PDB Short entry for 1QVD HEADER HYDROLASE 27-AUG-03 1QVD TITLE THE COMMON ACUTE LYMPHOBLASTIC LEUKEMIA ANTIGEN IN COMPLEX TITLE 2 WITH A NATURAL P5-P2' SUBSTRATE, BEFORE, DURING AND AFTER TITLE 3 MOLECULAR SIMULATION IN WATER. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEPRILYSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ECTODOMAIN; COMPND 5 SYNONYM: NEUTRAL ENDOPEPTIDASE, NEP, ENKEPHALINASE, COMMON COMPND 6 ACUTE LYMPHOCYTIC LEUKEMIA ANTIGEN, CALLA, NEUTRAL COMPND 7 ENDOPEPTIDASE 24.11, CD10; COMPND 8 EC: 3.4.24.11; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: P5-P2' OLIGOPEPTIDE SUBSTRATE; COMPND 11 CHAIN: B; COMPND 12 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: THIS PEPTIDE IS A SYNTHETIC CONSTRUCT KEYWDS NEPRILYSIN, CD10, CALLA, COMMON ACUTE LYMPHOBLASTIC KEYWDS 2 LAEUKEMIA ANTIGEN, NEUTRAL ENDOPEPTIDASE 24.11, SUBSTRATE EXPDTA THEORETICAL MODEL AUTHOR S.MANZETTI REVDAT 2 28-OCT-03 1QVD 1 JRNL REVDAT 1 16-SEP-03 1QVD 0 SPRSDE 16-SEP-03 1QVD 1MB7 JRNL AUTH S.MANZETTI JRNL TITL COMPUTER MODELING AND NANOSECOND SIMULATION OF THE JRNL TITL 2 ENZYME-SUBSTRATE COMPLEX OF THE COMMON JRNL TITL 3 LYMPHOBLASTIC LEUKEMIA ANTIGEN (NEPRILYSIN) JRNL TITL 4 INDICATES SHARED RESIDUES AT THE PRIMARY JRNL TITL 5 SPECIFICITY POCKET (S1') WITH MATRIX JRNL TITL 6 METALLOPROTEASES. JRNL REF J.MOL.MODEL. V. 9 348 2003 JRNL REFN GE ESSN 0948-5023 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS 3.1 REMARK 3 AUTHORS : JONES,ZOU,COWAN,KJELDGAARD REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QVD COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-2003. REMARK 100 THE RCSB ID CODE IS RCSB020113. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: (FROM PUBLICATION:)THE NANOSECOND SIMULATION OF NEP AND REMARK 220 SUBSTRATE WAS PREPARED IN A VIRTUAL BOX OF 730 NM3 REMARK 220 (VECTOR UNITS 999) FILLED WITH 20,639 WATER MOLECULES REMARK 220 ENCOMPASSING A SYSTEM OF 73,060 ATOMS. ALL N/C TERMINI REMARK 220 WERE ASSIGNED THE NEUTRAL STATE AND THE HISTIDINE REMARK 220 RESIDUES WERE PROTONATED AT THEIR DELTA NITROGEN. THE REMARK 220 NEUTRAL TERMINI WERE CHOSEN BECAUSE THE SYSTEM WAS NOT REMARK 220 NEUTRALIZED, SO TO AVOID INTERFERENCE OF NEUTRALIZING REMARK 220 IONS AT THE ZINCSUBSTRATE INTERFACE. FLEXIBLE WATER REMARK 220 MOLECULES [32] WERE ADAPTED TO THE ENZYMESUBSTRATE REMARK 220 COMPLEX WITH 500 STEPS OF ENERGY MINIMIZATION (STEEPEST REMARK 220 DESCENT). THE ENZYME WAS IMMOBILIZED (IN THE INPUT REMARK 220 PARAMETER FILE) SO THE FLEXIBLE WATERS COULD ADJUST TO REMARK 220 ITS EMPIRICAL STATE, WHILE THE SUBSTRATE WAS NOT REMARK 220 IMMOBILIZED AND ADJUSTABLE WITH THE ENZYME AND SOLVENT REMARK 220 ACCORDING TO CHEMICAL AND GEOMETRICAL SATISFACTION. THE REMARK 220 SIMULATION WAS PERFORMED USING THE GROMACS 3.1.4 PACKAGE REMARK 220 [33] WITH THE OPLS-AA/L FORCE FIELD. [34] THE SPC WATER REMARK 220 MODEL (SINGLE POINT CHARGE [35]) WAS USED TO SIMULATE REMARK 220 THE SOLVENT PHASE, AND AN INTEGRATION STEP SIZE OF 2 FS REMARK 220 WAS APPLIED. ELECTROSTATICS WERE SIMULATED WITH A REMARK 220 GENERALIZED REACTION FIELD [36] (GRF) WITH A COULOMB CUT REMARK 220 -OFF OF 9 AND A LENNARD-JONES CUT-OFF OF 15 (IN THE REMARK 220 AUTHOR'S PERSONAL EXPERIENCE, THESE CUT-OFFS HAVE SHOWN REMARK 220 TO BE APPROPRIATE FOR LARGE SYSTEMS WHEN USING GRF). REMARK 220 TEMPERATURE COUPLING WAS SET TO 298 K AND THE PRESSURE REMARK 220 WAS KEPT AT 1 ATM USING THE BERENDSEN TEMPERATURE- AND REMARK 220 PRESSURE-COUPLING SCHEME. [37] H BONDS WERE SIMULATED REMARK 220 USING THE LINCS ALGORITHM, [38] AND ALL OTHER BONDS WERE REMARK 220 SIMULATED USING A HARMONIC POTENTIAL. THE TWO HISTIDINE REMARK 220 RESIDUES (HEXXH MOTIF) AND THE CATALYTIC ZINC ION THEY REMARK 220 CHELATE WERE KEPT IMMOBILIZED DURING THE SIMULATION, REMARK 220 BECAUSE THESE RESIDUES ARE STRUCTURALLY STABLE AT REMARK 220 GROUND/TRANSITION STATE. [39] IN THIS WAY, THE POSITION REMARK 220 OF THE SUBSTRATE AND SURROUNDING RESIDUES WOULD ADAPT TO REMARK 220 THE RIGID CATALYTIC CENTER, WHICH HAS PREVIOUSLY SHOWN REMARK 220 TO BECOME VICTIM TO ARTIFACTS EASILY BECAUSE OF AN REMARK 220 IMPERFECT TOPOLOGY FOR THE SPECIAL CATALYTIC ZINC ION REMARK 220 (DAVID VAN DER SPOEL, PERSONAL COMMUNICATION). MODEL 1 REMARK 220 REPRESENTS THE STRUCTURE BEFORE MD SIMULATION, WHILE REMARK 220 MODELS 2 AND 3 REPRESENT THE STRUCTURES AT 500 AND REMARK 220 1000PS INTO THE MD SIMULATION RESPECTIVELY. 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: 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 1 PRO A 266 C - N - CA ANGL. DEV. = 19.8 DEGREES REMARK 500 1 ALA B 699 N - CA - CB ANGL. DEV. =-21.2 DEGREES REMARK 500 1 ALA B 699 CA - C - O ANGL. DEV. =-18.9 DEGREES REMARK 500 1 ALA B 701 N - CA - CB ANGL. DEV. =-22.1 DEGREES 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 1 LEU A 146 -54.41 67.56 REMARK 500 1 THR B 700 133.47 109.79 REMARK 500 2 LEU A 146 -33.47 68.21 REMARK 500 3 LEU A 146 -39.77 69.91 REMARK 500 3 ASN A 263 -33.53 94.62 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 PHE B 703 GLY B 704 1 -121.71 REMARK 500 LYS A 265 PRO A 266 2 -38.37 REMARK 500 GLN A 514 GLN A 515 2 144.77 REMARK 500 ILE A 426 GLY A 427 3 148.32 REMARK 500 PHE B 703 GLY B 704 3 -148.64 REMARK 999 REMARK 999 SEQUENCE REMARK 999 AN APPROPRIATE SEQUENCE DATABASE REFERENCE REMARK 999 FOR P5-P2' OLIGOPEPTIDE SUBSTRATE WAS NOT REMARK 999 AVAILABLE AT THE TIME OF PROCESSING. DBREF 1QVD A 1 696 UNP P08473 NEP_HUMAN 54 749 SEQRES 1 A 696 GLY ILE CYS LYS SER SER ASP CYS ILE LYS SER ALA ALA SEQRES 2 A 696 ARG LEU ILE GLN ASN MET ASP ALA THR THR GLU PRO CYS SEQRES 3 A 696 THR ASP PHE PHE LYS TYR ALA CYS GLY GLY TRP LEU LYS SEQRES 4 A 696 ARG ASN VAL ILE PRO GLU THR SER SER ARG TYR GLY ASN SEQRES 5 A 696 PHE ASP ILE LEU ARG ASP GLU LEU GLU VAL VAL LEU LYS SEQRES 6 A 696 ASP VAL LEU GLN GLU PRO LYS THR GLU ASP ILE VAL ALA SEQRES 7 A 696 VAL GLN LYS ALA LYS ALA LEU TYR ARG SER CYS ILE ASN SEQRES 8 A 696 GLU SER ALA ILE ASP SER ARG GLY GLY GLU PRO LEU LEU SEQRES 9 A 696 LYS LEU LEU PRO ASP ILE TYR GLY TRP PRO VAL ALA THR SEQRES 10 A 696 GLU ASN TRP GLU GLN LYS TYR GLY ALA SER TRP THR ALA SEQRES 11 A 696 GLU LYS ALA ILE ALA GLN LEU ASN SER LYS TYR GLY LYS SEQRES 12 A 696 LYS VAL LEU ILE ASN LEU PHE VAL GLY THR ASP ASP LYS SEQRES 13 A 696 ASN SER VAL ASN HIS VAL ILE HIS ILE ASP GLN PRO ARG SEQRES 14 A 696 LEU GLY LEU PRO SER ARG ASP TYR TYR GLU CYS THR GLY SEQRES 15 A 696 ILE TYR LYS GLU ALA CYS THR ALA TYR VAL ASP PHE MET SEQRES 16 A 696 ILE SER VAL ALA ARG LEU ILE ARG GLN GLU GLU ARG LEU SEQRES 17 A 696 PRO ILE ASP GLU ASN GLN LEU ALA LEU GLU MET ASN LYS SEQRES 18 A 696 VAL MET GLU LEU GLU LYS GLU ILE ALA ASN ALA THR ALA SEQRES 19 A 696 LYS PRO GLU ASP ARG ASN ASP PRO MET LEU LEU TYR ASN SEQRES 20 A 696 LYS MET THR LEU ALA GLN ILE GLN ASN ASN PHE SER LEU SEQRES 21 A 696 GLU ILE ASN GLY LYS PRO PHE SER TRP LEU ASN PHE THR SEQRES 22 A 696 ASN GLU ILE MET SER THR VAL ASN ILE SER ILE THR ASN SEQRES 23 A 696 GLU GLU ASP VAL VAL VAL TYR ALA PRO GLU TYR LEU THR SEQRES 24 A 696 LYS LEU LYS PRO ILE LEU THR LYS TYR SER ALA ARG ASP SEQRES 25 A 696 LEU GLN ASN LEU MET SER TRP ARG PHE ILE MET ASP LEU SEQRES 26 A 696 VAL SER SER LEU SER ARG THR TYR LYS GLU SER ARG ASN SEQRES 27 A 696 ALA PHE ARG LYS ALA LEU TYR GLY THR THR SER GLU THR SEQRES 28 A 696 ALA THR TRP ARG ARG CYS ALA ASN TYR VAL ASN GLY ASN SEQRES 29 A 696 MET GLU ASN ALA VAL GLY ARG LEU TYR VAL GLU ALA ALA SEQRES 30 A 696 PHE ALA GLY GLU SER LYS HIS VAL VAL GLU ASP LEU ILE SEQRES 31 A 696 ALA GLN ILE ARG GLU VAL PHE ILE GLN THR LEU ASP ASP SEQRES 32 A 696 LEU THR TRP MET ASP ALA GLU THR LYS LYS ARG ALA GLU SEQRES 33 A 696 GLU LYS ALA LEU ALA ILE LYS GLU ARG ILE GLY TYR PRO SEQRES 34 A 696 ASP ASP ILE VAL SER ASN ASP ASN LYS LEU ASN ASN GLU SEQRES 35 A 696 TYR LEU GLU LEU ASN TYR LYS GLU ASP GLU TYR PHE GLU SEQRES 36 A 696 ASN ILE ILE GLN ASN LEU LYS PHE SER GLN SER LYS GLN SEQRES 37 A 696 LEU LYS LYS LEU ARG GLU LYS VAL ASP LYS ASP GLU TRP SEQRES 38 A 696 ILE SER GLY ALA ALA VAL VAL ASN ALA PHE TYR SER SER SEQRES 39 A 696 GLY ARG ASN GLN ILE VAL PHE PRO ALA GLY ILE LEU GLN SEQRES 40 A 696 PRO PRO PHE PHE SER ALA GLN GLN SER ASN SER LEU ASN SEQRES 41 A 696 TYR GLY GLY ILE GLY MET VAL ILE GLY HIS GLU ILE THR SEQRES 42 A 696 HIS GLY PHE ASP ASP ASN GLY ARG ASN PHE ASN LYS ASP SEQRES 43 A 696 GLY ASP LEU VAL ASP TRP TRP THR GLN GLN SER ALA SER SEQRES 44 A 696 ASN PHE LYS GLU GLN SER GLN CYS MET VAL TYR GLN TYR SEQRES 45 A 696 GLY ASN PHE SER TRP ASP LEU ALA GLY GLY GLN HIS LEU SEQRES 46 A 696 ASN GLY ILE ASN THR LEU GLY GLU ASN ILE ALA ASP ASN SEQRES 47 A 696 GLY GLY LEU GLY GLN ALA TYR ARG ALA TYR GLN ASN TYR SEQRES 48 A 696 ILE LYS LYS ASN GLY GLU GLU LYS LEU LEU PRO GLY LEU SEQRES 49 A 696 ASP LEU ASN HIS LYS GLN LEU PHE PHE LEU ASN PHE ALA SEQRES 50 A 696 GLN VAL TRP CYS GLY THR TYR ARG PRO GLU TYR ALA VAL SEQRES 51 A 696 ASN SER ILE LYS THR ASP VAL HIS SER PRO GLY ASN PHE SEQRES 52 A 696 ARG ILE ILE GLY THR LEU GLN ASN SER ALA GLU PHE SER SEQRES 53 A 696 GLU ALA PHE HIS CYS ARG LYS ASN SER TYR MET ASN PRO SEQRES 54 A 696 GLU LYS LYS CYS ARG VAL TRP SEQRES 1 B 7 LEU ALA THR ALA CYS PHE GLY HET ZN A 697 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ FORMUL 4 HOH *1356(H2 O1) HELIX 1 1 SER A 5 MET A 19 1 15 HELIX 2 2 ASP A 28 ASN A 41 1 14 HELIX 3 3 ASN A 52 GLN A 69 1 18 HELIX 4 4 ILE A 76 ASN A 91 1 16 HELIX 5 5 ASN A 91 ARG A 98 1 8 HELIX 6 6 GLY A 100 LEU A 107 1 8 HELIX 7 7 PRO A 108 TYR A 111 5 4 HELIX 8 8 TRP A 113 THR A 117 5 5 HELIX 9 9 ASN A 119 TYR A 124 1 6 HELIX 10 10 THR A 129 GLY A 142 1 14 HELIX 11 11 SER A 174 CYS A 180 5 7 HELIX 12 12 THR A 181 ILE A 183 5 3 HELIX 13 13 TYR A 184 GLU A 206 1 23 HELIX 14 14 ASP A 211 THR A 233 1 23 HELIX 15 15 LYS A 235 ARG A 239 5 5 HELIX 16 16 ASP A 241 TYR A 246 1 6 HELIX 17 17 LEU A 251 PHE A 258 1 8 HELIX 18 18 SER A 268 SER A 278 1 11 HELIX 19 19 THR A 279 ASN A 281 5 3 HELIX 20 20 ALA A 294 THR A 306 1 13 HELIX 21 21 SER A 309 VAL A 326 1 18 HELIX 22 22 SER A 327 LEU A 329 5 3 HELIX 23 23 SER A 330 SER A 336 1 7 HELIX 24 24 ARG A 337 GLY A 346 1 10 HELIX 25 25 ALA A 352 MET A 365 1 14 HELIX 26 26 MET A 365 PHE A 378 1 14 HELIX 27 27 GLU A 381 LEU A 404 1 24 HELIX 28 28 ASP A 408 ILE A 422 1 15 HELIX 29 29 ASP A 430 ASN A 435 1 6 HELIX 30 30 ASN A 435 TYR A 443 1 9 HELIX 31 31 GLU A 452 LYS A 470 1 19 HELIX 32 32 GLY A 504 LEU A 506 5 3 HELIX 33 33 SER A 516 GLY A 523 1 8 HELIX 34 34 GLY A 523 GLY A 535 1 13 HELIX 35 35 ASN A 539 PHE A 543 5 5 HELIX 36 36 THR A 554 ASN A 574 1 21 HELIX 37 37 TRP A 577 GLY A 581 5 5 HELIX 38 38 THR A 590 GLY A 616 1 27 HELIX 39 39 ASN A 627 TRP A 640 1 14 HELIX 40 40 ARG A 645 ASP A 656 1 12 HELIX 41 41 PRO A 660 ASN A 671 1 12 HELIX 42 42 SER A 672 PHE A 679 1 8 SHEET 1 A 2 ARG A 49 GLY A 51 0 SHEET 2 A 2 GLY A 642 TYR A 644 -1 O THR A 643 N TYR A 50 SHEET 1 B 4 ASN A 148 ASP A 154 0 SHEET 2 B 4 ASN A 157 ASP A 166 -1 O ASN A 160 N ASP A 154 SHEET 3 B 4 ASP A 289 VAL A 292 1 O VAL A 291 N ILE A 165 SHEET 4 B 4 LYS A 248 THR A 250 -1 N MET A 249 O VAL A 290 SHEET 1 C 4 LYS A 423 GLY A 427 0 SHEET 2 C 4 GLN A 498 PRO A 502 1 O PHE A 501 N GLY A 427 SHEET 3 C 4 ALA A 490 SER A 493 -1 N PHE A 491 O VAL A 500 SHEET 4 C 4 THR B 700 PHE B 703 -1 O ALA B 701 N TYR A 492 SSBOND 1 CYS A 3 CYS A 8 SSBOND 2 CYS A 26 CYS A 681 SSBOND 3 CYS A 34 CYS A 641 SSBOND 4 CYS A 89 CYS A 357 SSBOND 5 CYS A 180 CYS A 188 SSBOND 6 CYS A 567 CYS A 693 CISPEP 1 LYS A 265 PRO A 266 1 -0.95 CISPEP 2 PRO A 508 PRO A 509 1 0.33 CISPEP 3 PRO A 508 PRO A 509 2 4.31 CISPEP 4 LYS A 265 PRO A 266 3 -7.43 CISPEP 5 PRO A 508 PRO A 509 3 21.16 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