PDB Short entry for 1M1V HEADER HYDROLASE 20-JUN-02 1M1V TITLE EXPLORING THE SUBSTRATE AFFINITIES OF MMP-3, ADAM-9 AND TITLE 2 ADAM-10 USING MOLECULAR MODELLING AND DYNAMICS SIMULATIONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: MELTRIN GAMMA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN; COMPND 5 SYNONYM: A DISINTEGRIN AND METALLOPROTEINASE DOMAIN 9; COMPND 6 METALLOPROTEASE/DISINTEGRIN/CYSTEINE-RICH PROTEIN; ADAM-9; COMPND 7 EC: 3.4.24.17; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: EMPIRICAL SUBSTRATE; COMPND 10 CHAIN: B; COMPND 11 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 KEYWDS ZN-BINDING, METALLOPROTEASE, SIMILAR TO SNAKE VENOME KEYWDS 2 ACUTOLYSIN-C, ADAMALYSIN FOLD, DIMERIC, SUBSTRATE EXPDTA THEORETICAL MODEL AUTHOR S.MANZETTI,D.R.MCCULLOCH,A.C.HERINGTON REVDAT 2 04-APR-05 1M1V 1 JRNL REMARK REVDAT 1 05-JUL-02 1M1V 0 SPRSDE 05-JUL-02 1M1V 1KNH JRNL AUTH S.MANZETTI,D.R.MCCULLOCH,A.C.HERINGTON, JRNL AUTH 2 D.VAN DER SPOEL JRNL TITL MODELING OF ENZYME-SUBSTRATE COMPLEXES FOR THE JRNL TITL 2 METALLOPROTEASES MMP-3, ADAM-9 AND ADAM-10 JRNL REF COMPUT.AIDED DES. V. 17 551 2003 JRNL REFN ASTM CAIDA5 UK ISSN 0010-4485 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 1M1V COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PRAGUE ON 27-JUN-2002. REMARK 100 THE RCSB ID CODE IS RCSB016494. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: SIMULATED IN VIRTUAL 125NM3-BOX FILLED WITH ~3200 WATER REMARK 220 MOLECULES AND MINIMIZED WITH THE SOLVENT WITH 100 STEPS REMARK 220 (SD). THE SIMULATION WAS CARRIED OUT AT 300K IN A 2.1NS- REMARK 220 INTERVAL WITH A TIME-STEP OF 1FS USING THE GROMOS96 43A2 REMARK 220 FORCE FIELD IN THE GROMACS 3.1.1 PACKAGE. SINGLE POINT REMARK 220 CHARGE (SPC) WATER MOLECULES WERE USED BECAUSE THIS REMARK 220 MODEL WAS RECENTLY RECOMMENDED. THE POSITIONS OF THE REMARK 220 WATER MOLECULES WERE OPTIMISED WITH A 100-STEP SD REMARK 220 MINIMIZATION ALL WATER MOLECULES WERE CONSTRAINED USING REMARK 220 THE SETTLE ALGORITHM. ALL N- AND C-TERMINI WERE ASSIGNED REMARK 220 A NEUTRAL STATE AND THE ZN-CHELATING HISTIDINE RESIDUES REMARK 220 WERE PROTONATED AT THE δ-NITROGEN, AND THE OVERALL REMARK 220 CHARGE WAS NEUTRALIZED BY ADDING AN ARBITRARY NUMBER OF REMARK 220 SODIUM AND CHLORINE ATOMS TO THE SYSTEM. DISTANCE REMARK 220 RESTRAINTS WERE APPLIED FOR THE ZN-ION WITH ITS SELECTED REMARK 220 ATOMS: ZN2+-εN: 2-2.1 ,. THE CHOICE OF CALCIUM- REMARK 220 CHELATING ATOMS IN THE DISTANCE RESTRAINTS DERIVES FROM REMARK 220 EXPERIMENTAL DATA OF THE CRYSTAL STRUCTURES OF MMP-3. REMARK 220 CHEMICAL BONDS WERE SIMULATED USING THE LINCS ALGORITHM. REMARK 220 ENERGIES WERE COMPUTED ONCE PER PICOSECOND BY AVERAGING REMARK 220 OVER 100FS INTERVALS, AND TEMPERATURE COUPLING WAS REMARK 220 CARRIED OUT USING THE BERENDSEN SCHEME. SHORT- AND LONG- REMARK 220 RANGE ELECTROSTATICS WERE SIMULATED USING PARTICLE-MESH REMARK 220 EWALD METHOD WITH A DISTANCE TO NEIGHBOURS: OF 1NM; A REMARK 220 VAN DER WAAL CUT-OFF OF 1NM; AN ELECTROSTATIC CUT-OFF OF REMARK 220 1NM AND A DIELECTRIC CONSTANT OF 1. 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O ALA A 110 CB ALA B 2 1.84 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 1 HIS A 145 CG HIS A 145 ND1 -0.085 REMARK 500 2 ASN A 198 C ASN A 198 O 0.131 REMARK 500 2 GLY B 8 C GLY B 8 O 0.132 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 MET A 166 CG - SD - CE ANGL. DEV. = 19.9 DEGREES REMARK 500 1 ASN A 167 C - N - CA ANGL. DEV. = 23.0 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 SER A 119 6.28 117.34 REMARK 500 1 ASP A 152 117.51 119.06 REMARK 500 1 ILE A 165 -140.22 130.64 REMARK 500 1 ALA A 170 -99.46 -174.28 REMARK 500 2 SER A 173 -85.09 42.12 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 ASN A 150 HIS A 151 1 -145.24 REMARK 500 CYS A 164 ILE A 165 1 123.11 REMARK 500 ALA A 170 SER A 171 1 -103.53 DBREF 1M1V A 2 198 GB 4501915 NP_003807 208 404 SEQRES 1 A 197 LEU PRO GLN THR ARG TYR VAL GLU LEU PHE ILE VAL VAL SEQRES 2 A 197 ASP LYS GLU ARG TYR ASP MET MET GLY ARG ASN GLN THR SEQRES 3 A 197 ALA VAL ARG GLU GLU MET ILE LEU LEU ALA ASN TYR LEU SEQRES 4 A 197 ASP SER MET TYR ILE MET LEU ASN ILE ARG ILE VAL LEU SEQRES 5 A 197 VAL GLY LEU GLU ILE TRP THR ASN GLY ASN LEU ILE ASN SEQRES 6 A 197 ILE VAL GLY GLY ALA GLY ASP VAL LEU GLY ASN PHE VAL SEQRES 7 A 197 GLN TRP ARG GLU LYS PHE LEU ILE THR ARG ARG ARG HIS SEQRES 8 A 197 ASP SER ALA GLN LEU VAL LEU LYS LYS GLY PHE GLY GLY SEQRES 9 A 197 THR ALA GLY MET ALA PHE VAL GLY THR VAL CYS SER ARG SEQRES 10 A 197 SER HIS ALA GLY GLY ILE ASN VAL PHE GLY GLN ILE THR SEQRES 11 A 197 VAL GLU THR PHE ALA SER ILE VAL ALA HIS GLU LEU GLY SEQRES 12 A 197 HIS ASN LEU GLY MET ASN HIS ASP ASP GLY ARG ASP CYS SEQRES 13 A 197 SER CYS GLY ALA LYS SER CYS ILE MET ASN SER GLY ALA SEQRES 14 A 197 SER GLY SER ARG ASN PHE SER SER CYS SER ALA GLU ASP SEQRES 15 A 197 PHE GLU LYS LEU THR LEU ASN LYS GLY GLY ASN CYS LEU SEQRES 16 A 197 LEU ASN SEQRES 1 B 8 ALA ALA LEU TYR LEU VAL CYS GLY HET ZN A 1 1 HETNAM ZN ZINC ION FORMUL 3 ZN ZN 2+ HELIX 1 1 ASP A 15 MET A 22 1 8 HELIX 2 2 ASN A 25 ILE A 45 1 21 HELIX 3 3 GLY A 70 PHE A 85 1 16 HELIX 4 4 GLU A 133 LEU A 147 1 15 HELIX 5 5 SER A 177 GLY A 192 1 16 HELIX 6 6 GLY A 193 LEU A 197 5 5 SHEET 1 A 6 ILE A 49 ILE A 58 0 SHEET 2 A 6 ARG A 6 VAL A 14 1 N VAL A 14 O GLU A 57 SHEET 3 A 6 SER A 94 LEU A 99 1 O VAL A 98 N VAL A 13 SHEET 4 A 6 ALA A 121 ASN A 125 1 O ILE A 124 N LEU A 97 SHEET 5 A 6 GLY A 105 ALA A 110 -1 N MET A 109 O GLY A 123 SHEET 6 A 6 LEU B 3 CYS B 7 -1 O LEU B 3 N ALA A 110 SSBOND 1 CYS A 116 CYS A 195 SSBOND 2 CYS A 157 CYS A 179 SSBOND 3 CYS A 159 CYS A 164 CISPEP 1 GLY A 104 GLY A 105 1 -6.86 CISPEP 2 ASP A 156 CYS A 157 1 3.37 CISPEP 3 MET A 166 ASN A 167 1 4.65 CISPEP 4 GLY A 169 ALA A 170 1 12.44 CISPEP 5 PHE A 176 SER A 177 1 15.17 CISPEP 6 GLY A 104 GLY A 105 2 2.13 CISPEP 7 ASP A 156 CYS A 157 2 19.86 CISPEP 8 MET A 166 ASN A 167 2 -1.48 CISPEP 9 GLY A 169 ALA A 170 2 0.27 CISPEP 10 ALA A 170 SER A 171 2 4.82 CISPEP 11 PHE A 176 SER A 177 2 -2.41 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