HEADER SERINE PROTEASE 08-AUG-94 1PFA TITLE A STRUCTURAL MODEL FOR THE PROSTATE DISEASE MARKER, TITLE 2 PROSTATE SPECIFIC ANTIGEN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROSTATE SPECIFIC ANTIGEN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1 KEYWDS SERINE PROTEASE EXPDTA THEORETICAL MODEL AUTHOR B.O.VILLOUTREIX,E.D.GETZOFF,J.H.GRIFFIN REVDAT 1 26-JAN-95 1PFA 0 JRNL AUTH B.O.VILLOUTREIX,E.D.GETZOFF,J.H.GRIFFIN JRNL TITL A STRUCTURAL MODEL FOR THE PROSTATE DISEASE JRNL TITL 2 MARKER, HUMAN PROSTATE-SPECIFIC ANTIGEN. JRNL REF PROTEIN SCI. V. 3 2033 1994 JRNL REFN ASTM PRCIEI US ISSN 0961-8368 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: NULL REMARK 4 REMARK 4 1PFA COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 5 REMARK 5 THESE COORDINATES WERE GENERATED BY HOMOLOGY MODELING REMARK 5 ONTO THE X-RAY CRYSTAL STRUCTURES OF CHYMOTRYPSIN, REMARK 5 KALLIKREIN, TONIN AND TRYPSIN. THE KALLIKREIN LOOP OF REMARK 5 PSA (AT RESIDUE 95) WAS SUBMITTED TO A 50-PS REMARK 5 HIGH-TEMPERATURE MOLECULAR DYNAMICS SIMULATION. REMARK 5 CALCULATION OF THE SOLVATION ENERGY WAS CARRIED OUT FOR REMARK 5 EACH STRUCTURE. THE MODEL REPORTED IN THIS FILE REMARK 5 CORRESPONDS TO THE LOOP STRUCTURE HAVING THE LOWEST REMARK 5 SOLVATION ENERGY. THIS STRUCTURE WAS JUDGED APPROPRIATE REMARK 5 FOR THE STRUCTURAL ANALYSIS OF THE MODEL. REMARK 6 REMARK 6 THE CHYMOTRYPSINOGEN NUMBERING IS MAINTAINED THROUGHOUT REMARK 6 THIS FILE. REMARK 7 REMARK 7 CAT IS THE SERINE PROTEASE CATALYTIC TRIAD (SEE SITE REMARK 7 RECORDS BELOW). REMARK 8 REMARK 8 PSA HAS 15 RESIDUES AT THE N-TERMINUS. THE FIRST 8 ARE REMARK 8 CLEAVED. THE ENZYME IS CALLED PREPROENZYME. NO X-RAY REMARK 8 STRUCTURES OF PREPROENZYME ARE KNOWN. THE FOLLOWING 7 REMARK 8 RESIDUES ARE ALSO CLEAVED, AND IT SEEMS THAT NO GROUPS HAVE REMARK 8 BEEN ABLE TO IDENTIFY A CIRCULATING PSA PROTEIN WITH THESE REMARK 8 7 RESIDUES. REMARK 9 REMARK 9 CROSS REFERENCE TO SEQUENCE DATABASE REMARK 9 SWISS-PROT ENTRY NAME PDB ENTRY CHAIN NAME REMARK 9 PROS_HUMAN REMARK 9 REMARK 9 THE FOLLOWING RESIDUES ARE MISSING FROM THE N-TERMINUS REMARK 9 SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY REMARK 9 LEU 10 REMARK 9 SER 11 REMARK 9 VAL 12 REMARK 9 THR 13 REMARK 9 TRP 14 REMARK 9 ILE 15 REMARK 9 GLY 16 REMARK 9 ALA 17 REMARK 9 ALA 18 REMARK 9 PRO 19 REMARK 9 LEU 20 REMARK 9 ILE 21 REMARK 9 LEU 22 REMARK 9 SER 23 REMARK 9 ARG 24 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 LEU A 1 REMARK 465 SER A 2 REMARK 465 VAL A 3 REMARK 465 THR A 4 REMARK 465 TRP A 5 REMARK 465 ILE A 6 REMARK 465 GLY A 7 REMARK 465 ALA A 8 REMARK 465 ALA A 9 REMARK 465 PRO A 10 REMARK 465 LEU A 11 REMARK 465 ILE A 12 REMARK 465 LEU A 13 REMARK 465 SER A 14 REMARK 465 ARG A 15 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 142 SER A 143 -149.36 REMARK 500 SER A 189 THR A 190 148.39 REMARK 500 ALA A 221A LEU A 221 149.81 DBREF 1PFA A 1 246 UNP P07288 KLK3_HUMAN 10 261 SEQRES 1 A 252 LEU SER VAL THR TRP ILE GLY ALA ALA PRO LEU ILE LEU SEQRES 2 A 252 SER ARG ILE VAL GLY GLY TRP GLU CYS GLU LYS HIS SER SEQRES 3 A 252 GLN PRO TRP GLN VAL LEU VAL ALA SER ARG GLY ARG ALA SEQRES 4 A 252 VAL CYS GLY GLY VAL LEU VAL HIS PRO GLN TRP VAL LEU SEQRES 5 A 252 THR ALA ALA HIS CYS ILE ARG ASN LYS SER VAL ILE LEU SEQRES 6 A 252 LEU GLY ARG HIS SER LEU PHE HIS PRO GLU ASP THR GLY SEQRES 7 A 252 GLN VAL PHE GLN VAL SER HIS SER PHE PRO HIS PRO LEU SEQRES 8 A 252 TYR ASP MET SER LEU LEU LYS ASN ARG PHE LEU ARG PRO SEQRES 9 A 252 GLY ASP ASP SER SER HIS ASP LEU MET LEU LEU ARG LEU SEQRES 10 A 252 SER GLU PRO ALA GLU LEU THR ASP ALA VAL LYS VAL MET SEQRES 11 A 252 ASP LEU PRO THR GLN GLU PRO ALA LEU GLY THR THR CYS SEQRES 12 A 252 TYR ALA SER GLY TRP GLY SER ILE GLU PRO GLU GLU PHE SEQRES 13 A 252 LEU THR PRO LYS LYS LEU GLN CYS VAL ASP LEU HIS VAL SEQRES 14 A 252 ILE SER ASN ASP VAL CYS ALA GLN VAL HIS PRO GLN LYS SEQRES 15 A 252 VAL THR LYS PHE MET LEU CYS ALA GLY ARG TRP THR GLY SEQRES 16 A 252 GLY LYS SER THR CYS SER GLY ASP SER GLY GLY PRO LEU SEQRES 17 A 252 VAL CYS ASN GLY VAL LEU GLN GLY ILE THR SER TRP GLY SEQRES 18 A 252 SER GLU PRO CYS ALA LEU PRO GLU ARG PRO SER LEU TYR SEQRES 19 A 252 THR LYS VAL VAL HIS TYR ARG LYS TRP ILE LYS ASP THR SEQRES 20 A 252 ILE VAL ALA ASN PRO FTNOTE 1 GLY 142 - SER 143 OMEGA = 210.64 PEPTIDE BOND DEVIATES FTNOTE 1 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 2 SER 189 - THR 190 OMEGA = 148.39 PEPTIDE BOND DEVIATES FTNOTE 2 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 3 CIS PROLINE - PRO 219 FTNOTE 4 ALA 221A - LEU 221 OMEGA = 149.81 PEPTIDE BOND DEVIATES FTNOTE 4 SIGNIFICANTLY FROM TRANS CONFORMATION HELIX 1 1 GLU A 23 GLN A 27 5 5 HELIX 2 2 ALA A 55 ILE A 59 5 5 HELIX 3 3 SER A 164 HIS A 172 1 9 HELIX 4 4 TYR A 234 ASN A 245 1 12 SHEET 1 A 7 GLN A 30 SER A 35 0 SHEET 2 A 7 ARG A 39 HIS A 48 -1 N ARG A 39 O SER A 35 SHEET 3 A 7 TRP A 51 THR A 54 -1 N TRP A 51 O HIS A 48 SHEET 4 A 7 MET A 104 LEU A 108 -1 O MET A 104 N THR A 54 SHEET 5 A 7 GLN A 81 PRO A 90 -1 N SER A 86 O ARG A 107 SHEET 6 A 7 VAL A 64 LEU A 67 -1 O ILE A 65 N PHE A 83 SHEET 7 A 7 GLN A 30 SER A 35 -1 N LEU A 32 O LEU A 66 SSBOND 1 CYS A 22 CYS A 157 SSBOND 2 CYS A 42 CYS A 58 SSBOND 3 CYS A 136 CYS A 201 SSBOND 4 CYS A 168 CYS A 182 SSBOND 5 CYS A 191 CYS A 220 CISPEP 1 GLU A 218 PRO A 219 0 11.36 SITE 1 CAT 3 HIS A 57 ASP A 102 SER A 195 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 101 4 0 4 7 0 1 6 0 0 0 20 END