10 20 30 40 50 60 70 80 1XZS - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LYASE/DNA 12-NOV-04 1XZS
TITLE THEORETICAL MODEL OF BOVINE AP LYASE, BAP1 MUTANT: 282 ASP TITLE 2 TO ALA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AP LYASE; COMPND 5 SYNONYM: AP ENDONUCLEASE 1, APEX NUCLEASE, APEN; COMPND 6 EC: 4.2.99.18; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*GP*CP*GP*TP*CP*CP*(3DR) COMPND 10 P*CP*GP*AP*CP*GP*AP*CP*G)-3'; COMPND 11 CHAIN: X; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*GP*TP*CP*GP*TP*CP*GP*GP*GP*GP*AP*CP*GP*C)- COMPND 15 3'; COMPND 16 CHAIN: Y; COMPND 17 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: BOVINE; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 MOL_ID: 3; SOURCE 7 SYNTHETIC: YES
KEYWDS THEORETICAL MODEL, ENDONUCLEASE, AP LYASE, DNA REPAIR ENZYME
EXPDTA THEORETICAL MODEL
AUTHOR R.KHURSHID,A.SALIM,A.ABBASI
REVDAT 2 15-MAR-05 1XZS 1 JRNL REVDAT 1 23-NOV-04 1XZS 0
JRNL AUTH R.KHURSHID,A.SALIM,A.ABBASI JRNL TITL THREE-DIMENSIONAL STRUCTURE PREDICTION OF BOVINE JRNL TITL 2 AP LYASE, BAP1: PREDICTION OF INTERACTION WITH DNA JRNL TITL 3 AND ALTERATIONS AS A RESULT OF ARG176-->ALA, JRNL TITL 4 ASP282-->ALA, AND HIS308-->ASN MUTATIONS. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 326 711 2005 JRNL REFN ASTM BBRCA9 US ISSN 0006-291X
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MODELLER 4 REMARK 3 AUTHORS : A.SALI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1XZS COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-NOV-2004. REMARK 100 THE RCSB ID CODE IS RCSB030935.
REMARK 103 REMARK 103 THERE ARE NON-WATSON-CRICK HYDROGEN BONDS BETWEEN THE REMARK 103 FOLLOWING ATOMS: REMARK 103 O2 C X 11 AND N1 G Y 20
REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: COMPARATIVE MODELING WAS USED FOR REFINEMENT METHOD
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
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 REMARK 500 O2P C X 6 OD1 ASN A 173 1.15 REMARK 500 P C X 6 OD1 ASN A 173 1.23 REMARK 500 O1P A X 10 CE LYS A 275 1.37 REMARK 500 O1P A X 10 NZ LYS A 275 1.39 REMARK 500 O1P C X 6 ND2 ASN A 173 1.49 REMARK 500 O5* C X 6 CG ASN A 173 1.57 REMARK 500 P C X 6 CG ASN A 173 1.65 REMARK 500 O1P C X 6 CG ASN A 173 1.73 REMARK 500 O5* C X 6 ND2 ASN A 173 1.74 REMARK 500 N2 G Y 23 CE MET A 270 1.74 REMARK 500 O5* G X 9 CG1 VAL A 277 1.76 REMARK 500 C5* C X 6 ND2 ASN A 173 1.84 REMARK 500 P C X 6 ND2 ASN A 173 1.87 REMARK 500 O1P C X 6 OD1 ASN A 173 1.89 REMARK 500 O5* C X 6 OD1 ASN A 173 1.93 REMARK 500 O1P A X 10 CD LYS A 275 1.96 REMARK 500 C5* G Y 29 O GLU A 125 2.00 REMARK 500 P A X 10 NZ LYS A 275 2.18 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ALA A 282 CB - CA - C ANGL. DEV. =-13.7 DEGREES
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XZR RELATED DB: PDB REMARK 900 RELATED ID: 1XZT RELATED DB: PDB
DBREF 1XZS A 39 317 UNP P23196 APE1_BOVIN 39 317
SEQADV 1XZS ALA A 282 UNP P23196 ASP 282 ENGINEERED
SEQRES 1 A 279 GLU GLY ALA VAL LEU TYR GLU ASP PRO PRO ASP GLN LYS SEQRES 2 A 279 THR SER PRO SER GLY LYS SER ALA THR LEU LYS ILE CYS SEQRES 3 A 279 SER TRP ASN VAL ASP GLY LEU ARG ALA TRP ILE LYS LYS SEQRES 4 A 279 LYS GLY LEU ASP TRP VAL LYS GLU GLU ALA PRO ASP ILE SEQRES 5 A 279 LEU CYS LEU GLN GLU THR LYS CYS SER GLU ASN LYS LEU SEQRES 6 A 279 PRO VAL GLU LEU GLN GLU LEU SER GLY LEU SER HIS GLN SEQRES 7 A 279 TYR TRP SER ALA PRO SER ASP LYS GLU GLY TYR SER GLY SEQRES 8 A 279 VAL GLY LEU LEU SER ARG GLN CYS PRO LEU LYS VAL SER SEQRES 9 A 279 TYR GLY ILE GLY GLU GLU GLU HIS ASP GLN GLU GLY ARG SEQRES 10 A 279 VAL ILE VAL ALA GLU TYR ASP ALA PHE VAL LEU VAL THR SEQRES 11 A 279 ALA TYR VAL PRO ASN ALA GLY ARG GLY LEU VAL ARG LEU SEQRES 12 A 279 GLU TYR ARG GLN ARG TRP ASP GLU ALA PHE ARG LYS PHE SEQRES 13 A 279 LEU LYS GLY LEU ALA SER ARG LYS PRO LEU VAL LEU CYS SEQRES 14 A 279 GLY ASP LEU ASN VAL ALA HIS GLU GLU ILE ASP LEU ARG SEQRES 15 A 279 ASN PRO LYS GLY ASN LYS LYS ASN ALA GLY PHE THR PRO SEQRES 16 A 279 GLN GLU ARG GLN GLY PHE GLY GLU LEU LEU GLN ALA VAL SEQRES 17 A 279 PRO LEU THR ASP SER PHE ARG HIS LEU TYR PRO ASN THR SEQRES 18 A 279 ALA TYR ALA TYR THR PHE TRP THR TYR MET MET ASN ALA SEQRES 19 A 279 ARG SER LYS ASN VAL GLY TRP ARG LEU ALA TYR PHE LEU SEQRES 20 A 279 LEU SER GLN SER VAL LEU PRO ALA LEU CYS ASP SER LYS SEQRES 21 A 279 ILE ARG SER LYS ALA LEU GLY SER ASP HIS CYS PRO ILE SEQRES 22 A 279 THR LEU TYR LEU ALA LEU SEQRES 1 X 15 G C G T C C 3DR C G A C G A SEQRES 2 X 15 C G SEQRES 1 Y 14 G T C G T C G G G G A C G SEQRES 2 Y 14 C
HET 3DR X 7 20
HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
HETSYN 3DR ABASIC DIDEOXYRIBOSE
FORMUL 1 3DR C5 H11 O6 P
HELIX 1 1 GLY A 70 LYS A 77 1 8 HELIX 2 2 LYS A 78 ALA A 87 1 10 HELIX 3 3 PRO A 104 GLU A 109 5 6 HELIX 4 4 LEU A 110 SER A 114 5 5 HELIX 5 5 GLU A 147 ASP A 151 5 5 HELIX 6 6 ARG A 180 LYS A 202 1 23 HELIX 7 7 GLU A 215 LEU A 219 5 5 HELIX 8 8 THR A 232 VAL A 246 1 15 HELIX 9 9 SER A 251 TYR A 256 1 6 HELIX 10 10 ASN A 271 ASN A 276 1 6 HELIX 11 11 GLN A 288 PRO A 292 5 5
SHEET 1 A 6 HIS A 115 SER A 119 0 SHEET 2 A 6 VAL A 130 SER A 134 -1 O LEU A 132 N TYR A 117 SHEET 3 A 6 ILE A 90 GLN A 94 -1 N LEU A 93 O GLY A 131 SHEET 4 A 6 LEU A 61 ASN A 67 1 N CYS A 64 O CYS A 92 SHEET 5 A 6 ILE A 311 LEU A 315 -1 O LEU A 313 N ILE A 63 SHEET 6 A 6 LEU A 294 ILE A 299 -1 N LYS A 298 O THR A 312 SHEET 1 B 6 LYS A 140 TYR A 143 0 SHEET 2 B 6 VAL A 156 GLU A 160 -1 O VAL A 158 N SER A 142 SHEET 3 B 6 VAL A 165 TYR A 170 -1 O LEU A 166 N ALA A 159 SHEET 4 B 6 LEU A 204 ASP A 209 1 O CYS A 207 N VAL A 167 SHEET 5 B 6 ALA A 282 LEU A 286 -1 O LEU A 285 N LEU A 206 SHEET 6 B 6 THR A 249 ASP A 250 -1 N THR A 249 O LEU A 286
CISPEP 1 VAL A 246 PRO A 247 0 -5.52
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