTRAINTS, AND
REMARK 3 40 DISTANCE RESTRAINTS FROM HYDROGEN BONDS
REMARK 4
REMARK 4 1TKQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-04.
REMARK 100 THE DEPOSITION ID IS D_1000022727.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 293
REMARK 210 PH : NULL
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : 3MM SATURATED WITH CSCL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; 2D NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : SYBYL/DYANA 6.8
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : MINIMIZED AVERAGE STRUCTURE OF
REMARK 210 11 STRUCTURES WITH THE LOWEST
REMARK 210 TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: VARIABLE TEMPERATURE EXPERIMENTS WERE PERFORMED TO HAVE
REMARK 210 THE TEMPERATURE DEPENDENCE OF NH CHEMICAL SHIFTS, THEREFORE
REMARK 210 PROVIDE EVIDENCE FOR HYDROGEN BONDING.
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: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 760 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 2810 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 6.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS
REMARK 400 INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM
REMARK 400 BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D
REMARK 400 HERE, MODIFIDED GRAMICIDIN A IS REPRESENTED BY TWO SEQUENCES (SEQRES
REMARK 400 AND ONE HET (SIN)
REMARK 400
REMARK 400 THE MINI-GRAMICIDIN A - GRAMICIDIN A DIMER IS POLYPEPTIDE, A MEMBER
REMARK 400 OF ANTIBIOTIC CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: MINI-GRAMICIDIN A - GRAMICIDIN A DIMER
REMARK 400 CHAIN: A, B
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 COMPONENT_2: PEPTIDE LIKE POLYMER
REMARK 400 COMPONENT_3: RESIDUE SIN
REMARK 400 DESCRIPTION: THE N-TERMINI OF THE TWO PEPTIDES, EACH A TRUNCATED
REMARK 400 GRAMICIDIN A, WERE LINKED BY A SUCCINIC ACID IN A
REMARK 400 HEAD-TO-HEAD MANNER.
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 TRP A 15 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES
REMARK 500 TRP B 9 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES
REMARK 500 TRP B 11 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES
REMARK 500 TRP B 13 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES
REMARK 500 TRP B 15 CE2 - CD2 - CG ANGL. DEV. = -4.9 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1TK2 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN S COMPLEXED WITH ALKALINE
REMARK 900 PROTEINASE SAVINASE
REMARK 900 RELATED ID: 2XDC RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID
REMARK 900 CUBIC PHASE.
REMARK 900 RELATED ID: 1AV2 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE
REMARK 900 RELATED ID: 1BDW RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A FROM BACILLUS BREVIS
REMARK 900 RELATED ID: 1C4D RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE
REMARK 900 RELATED ID: 1GMK RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLRXED WITH POTASSIUM
REMARK 900 THIOCYANATE
REMARK 900 RELATED ID: 1GRM RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF THE GRAMICIDIN A
REMARK 900 RELATED ID: 1JNO RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN SODIUM DODECYL SULFATE
REMARK 900 MICELLES
REMARK 900 RELATED ID: 1KQE RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A IN BENZENE/
REMARK 900 ACETONE 10:1
REMARK 900 RELATED ID: 1MAG RELATED DB: PDB
REMARK 900 SOLID STATE NMR STRUCTURE OF GRAMICIDIN A IN HYDRATED DMPC BILAYERS,
REMARK 900 RELATED ID: 1MIC RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN METHANOL IN THE PRESENCE OF
REMARK 900 CACL
REMARK 900 RELATED ID: 1NG8 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A (W15G) IN SODIUM DODECYL SULFATE
REMARK 900 MICELLES
REMARK 900 RELATED ID: 1NRM RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE
REMARK 900 MICELLES
REMARK 900 RELATED ID: 1NRU RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE
REMARK 900 MICELLES IN THE PRESENCE OF EXCESS NA+
REMARK 900 RELATED ID: 1NT5 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN A (V1F) IN SODIUM DODECYL SULFATE
REMARK 900 MICELLES
REMARK 900 RELATED ID: 1JO3 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN B IN SODIUM DODECYL SULFATE
REMARK 900 MICELLES
REMARK 900 RELATED ID: 1JO4 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF GRAMICIDIN C IN SODIUM DODECYL SULFATE
REMARK 900 MICELLES
REMARK 900 RELATED ID: 1NT6 RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE
REMARK 900 MICELLES
REMARK 900 RELATED ID: 1W5U RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL
REMARK 900 RELATED ID: 2IZQ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH KI IN METHANOL
REMARK 900 RELATED ID: 3L8L RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI
REMARK 900 RELATED ID: 1AL4 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN N-PROPANOL
REMARK 900 RELATED ID: 1ALX RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN METHANOL
REMARK 900 RELATED ID: 1ALZ RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 BOTH OF THE C-TERMINI HAVE ETHANOLAMINE ATTACHED WITH
REMARK 999 THE CAPPING GROUP T-BUTYLDIPHENYLSILYL, WHICH WAS APPLIED
REMARK 999 TO ENHANCE THE SOLUBILITY AND STABILITY OF THE STRUCTURE
REMARK 999 IN ORGANIC SOLVENTS. OWING TO AMBIGUITY IN RESONANCE
REMARK 999 ASSIGNMENT OF THE TERMINI AND THEREFORE A LACK OF ENOUGH
REMARK 999 NOE CONSTRAINTS, THE T-BUTYLDIPHENYLSILYL TERMINI WERE
REMARK 999 OMITTED IN THE STRUCTURE CALCULATION.
DBREF 1TKQ A 5 15 NOR NOR00243 NOR00243 5 15
DBREF 1TKQ B 1 15 NOR NOR00243 NOR00243 1 15
SEQRES 1 A 11 ALA DVA VAL DVA TRP DLE TRP DLE TRP DLE TRP
SEQRES 1 B 15 VAL GLY ALA DLE ALA DVA VAL DVA TRP DLE TRP DLE TRP
SEQRES 2 B 15 DLE TRP
HET DVA A 6 15
HET DVA A 8 15
HET DLE A 10 19
HET DLE A 12 19
HET DLE A 14 19
HET DLE B 4 19
HET DVA B 6 15
HET DVA B 8 15
HET DLE B 10 19
HET DLE B 12 19
HET DLE B 14 19
HET SIN B 101 8
HETNAM DVA D-VALINE
HETNAM DLE D-LEUCINE
HETNAM SIN SUCCINIC ACID
FORMUL 1 DVA 4(C5 H11 N O2)
FORMUL 1 DLE 7(C6 H13 N O2)
FORMUL 3 SIN C4 H6 O4
SHEET 1 AA 3 DLE A 12 TRP A 15 0
SHEET 2 AA 3 DVA A 6 TRP A 9 1 O DVA A 6 N TRP A 13
SHEET 3 AA 3 GLY B 2 TRP B 15 -1 O ALA B 3 N VAL A 7
LINK C ALA A 5 N DVA A 6 1555 1555 1.36
LINK C DVA A 6 N VAL A 7 1555 1555 1.35
LINK C VAL A 7 N DVA A 8 1555 1555 1.36
LINK C DVA A 8 N TRP A 9 1555 1555 1.36
LINK C TRP A 9 N DLE A 10 1555 1555 1.36
LINK C DLE A 10 N TRP A 11 1555 1555 1.36
LINK C TRP A 11 N DLE A 12 1555 1555 1.36
LINK C DLE A 12 N TRP A 13 1555 1555 1.36
LINK C TRP A 13 N DLE A 14 1555 1555 1.36
LINK C DLE A 14 N TRP A 15 1555 1555 1.35
LINK C ALA B 3 N DLE B 4 1555 1555 1.35
LINK C DLE B 4 N ALA B 5 1555 1555 1.35
LINK C ALA B 5 N DVA B 6 1555 1555 1.36
LINK C DVA B 6 N VAL B 7 1555 1555 1.35
LINK C VAL B 7 N DVA B 8 1555 1555 1.35
LINK C DVA B 8 N TRP B 9 1555 1555 1.36
LINK C TRP B 9 N DLE B 10 1555 1555 1.35
LINK C DLE B 10 N TRP B 11 1555 1555 1.36
LINK C TRP B 11 N DLE B 12 1555 1555 1.35
LINK C DLE B 12 N TRP B 13 1555 1555 1.35
LINK C TRP B 13 N DLE B 14 1555 1555 1.35
LINK C DLE B 14 N TRP B 15 1555 1555 1.35
LINK C4 SIN B 101 N VAL B 1 1555 1555 1.35
LINK C1 SIN B 101 N ALA A 5 1555 1555 1.35
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
Complete list - 25 201 Bytes