Header list of 2gkd.pdb file
Complete list - 9 20 Bytes
HEADER TOXIN/DNA 01-APR-06 2GKD TITLE STRUCTURAL INSIGHT INTO SELF-SACRIFICE MECHANISM OF ENEDIYNE TITLE 2 RESISTANCE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*AP*TP*AP*TP*GP*AP*TP*AP*G)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*CP*TP*AP*TP*CP*AP*TP*AP*TP*GP*C)-3'; COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: CALC; COMPND 11 CHAIN: A; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: MICROMONOSPORA ECHINOSPORA; SOURCE 7 ORGANISM_TAXID: 1877; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS START DOMAIN PROTEIN, TOXIN-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR S.SINGH,J.S.THORSON REVDAT 4 09-MAR-22 2GKD 1 REMARK REVDAT 3 31-MAR-09 2GKD 1 REMARK REVDAT 2 24-FEB-09 2GKD 1 VERSN REVDAT 1 22-AUG-06 2GKD 0 JRNL AUTH S.SINGH,M.H.HAGER,C.ZHANG,B.R.GRIFFITH,M.S.LEE,K.HALLENGA, JRNL AUTH 2 J.L.MARKLEY,J.S.THORSON JRNL TITL STRUCTURAL INSIGHT INTO THE SELF-SACRIFICE MECHANISM OF JRNL TITL 2 ENEDIYNE RESISTANCE. JRNL REF ACS CHEM.BIOL. V. 1 451 2006 JRNL REFN ISSN 1554-8929 JRNL PMID 17168523 JRNL DOI 10.1021/CB6002898 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, HADDOCK 1.1 REMARK 3 AUTHORS : BRUNGER A.T. (CNS), BONVIN, AMJJ (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037226. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : U-15N, CALC, 50MM PHOSPHATE REMARK 210 BUFFER, 150 MM NACL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, DOCKING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 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: NMR CHEMICAL SHIFT PERTURBATION INFORMATION WAS USED FOR REMARK 210 DOCKING. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C, 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 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 HD3 LYS A 39 H VAL A 40 1.26 REMARK 500 OE2 GLU A 55 HE2 HIS A 63 1.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DA B 10 O3' DA B 10 C3' -0.047 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 DT B 4 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DA B 5 O3' - P - OP2 ANGL. DEV. = -16.8 DEGREES REMARK 500 DA B 5 O3' - P - OP1 ANGL. DEV. = 20.8 DEGREES REMARK 500 DA B 5 O4' - C4' - C3' ANGL. DEV. = -2.6 DEGREES REMARK 500 DT B 9 O4' - C1' - N1 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA B 10 O4' - C1' - C2' ANGL. DEV. = 3.0 DEGREES REMARK 500 DG B 11 O5' - P - OP1 ANGL. DEV. = -5.9 DEGREES REMARK 500 DT C 15 O3' - P - OP1 ANGL. DEV. = 11.6 DEGREES REMARK 500 DA C 17 N1 - C6 - N6 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA C 17 C5 - C6 - N6 ANGL. DEV. = -5.4 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 ASP A 15 165.55 141.65 REMARK 500 TRP A 31 21.19 -142.00 REMARK 500 PHE A 35 46.77 -74.51 REMARK 500 LYS A 39 -146.37 -146.02 REMARK 500 PRO A 43 66.69 -69.40 REMARK 500 LEU A 44 -85.71 -174.77 REMARK 500 HIS A 63 133.60 -31.41 REMARK 500 ASP A 72 63.50 -101.64 REMARK 500 GLU A 73 -170.39 48.27 REMARK 500 PRO A 74 84.12 -60.36 REMARK 500 ASP A 75 -70.00 -172.86 REMARK 500 ARG A 82 149.58 -177.78 REMARK 500 LEU A 83 -159.99 -138.86 REMARK 500 PHE A 86 -152.54 -130.87 REMARK 500 PRO A 91 41.57 -67.41 REMARK 500 SER A 94 -48.44 68.12 REMARK 500 SER A 95 87.25 29.33 REMARK 500 GLN A 106 19.60 58.09 REMARK 500 LYS A 107 14.17 -142.40 REMARK 500 HIS A 117 -69.45 -175.12 REMARK 500 MET A 121 4.56 -60.90 REMARK 500 THR A 123 -93.19 82.37 REMARK 500 ALA A 153 -53.55 -172.56 REMARK 500 LYS A 154 -64.92 -91.52 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 DA B 10 0.15 SIDE CHAIN REMARK 500 DA C 17 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.79751 RELATED DB: TARGETDB REMARK 900 RELATED ID: 1ZXF RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF CALC REMARK 900 RELATED ID: 2GKC RELATED DB: PDB REMARK 900 STRUCTURE OF CALC-CALICHEAMICIN DBREF 2GKD A 1 155 UNP Q8KNF0 Q8KNF0_MICEC 27 181 DBREF 2GKD B 1 11 PDB 2GKD 2GKD 1 11 DBREF 2GKD C 12 22 PDB 2GKD 2GKD 12 22 SEQRES 1 B 11 DG DC DA DT DA DT DG DA DT DA DG SEQRES 1 C 11 DC DT DA DT DC DA DT DA DT DG DC SEQRES 1 A 155 ASN TYR ASP PRO PHE VAL ARG HIS SER VAL THR VAL LYS SEQRES 2 A 155 ALA ASP ARG LYS THR ALA PHE LYS THR PHE LEU GLU GLY SEQRES 3 A 155 PHE PRO GLU TRP TRP PRO ASN ASN PHE ARG THR THR LYS SEQRES 4 A 155 VAL GLY ALA PRO LEU GLY VAL ASP LYS LYS GLY GLY ARG SEQRES 5 A 155 TRP TYR GLU ILE ASP GLU GLN GLY GLU GLU HIS THR PHE SEQRES 6 A 155 GLY LEU ILE ARG LYS VAL ASP GLU PRO ASP THR LEU VAL SEQRES 7 A 155 ILE GLY TRP ARG LEU ASN GLY PHE GLY ARG ILE ASP PRO SEQRES 8 A 155 ASP ASN SER SER GLU PHE THR VAL THR PHE VAL ALA ASP SEQRES 9 A 155 GLY GLN LYS LYS THR ARG VAL ASP VAL GLU HIS THR HIS SEQRES 10 A 155 PHE ASP ARG MET GLY THR LYS HIS ALA LYS ARG VAL ARG SEQRES 11 A 155 ASN GLY MET ASP LYS GLY TRP PRO THR ILE LEU GLN SER SEQRES 12 A 155 PHE GLN ASP LYS ILE ASP GLU GLU GLY ALA LYS LYS HELIX 1 1 ASP A 15 GLU A 25 1 11 HELIX 2 2 GLY A 26 TRP A 30 5 5 HELIX 3 3 PHE A 118 GLY A 122 5 5 HELIX 4 4 THR A 123 ARG A 130 1 8 HELIX 5 5 GLY A 136 GLY A 152 1 17 SHEET 1 A 6 VAL A 6 VAL A 12 0 SHEET 2 A 6 LYS A 108 HIS A 115 -1 O THR A 109 N VAL A 12 SHEET 3 A 6 PHE A 97 ASP A 104 -1 N ASP A 104 O LYS A 108 SHEET 4 A 6 THR A 76 GLY A 80 -1 N LEU A 77 O VAL A 99 SHEET 5 A 6 GLY A 60 ASP A 72 -1 N ARG A 69 O VAL A 78 SHEET 6 A 6 ARG A 52 ASP A 57 -1 N TRP A 53 O GLY A 66 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 - 9 20 Bytes