PDB Short entry for 1U50 HEADER HYDROLASE 26-JUL-04 1U50 TITLE LIGAND 6PE DOCKED TO PHOSPHOLIPASE D (1F0I) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOLIPASE D; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.4.4 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES SP.; SOURCE 3 ORGANISM_COMMON: BACTERIA; SOURCE 4 STRAIN: PMF KEYWDS HYDROLASE EXPDTA THEORETICAL MODEL AUTHOR C.L.AIKENS,A.T.LAEDERACH,P.J.REILLY REVDAT 1 05-JUL-05 1U50 0 JRNL AUTH C.L.AIKENS,A.T.LAEDERACH,P.J.REILLY JRNL TITL VISUALIZING COMPLEXES OF PHOSPHOLIPIDS WITH JRNL TITL 2 STREPTOMYCES PHOSPHOLIPASE D BY AUTOMATED DOCKING JRNL REF PROTEINS V. 57 27 2004 JRNL REFN ASTM PSFGEY US ISSN 0887-3585 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.LEIROS,F.SECUNDO,C.ZAMBONELLI,S.SERVI,E.HOUGH REMARK 1 TITL THE FIRST CRYSTAL STRUCTURE OF A PHOSPHOLIPASE D REMARK 1 REF STRUCTURE V. 8 655 2000 REMARK 1 REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AUTODOCK 3.0 REMARK 3 AUTHORS : MORRIS, GOODSELL, HALLIDAY, HUEY, HART, BELEW, REMARK 3 OLSON REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1U50 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-SEP-2004. REMARK 100 THE RCSB ID CODE IS RCSB023252. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE :THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: STARTING MODEL 1F0I 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 VAL A 122 REMARK 465 TYR A 123 REMARK 465 GLY A 374 REMARK 465 ALA A 375 REMARK 465 VAL A 376 REMARK 465 GLY A 377 REMARK 465 SER A 378 REMARK 465 GLY A 379 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 124 CB CG ND1 CD2 CE1 NE2 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 226 C ASN A 227 N 0.115 REMARK 500 ILE A 228 C ALA A 229 N 0.099 REMARK 500 LEU A 285 C PRO A 286 N -0.089 REMARK 500 THR A 287 N THR A 287 CA 0.115 REMARK 500 PRO A 286 C THR A 287 N 0.073 REMARK 500 THR A 287 C ALA A 288 N 0.167 REMARK 500 VAL A 294 CB VAL A 294 CG1 0.129 REMARK 500 GLU A 491 C THR A 492 N 0.169 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 ASN A 227 CA - C - N ANGL. DEV. = 18.6 DEGREES REMARK 500 ILE A 228 C - N - CA ANGL. DEV. = 17.0 DEGREES REMARK 500 ALA A 229 C - N - CA ANGL. DEV. =-15.8 DEGREES REMARK 500 THR A 287 N - CA - CB ANGL. DEV. =-14.9 DEGREES REMARK 500 VAL A 294 CG1 - CB - CG2 ANGL. DEV. =-96.8 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F0I RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE USED FOR THE DOCKING SIMULATIONS REMARK 900 RELATED ID: 1TAI RELATED DB: PDB REMARK 900 LIGAND P2A COMPLEXED WITH PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1TAJ RELATED DB: PDB REMARK 900 LIGAND PC8 COMPLEXED WITH PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1TAK RELATED DB: PDB REMARK 900 LIGAND P10 COMPLEXED WITH PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1TAO RELATED DB: PDB REMARK 900 LIGAND PX4 COMPLEXED WITH PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1TAV RELATED DB: PDB REMARK 900 LIGAND P2I COMPLEXED WITH PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1TB1 RELATED DB: PDB REMARK 900 LIGAND PS1 COMPLEXED WITH PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1TB2 RELATED DB: PDB REMARK 900 LIGAND PG8 COMPLEXED WITH PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U4T RELATED DB: PDB REMARK 900 LIGAND PA8 DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U4U RELATED DB: PDB REMARK 900 LIGAND XPA DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U4V RELATED DB: PDB REMARK 900 LIGAND PX2 DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U4W RELATED DB: PDB REMARK 900 LIGAND X4P DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U4X RELATED DB: PDB REMARK 900 LIGAND X41 DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U4Y RELATED DB: PDB REMARK 900 LIGAND PX6 DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U4Z RELATED DB: PDB REMARK 900 LIGAND PX8 DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U51 RELATED DB: PDB REMARK 900 LIGAND X81 DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 900 RELATED ID: 1U52 RELATED DB: PDB REMARK 900 LIGAND PEX DOCKED TO PHOSPHOLIPASE D (1F0I) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS SEQUENCE HAS NOT YET BEEN DEPOSITED IN ANY REMARK 999 SEQUENCE DATABASE SEQRES 1 A 504 ALA ALA THR PRO HIS LEU ASP ALA VAL GLU GLN THR LEU SEQRES 2 A 504 ARG GLN VAL SER PRO GLY LEU GLU GLY ASP VAL TRP GLU SEQRES 3 A 504 ARG THR SER GLY ASN LYS LEU ASP GLY SER ALA ALA ASP SEQRES 4 A 504 PRO SER ASP TRP LEU LEU GLN THR PRO GLY CYS TRP GLY SEQRES 5 A 504 ASP ASP LYS CYS ALA ASP ARG VAL GLY THR LYS ARG LEU SEQRES 6 A 504 LEU ALA LYS MET THR GLU ASN ILE GLY ASN ALA THR ARG SEQRES 7 A 504 THR VAL ASP ILE SER THR LEU ALA PRO PHE PRO ASN GLY SEQRES 8 A 504 ALA PHE GLN ASP ALA ILE VAL ALA GLY LEU LYS GLU SER SEQRES 9 A 504 ALA ALA LYS GLY ASN SER LEU LYS VAL ARG ILE LEU VAL SEQRES 10 A 504 GLY ALA ALA PRO VAL TYR HIS MET ASN GLY ILE PRO SER SEQRES 11 A 504 LYS TYR ARG ASP LYS LEU THR ALA LYS LEU GLY LYS ALA SEQRES 12 A 504 ALA GLU ASN ILE THR LEU ASN VAL ALA SER MET THR THR SEQRES 13 A 504 SER LYS THR ALA PHE SER TRP ASN HIS SER LYS ILE LEU SEQRES 14 A 504 VAL VAL ASP GLY GLN SER ALA LEU THR GLY GLY ILE ASN SEQRES 15 A 504 SER TRP LYS ASP ASP TYR LEU ASP THR THR HIS PRO VAL SEQRES 16 A 504 SER ASP VAL ASP LEU ALA LEU THR GLY PRO ALA ALA GLY SEQRES 17 A 504 SER ALA GLY ARG TYR LEU ASP THR LEU TRP THR TRP THR SEQRES 18 A 504 CYS LYS ASN LYS SER ASN ILE ALA SER VAL TRP PHE ALA SEQRES 19 A 504 ALA SER GLY ASN ALA GLY CYS MET PRO THR MET HIS LYS SEQRES 20 A 504 ASP THR ASN PRO LYS ALA SER PRO ALA THR GLY ASN VAL SEQRES 21 A 504 PRO VAL ILE ALA VAL GLY GLY LEU GLY VAL GLY ILE LYS SEQRES 22 A 504 ASP VAL ASP PRO LYS SER THR PHE ARG PRO ASP LEU PRO SEQRES 23 A 504 THR ALA SER ASP THR LYS CYS VAL VAL GLY LEU HIS ASP SEQRES 24 A 504 ASN THR ASN ALA ASP ARG ASP TYR ASP THR VAL ASN PRO SEQRES 25 A 504 GLU GLU SER ALA LEU ARG ALA LEU VAL ALA SER ALA LYS SEQRES 26 A 504 GLY HIS ILE GLU ILE SER GLN GLN ASP LEU ASN ALA THR SEQRES 27 A 504 CYS PRO PRO LEU PRO ARG TYR ASP ILE ARG LEU TYR ASP SEQRES 28 A 504 ALA LEU ALA ALA LYS MET ALA ALA GLY VAL LYS VAL ARG SEQRES 29 A 504 ILE VAL VAL SER ASP PRO ALA ASN ARG GLY ALA VAL GLY SEQRES 30 A 504 SER GLY GLY TYR SER GLN ILE LYS SER LEU SER GLU ILE SEQRES 31 A 504 SER ASP THR LEU ARG ASN ARG LEU ALA ASN ILE THR GLY SEQRES 32 A 504 GLY GLN GLN ALA ALA LYS THR ALA MET CYS SER ASN LEU SEQRES 33 A 504 GLN LEU ALA THR PHE ARG SER SER PRO ASN GLY LYS TRP SEQRES 34 A 504 ALA ASP GLY HIS PRO TYR ALA GLN HIS HIS LYS LEU VAL SEQRES 35 A 504 SER VAL ASP SER SER THR PHE TYR ILE GLY SER LYS ASN SEQRES 36 A 504 LEU TYR PRO SER TRP LEU GLN ASP PHE GLY TYR ILE VAL SEQRES 37 A 504 GLU SER PRO GLU ALA ALA LYS GLN LEU ASP ALA LYS LEU SEQRES 38 A 504 LEU ASP PRO GLN TRP LYS TYR SER GLN GLU THR ALA THR SEQRES 39 A 504 VAL ASP TYR ALA ARG GLY ILE CYS GLY ALA HET 6PE 1 60 HETNAM 6PE 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE FORMUL 2 6PE C17 H33 N O8 P 1- HELIX 1 1 THR A 3 SER A 17 1 15 HELIX 2 2 PRO A 18 GLU A 21 5 4 HELIX 3 3 ASP A 39 ASP A 42 5 4 HELIX 4 4 ARG A 59 ASN A 75 1 17 HELIX 5 5 ASN A 90 LYS A 107 1 18 HELIX 6 6 GLY A 127 GLY A 141 1 15 HELIX 7 7 LYS A 142 GLU A 145 5 4 HELIX 8 8 TRP A 184 LEU A 189 1 6 HELIX 9 9 GLY A 204 ASN A 224 1 21 HELIX 10 10 THR A 244 ASN A 250 1 7 HELIX 11 11 ASP A 304 ASN A 311 1 8 HELIX 12 12 ASN A 311 SER A 323 1 13 HELIX 13 13 ASP A 346 ALA A 359 1 14 HELIX 14 14 ASP A 369 ARG A 373 5 5 HELIX 15 15 LEU A 387 GLY A 403 1 17 HELIX 16 16 GLY A 404 ASN A 415 1 12 HELIX 17 17 SER A 470 LEU A 481 1 12 HELIX 18 18 LEU A 481 GLN A 490 1 10 HELIX 19 19 GLU A 491 ALA A 493 5 3 HELIX 20 20 ALA A 498 GLY A 500 5 3 SHEET 1 A 8 LEU A 44 THR A 47 0 SHEET 2 A 8 ASP A 197 THR A 203 -1 O ASP A 197 N THR A 47 SHEET 3 A 8 SER A 175 GLY A 179 -1 N THR A 178 O LEU A 200 SHEET 4 A 8 ILE A 168 VAL A 171 -1 N VAL A 171 O SER A 175 SHEET 5 A 8 THR A 79 LEU A 85 -1 N ASP A 81 O VAL A 170 SHEET 6 A 8 LEU A 111 GLY A 118 1 O ARG A 114 N ILE A 82 SHEET 7 A 8 ILE A 147 MET A 154 1 O THR A 148 N LEU A 111 SHEET 8 A 8 VAL A 231 ALA A 235 -1 O ALA A 234 N VAL A 151 SHEET 1 B12 LEU A 44 THR A 47 0 SHEET 2 B12 ASP A 197 THR A 203 -1 O ASP A 197 N THR A 47 SHEET 3 B12 TRP A 25 LEU A 33 -1 N LYS A 32 O THR A 203 SHEET 4 B12 VAL A 260 GLY A 266 -1 O ALA A 264 N GLU A 26 SHEET 5 B12 PHE A 464 GLU A 469 -1 O ILE A 467 N ILE A 263 SHEET 6 B12 THR A 448 GLY A 452 -1 N PHE A 449 O VAL A 468 SHEET 7 B12 LYS A 440 VAL A 444 -1 N VAL A 444 O THR A 448 SHEET 8 B12 HIS A 327 GLN A 332 -1 N GLU A 329 O SER A 443 SHEET 9 B12 LYS A 362 VAL A 367 1 O ARG A 364 N ILE A 330 SHEET 10 B12 LEU A 416 THR A 420 1 O GLN A 417 N ILE A 365 SHEET 11 B12 VAL A 495 ASP A 496 -1 O VAL A 495 N LEU A 418 SHEET 12 B12 ILE A 501 CYS A 502 -1 O ILE A 501 N ASP A 496 SSBOND 1 CYS A 50 CYS A 56 SSBOND 2 CYS A 222 CYS A 241 SSBOND 3 CYS A 293 CYS A 339 SSBOND 4 CYS A 413 CYS A 502 CISPEP 1 THR A 47 PRO A 48 0 0.47 CISPEP 2 ALA A 86 PRO A 87 0 0.61 CISPEP 3 CYS A 339 PRO A 340 0 -11.57 CISPEP 4 PRO A 340 PRO A 341 0 0.77 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