2PSA - Header Asymmetric Unit

HEADER KALLIKREIN 11-MAR-99 2PSA

TITLE KNOWLEDGE BASED MODEL OF PROSTATE SPECIFIC ANTIGEN TITLE 2 (THEORETICAL MODEL) BOUND TO A CONSENSUS PEPTIDE SUBSTRATE

COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (PROSTATE SPECIFIC ANTIGEN); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PSA; COMPND 5 EC: 3.4.21.77; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN (CONSENSUS PEPTIDE SUBSTRATE); COMPND 9 CHAIN: I; COMPND 10 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: HEXAPEPTIDE

KEYWDS KALLIKREIN, SERINE PROTEASE, PSA, SUBSTRATE PHAGE DISPLAY

EXPDTA THEORETICAL MODEL

AUTHOR J.L.PELLEQUER

REVDAT 1 16-MAR-99 2PSA 0

JRNL AUTH G.S.COOMBS,R.C.BERGSTROM,J.L.PELLEQUER,S.I.BAKER, JRNL AUTH 2 M.NAVRE,M.M.SMITH,J.A.TAINER,E.L.MADISON,D.R.COREY JRNL TITL SUBSTRATE SPECIFICITY OF PROSTATE-SPECIFIC ANTIGEN JRNL TITL 2 (PSA). JRNL REF CHEM.BIOL. V. 5 475 1998 JRNL REFN ASTM CBOLE2 UK ISSN 1074-5521

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: NUMBER OF ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS: 3641 PROTEIN HEAVY ATOMS : 1832 RMS DEVIATIONS REMARK 3 FROM IDEAL VALUES. BOND LENGTHS (A): 0.015 BOND ANGLES REMARK 3 (DEGREES): 2.459 DIHEDRAL ANGLES (DEGREES): NULL IMPROPER REMARK 3 ANGLES (DEGREES) : 2.110 PARAMETER FILE 1 : PARALLH22X.PRO REMARK 3 PARAMETER FILE 2 : JLP22ADD.PAR TOPOLOGY FILE 1 : REMARK 3 TOPALLH22X.PRO TOPOLOGY FILE 2 : NULL OTHER REFINEMENT REMARK 3 REMARKS: RAMACHANDRAM MAP AS DETERMINED BY PROCHECK MOST REMARK 3 FAVOURED : 163 (81.9%) ADDITIONAL ALLOWED REGIONS: 36 18.1% REMARK 3 GENEROUSLY ALLOWED REGIONS: 0 0.0% DISALLOWED REGIONS : 0 0.0%

REMARK 4 REMARK 4 2PSA COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 6 REMARK 6 THE CHYMOTRYPSINOGEN NUMBERING IS MAINTAINED THROUGHOUT REMARK 6 THIS FILE. THE MODELED PEPTIDE SUBSTRATE USES THE SAME REMARK 6 NUMBERING AS IN THE COMPLEX BETWEEN KALLIKREIN AND REMARK 6 HIRUSTATIN IN 1HIA.PDB (RESIDUE 27 TO 32).

REMARK 7 REMARK 7 THE FIRST 18 RESIDUES IN PSA FORM THE SIGNAL PEPTIDE. REMARK 7 RESIDUES 19 TO 24 FORM THE "ACTIVATION PEPTIDE" THAT REMARK 7 IS CLEAVED IN ACTIVE PSA. THE MODEL PRESENT COORDINATES REMARK 7 FOR RESIDUES 25 TO 261 IN PSA NUMBERING.

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-1999. REMARK 100 THE RCSB ID CODE IS RCSB000629.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: PSA WAS MODELED USING THE PORCINE TISSUE KALLIKREIN REMARK 220 (2KAI.PDB, 60% IDENTICAL RESIDUES). THE CONSENSUS REMARK 220 PEPTIDE SUBSTRATE WAS IDENTIFIED BY A SUBSTRATE PHAGE REMARK 220 DISPLAY METHOD WITH AN ITERATIVE OPTIMIZATION OF NATIVE REMARK 220 SUBSTRATE SEQUENCES FROM P4 TO P2'. THE CONSENSUS REMARK 220 PEPTIDE SUBSTRATE WAS DOCKED IN A CANONICAL CONFORMATION REMARK 220 CHARACTERIZED BY A PRECISE SET OF HYDROGEN BONDING REMARK 220 PATTERN. THE SUBSTRATE FORMS A TYPE VIA2 TURN AT THE P2- REMARK 220 P1 POSITION. A MOLECULAR DYNAMICS SIMULATION WAS CARRIED REMARK 220 OUT ON THE LOOP 95-96 (11 RESIDUES) IN THE PRESENCE OF REMARK 220 THE PEPTIDE SUBSTRATE: A 50 PS DYNAMICS AT 300K USING REMARK 220 THE VERLET ALGORITHM IN XPLOR (GAS PHASE WITH NO REMARK 220 ELECTROSTATIC TERM TURNED ON).

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 600 REMARK 600 HETEROGEN REMARK 600 THE N-TERMINUS OF CHAIN I IS ACETYLATED. REMARK 600 REMARK 600 THE C-TERMINUS OF CHAIN I IS AMIDATED.

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CAT REMARK 800 SITE_DESCRIPTION: REMARK 800 CATALYTIC TRIAD

DBREF 2PSA A 16 246 UNP P07288 PROS_HUMAN 25 261

SEQRES 1 A 237 ILE VAL GLY GLY TRP GLU CYS GLU LYS HIS SER GLN PRO SEQRES 2 A 237 TRP GLN VAL LEU VAL ALA SER ARG GLY ARG ALA VAL CYS SEQRES 3 A 237 GLY GLY VAL LEU VAL HIS PRO GLN TRP VAL LEU THR ALA SEQRES 4 A 237 ALA HIS CYS ILE ARG ASN LYS SER VAL ILE LEU LEU GLY SEQRES 5 A 237 ARG HIS SER LEU PHE HIS PRO GLU ASP THR GLY GLN VAL SEQRES 6 A 237 PHE GLN VAL SER HIS SER PHE PRO HIS PRO LEU TYR ASP SEQRES 7 A 237 MET SER LEU LEU LYS ASN ARG PHE LEU ARG PRO GLY ASP SEQRES 8 A 237 ASP SER SER HIS ASP LEU MET LEU LEU ARG LEU SER GLU SEQRES 9 A 237 PRO ALA GLU LEU THR ASP ALA VAL LYS VAL MET ASP LEU SEQRES 10 A 237 PRO THR GLN GLU PRO ALA LEU GLY THR THR CYS TYR ALA SEQRES 11 A 237 SER GLY TRP GLY SER ILE GLU PRO GLU GLU PHE LEU THR SEQRES 12 A 237 PRO LYS LYS LEU GLN CYS VAL ASP LEU HIS VAL ILE SER SEQRES 13 A 237 ASN ASP VAL CYS ALA GLN VAL HIS PRO GLN LYS VAL THR SEQRES 14 A 237 LYS PHE MET LEU CYS ALA GLY ARG TRP THR GLY GLY LYS SEQRES 15 A 237 SER THR CYS SER GLY ASP SER GLY GLY PRO LEU VAL CYS SEQRES 16 A 237 ASN GLY VAL LEU GLN GLY ILE THR SER TRP GLY SER GLU SEQRES 17 A 237 PRO CYS ALA LEU PRO GLU ARG PRO SER LEU TYR THR LYS SEQRES 18 A 237 VAL VAL HIS TYR ARG LYS TRP ILE LYS ASP THR ILE VAL SEQRES 19 A 237 ALA ASN PRO SEQRES 1 I 8 ACE SER SER TYR TYR SER GLY NH2

HET ACE I 26 6 HET NH2 I 33 3

HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP

FORMUL 2 ACE C2 H4 O FORMUL 2 NH2 H3 N

HELIX 1 1 ALA A 56 CYS A 58 5 3 HELIX 2 2 ASN A 165 VAL A 171 1 7 HELIX 3 3 VAL A 231 ALA A 244 5 14

SHEET 1 A 7 GLN A 81 GLN A 84 0 SHEET 2 A 7 VAL A 64 LEU A 67 -1 N LEU A 67 O GLN A 81 SHEET 3 A 7 GLN A 30 SER A 35 -1 N ALA A 34 O VAL A 64 SHEET 4 A 7 ARG A 39 HIS A 48 -1 N GLY A 44 O VAL A 31 SHEET 5 A 7 TRP A 51 THR A 54 -1 N LEU A 53 O VAL A 45 SHEET 6 A 7 MET A 104 LEU A 108 -1 N LEU A 106 O VAL A 52 SHEET 7 A 7 VAL A 85 PRO A 90 -1 N PHE A 89 O LEU A 105 SHEET 1 B 7 GLN A 156 HIS A 161 0 SHEET 2 B 7 THR A 135 GLY A 140 -1 N GLY A 140 O GLN A 156 SHEET 3 B 7 PRO A 198 CYS A 201 -1 N VAL A 200 O TYR A 137 SHEET 4 B 7 VAL A 208 TRP A 215 -1 N GLY A 211 O LEU A 199 SHEET 5 B 7 SER A 226 LYS A 230 -1 N THR A 229 O ILE A 212 SHEET 6 B 7 MET A 180 GLY A 184A-1 N ALA A 183 O SER A 226 SHEET 7 B 7 HIS A 161 ILE A 163 -1 N ILE A 163 O CYS A 182

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 9.80

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