HEADER TRANSFERASE, TRANSPORT PROTEIN 15-JAN-03 1NNZ TITLE DOCKING MODEL FOR MAT AND ACP COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALONYL COA:ACYL CARRIER PROTEIN COMPND 3 MALONYLTRANSFERASE; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: MALONYL-COA:ACP TRANSACYLASE; COMPND 6 EC: 2.3.1.39; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: ACTINORHODIN POLYKETIDE SYNTHASE ACYL CARRIER COMPND 10 PROTEIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: ACYL CARRIER PROTEIN; COMPND 13 SYNONYM: ACTI ORF3; COMPND 14 EC: 2.7.8.7; COMPND 15 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR A3; SOURCE 3 ORGANISM_COMMON: 2; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: STREPTOMYCES COELICOLOR; SOURCE 6 GENE: SCO5089 OR SCBAC28G1.15 KEYWDS MAT-ACP INTERFACE, ACP DOCKING SITE EXPDTA THEORETICAL MODEL AUTHOR A.T.KEATINGE-CLAY,A.A.SHELAT,D.F.SAVAGE,S.TSAI, AUTHOR 2 L.J.W.MIERCKE,J.D.O'CONNELL III,C.KHOSLA,R.M STROUD REVDAT 2 11-FEB-03 1NNZ 1 KEYWDS REVDAT 1 28-JAN-03 1NNZ 0 JRNL AUTH A.T.KEATINGE-CLAY,A.A.SHELAT,D.F.SAVAGE,S.TSAI, JRNL AUTH 2 L.J.W.MIERCKE,J.D.O'CONNELL III,C.KHOSLA,R.M.STROUD JRNL TITL CATALYSIS, SPECIFICITY, AND ACP DOCKING SITE OF JRNL TITL 2 STREPTOMYCES COELICOLOR MALONYL-COA:ACP JRNL TITL 3 TRANSACYLASE JRNL REF STRUCTURE V. 11 147 2003 JRNL REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RIGID DOCKING OF ACTINORHODIN ACP REMARK 3 (PDB CODE 2AF8) AND MAT WAS PERFORMED USING THE DOCK 4.0 REMARK 3 PROGRAM SUITE. TO EXHAUSTIVELY SEARCH THE BINDING SURFACE OF REMARK 3 MAT, TWO SPHERE SETS WERE GENERATED COVERING THE LARGE AND THE REMARK 3 SMALL SUBDOMAINS. ONE DOCKING EXPERIMENT WAS PERFORMED WITH REMARK 3 EACH SPHERE SET. THE MINIMUM NUMBER OF NODES ALLOWED IN A REMARK 3 CLIQUE WAS 5, WITH A MAXIMUM 10 MILLION ORIENTATIONS ALLOWED REMARK 3 FOR EACH SPHERE SET. ORIENTATIONS WERE RAPIDLY SCORED USING AN REMARK 3 ENERGY GRID WITH A 6-9 ATTRACTIVE-REPULSIVE VAN DER WAALS REMARK 3 POTENTIAL AND THE ELECTROSTATIC TERM WEIGHTED BY 0.01. THE REMARK 3 ENERGY MINIMIZATION OPTION WAS ACTIVATED WITH DEFAULT VALUES. REMARK 3 A BUMP FILTER WAS EMPLOYED TO DISCARD ORIENTATIONS WITH REMARK 3 GREATER THAN 100 MAJOR STERIC CLASHES. RESIDUES LYS 47, LYS REMARK 3 190, ARG 287, AND LYS 293 WERE MUTATED TO ALANINE PRIOR TO REMARK 3 DOCKING AS THEIR SIDE CHAINS HAD HIGH B-FACTORS; THESE SIDE REMARK 3 CHAINS WERE ADDED BACK FOR ALL SUBSEQUENT STEPS. THE TOP TEN REMARK 3 SCORING LIGAND ORIENTATIONS RESULTING FROM EACH DOCK RUN WERE REMARK 3 MINIMIZED USING THE GENERALIZED BORN/SURFACE AREA (GB/SA) REMARK 3 OPTION IN THE AMBER 7.0 SANDER MODULE (IGB=1, SALTCON=0.2M, REMARK 3 GBSA=1) BASED ON THE FOLLOWING PROTOCOL: 500 STEPS STEEPEST REMARK 3 DESCENT (SD) MINIMIZATION WITH A 5000 KCAL MOL-1 RESTRAINT ON REMARK 3 ALL HEAVY ATOMS, FOLLOWED BY 5 ROUNDS OF 500 STEPS OF SD REMARK 3 MINIMIZATION WITH 25, 20, 15, 10, AND 5 KCAL/MOL RESTRAINTS ON REMARK 3 ALL ATOMS, THEN 5000 STEPS OF SD MINIMIZATION WITH NO REMARK 3 RESTRAINTS. THE TOP 5 ORIENTATIONS SCORED SIMILARLY, AND WERE REMARK 3 SUBJECTED TO FURTHER REFINEMENT WITH MOLECULAR DYNAMICS IN REMARK 3 SANDER USING THE GB/SA OPTIONS PREVIOUSLY DESCRIBED AND A 20 REMARK 3 KCAL/MOL RESTRAINT ON BACKBONE HEAVY ATOMS. THE COMPLEX WAS REMARK 3 HEATED FROM 10 K TO 300 K OVER 10 PS, FOLLOWED BY REMARK 3 EQUILIBRATION AT 300 K FOR 15 PS. THE RESULTING STRUCTURES REMARK 3 WERE THEN SUBJECTED TO 2000 STEPS OF SD MINIMIZATION. THIS REMARK 3 SOLUTION HAS THE BEST ORIENTATION, SIGNIFICANTLY LOWER IN REMARK 3 ENERGY THAN ANY OTHER. REMARK 4 REMARK 4 1NNZ COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JAN-2003. REMARK 100 THE RCSB ID CODE IS RCSB018049. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 77 REMARK 465 THR A 78 REMARK 465 SER A 79 REMARK 465 VAL A 80 REMARK 465 ALA A 81 REMARK 465 ASP A 82 REMARK 465 ALA A 83 REMARK 465 THR A 84 REMARK 465 GLY A 85 REMARK 465 PRO A 86 REMARK 465 GLN A 315 REMARK 465 ALA A 316 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 96 ND1 CE1 NE2 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 M RES CSSEQI PSI PHI REMARK 500 SER A 97 -102.48 51.67 REMARK 500 SER B 42 -46.85 143.19 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NM2 RELATED DB: PDB REMARK 900 MALONYL-COA:ACP TRANSACYLASE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THERE ARE TEN RESIDUES THAT CANNOT BE SEEN REMARK 999 IN THE ELECTRON DENSITY BECAUSE REMARK 999 THEY EXIST ON A PRESUMABLY FLEXIBLE LOOP. REMARK 999 THUS, THERE IS NO DELETION, AND REMARK 999 THR76 AND GLY87 SHOULD NOT BE LINKED. REMARK 999 THAT THEY ARE SO CLOSE TO ONE ANOTHER REMARK 999 IS AN ARTIFACT FROM THE DOCKING SIMULATIONS. DBREF 1NNZ A 1 316 GB 21220854 NP_626633 1 316 DBREF 1NNZ B 1 86 UNP Q02054 ACPX_STRCO 1 86 SEQRES 1 A 316 MET LEU VAL LEU VAL ALA PRO GLY GLN GLY ALA GLN THR SEQRES 2 A 316 PRO GLY PHE LEU THR ASP TRP LEU ALA LEU PRO GLY ALA SEQRES 3 A 316 ALA ASP ARG VAL ALA ALA TRP SER ASP ALA ILE GLY LEU SEQRES 4 A 316 ASP LEU ALA HIS PHE GLY THR LYS ALA ASP ALA ASP GLU SEQRES 5 A 316 ILE ARG ASP THR SER VAL ALA GLN PRO LEU LEU VAL ALA SEQRES 6 A 316 ALA GLY ILE LEU SER ALA ALA ALA LEU GLY THR GLN THR SEQRES 7 A 316 SER VAL ALA ASP ALA THR GLY PRO GLY PHE THR PRO GLY SEQRES 8 A 316 ALA VAL ALA GLY HIS SER VAL GLY GLU ILE THR ALA ALA SEQRES 9 A 316 VAL PHE ALA GLY VAL LEU ASP ASP THR ALA ALA LEU SER SEQRES 10 A 316 LEU VAL ARG ARG ARG GLY LEU ALA MET ALA GLU ALA ALA SEQRES 11 A 316 ALA VAL THR GLU THR GLY MET SER ALA LEU LEU GLY GLY SEQRES 12 A 316 ASP PRO GLU VAL SER VAL ALA HIS LEU GLU ARG LEU GLY SEQRES 13 A 316 LEU THR PRO ALA ASN VAL ASN GLY ALA GLY GLN ILE VAL SEQRES 14 A 316 ALA ALA GLY THR MET GLU GLN LEU ALA ALA LEU ASN GLU SEQRES 15 A 316 ASP LYS PRO GLU GLY VAL ARG LYS VAL VAL PRO LEU LYS SEQRES 16 A 316 VAL ALA GLY ALA PHE HIS THR ARG HIS MET ALA PRO ALA SEQRES 17 A 316 VAL ASP LYS LEU ALA GLU ALA ALA LYS ALA LEU THR PRO SEQRES 18 A 316 ALA ASP PRO LYS VAL THR TYR VAL SER ASN LYS ASP GLY SEQRES 19 A 316 ARG ALA VAL ALA SER GLY THR GLU VAL LEU ASP ARG LEU SEQRES 20 A 316 VAL GLY GLN VAL ALA ASN PRO VAL ARG TRP ASP LEU CYS SEQRES 21 A 316 MET GLU THR PHE LYS GLU LEU GLY VAL THR ALA ILE ILE SEQRES 22 A 316 GLU VAL CYS PRO GLY GLY THR LEU THR GLY LEU ALA LYS SEQRES 23 A 316 ARG ALA LEU PRO GLY VAL LYS THR LEU ALA LEU LYS THR SEQRES 24 A 316 PRO ASP ASP LEU ASP ALA ALA ARG GLU LEU VAL ALA GLU SEQRES 25 A 316 HIS THR GLN ALA SEQRES 1 B 86 MET ALA THR LEU LEU THR THR ASP ASP LEU ARG ARG ALA SEQRES 2 B 86 LEU VAL GLU CYS ALA GLY GLU THR ASP GLY THR ASP LEU SEQRES 3 B 86 SER GLY ASP PHE LEU ASP LEU ARG PHE GLU ASP ILE GLY SEQRES 4 B 86 TYR ASP SER LEU ALA LEU MET GLU THR ALA ALA ARG LEU SEQRES 5 B 86 GLU SER ARG TYR GLY VAL SER ILE PRO ASP ASP VAL ALA SEQRES 6 B 86 GLY ARG VAL ASP THR PRO ARG GLU LEU LEU ASP LEU ILE SEQRES 7 B 86 ASN GLY ALA LEU ALA GLU ALA ALA HELIX 1 1 LEU A 17 ALA A 22 1 6 HELIX 2 2 GLY A 25 GLY A 38 1 14 HELIX 3 3 ASP A 40 LYS A 47 1 8 HELIX 4 4 ASP A 49 ARG A 54 1 6 HELIX 5 5 ASP A 55 GLY A 75 1 21 HELIX 6 6 VAL A 98 ALA A 107 1 10 HELIX 7 7 ASP A 111 VAL A 132 1 22 HELIX 8 8 ASP A 144 LEU A 155 1 12 HELIX 9 9 MET A 174 ASP A 183 1 10 HELIX 10 10 THR A 202 HIS A 204 5 3 HELIX 11 11 MET A 205 LYS A 217 1 13 HELIX 12 12 SER A 239 GLN A 250 1 12 HELIX 13 13 VAL A 251 ASN A 253 5 3 HELIX 14 14 ARG A 256 LEU A 267 1 12 HELIX 15 15 GLY A 279 LEU A 289 1 11 HELIX 16 16 THR A 299 ASP A 301 5 3 HELIX 17 17 ASP A 302 GLU A 312 1 11 HELIX 18 18 THR B 6 GLY B 19 1 14 HELIX 19 19 LEU B 33 GLY B 39 1 7 HELIX 20 20 SER B 42 GLY B 57 1 16 HELIX 21 21 PRO B 61 GLY B 66 1 6 HELIX 22 22 THR B 70 ALA B 85 1 16 SHEET 1 A 6 ALA A 236 VAL A 237 0 SHEET 2 A 6 THR A 227 VAL A 229 -1 N TYR A 228 O VAL A 237 SHEET 3 A 6 ALA A 92 GLY A 95 1 N VAL A 93 O THR A 227 SHEET 4 A 6 LEU A 2 ALA A 6 1 N LEU A 4 O ALA A 92 SHEET 5 A 6 ALA A 271 GLU A 274 1 O ILE A 273 N VAL A 5 SHEET 6 A 6 LYS A 293 ALA A 296 1 O LEU A 295 N GLU A 274 SHEET 1 B 4 THR A 158 VAL A 162 0 SHEET 2 B 4 ILE A 168 THR A 173 -1 O VAL A 169 N ASN A 161 SHEET 3 B 4 THR A 135 GLY A 142 -1 N LEU A 140 O ILE A 168 SHEET 4 B 4 VAL A 188 PRO A 193 -1 O VAL A 192 N ALA A 139 CISPEP 1 GLY A 87 GLY A 87 0 -3.47 CISPEP 2 CYS A 276 PRO A 277 0 -12.61 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 MASTER 109 0 0 22 10 0 0 6 0 0 0 32 END