10 20 30 40 50 60 70 80 1M1W - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 20-JUN-02 1M1W
TITLE MOLECULAR DYNAMICS OF MMP-3, ADAM-9 AND ADAM-10: NEW TITLE 2 IMPLICATIONS ON FAMILIARITY, STRUCTURE, FUNCTION AND TITLE 3 SUBSTRATE AFFINITY
COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMELYSIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MMP-3; MATRIX METALLOPROTEINASE-3; TRANSIN-1; SL- COMPND 5 1; COMPND 6 EC: 3.4.24.17; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: AGPLACTCVP SUBSTRATE; COMPND 9 CHAIN: B; 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
KEYWDS METALLOPROTEASE, METZINCIN, MMP, MATRIXIN, MATRILYSIN, KEYWDS 2 PEPTIDIC, SUBSTRATE, DIMER
EXPDTA THEORETICAL MODEL
AUTHOR S.MANZETTI,D.R.MCCULLOCH,A.C.HERINGTON
REVDAT 2 05-APR-05 1M1W 1 JRNL EXPDTA REMARK REVDAT 1 05-JUL-02 1M1W 0
SPRSDE 05-JUL-02 1M1W 1KN8
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 1M1W 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 RCSB016495.
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 ZN- AND CA2+-IONS WITH THEIR REMARK 220 RESPECTIVE CHELATING ATOMS: ZN2+-εN: 2-2.1 , CA2+- REMARK 220 C=O: 2.2-2.5. THE CHOICE OF CALCIUM-CHELATING ATOMS IN REMARK 220 THE DISTANCE RESTRAINTS DERIVES FROM EXPERIMENTAL DATA REMARK 220 OF THE CRYSTAL STRUCTURE OF MMP-3. CHEMICAL BONDS WERE REMARK 220 SIMULATED USING THE LINCS ALGORITHM. ENERGIES WERE REMARK 220 COMPUTED ONCE PER PICOSECOND BY AVERAGING OVER 100FS REMARK 220 INTERVALS, AND TEMPERATURE COUPLING WAS CARRIED OUT REMARK 220 USING THE BERENDSEN SCHEME. SHORT- AND LONG- RANGE REMARK 220 ELECTROSTATICS WERE SIMULATED USING PARTICLE-MESH EWALD REMARK 220 METHOD WITH A DISTANCE TO NEIGHBOURS: OF 1NM; A VAN DER REMARK 220 WAAL CUT-OFF OF 1NM; AN ELECTROSTATIC CUT-OFF OF 1NM AND REMARK 220 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 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 1 ASP A 184 REMARK 465 2 ASP A 184
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 138 CA HIS A 138 CB -0.098 REMARK 500 1 LEU B 187 CB LEU B 187 CG -0.093 REMARK 500 1 LEU B 187 CG LEU B 187 CD1 -0.086 REMARK 500 2 PRO A 183 C PRO A 183 O 0.134 REMARK 500 2 PRO B 192 C PRO B 192 O 0.133 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 LEU B 187 N - CA - CB ANGL. DEV. =-22.8 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 ASN A 95 -103.88 52.85 REMARK 500 2 ASN A 95 -95.52 49.33 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 B 185 PRO B 186 1 94.48
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1B3D RELATED DB: PDB REMARK 900 MMP-3, METALLOPROTEASE
DBREF 1M1W A 16 184 UNP P08254 MM03_HUMAN 100 268
SEQRES 1 A 169 PHE ARG THR PHE PRO GLY ILE PRO LYS TRP ARG LYS THR SEQRES 2 A 169 HIS LEU THR TYR ARG ILE VAL ASN TYR THR PRO ASP LEU SEQRES 3 A 169 PRO LYS ASP ALA VAL ASP SER ALA VAL GLU LYS ALA LEU SEQRES 4 A 169 LYS VAL TRP GLU GLU VAL THR PRO LEU THR PHE SER ARG SEQRES 5 A 169 LEU TYR GLU GLY GLU ALA ASP ILE MET ILE SER PHE ALA SEQRES 6 A 169 VAL ARG GLU HIS GLY ASP PHE TYR PRO PHE ASP GLY PRO SEQRES 7 A 169 GLY ASN VAL LEU ALA HIS ALA TYR ALA PRO GLY PRO GLY SEQRES 8 A 169 ILE ASN GLY ASP ALA HIS PHE ASP ASP ASP GLU GLN TRP SEQRES 9 A 169 THR LYS ASP THR THR GLY THR ASN LEU PHE LEU VAL ALA SEQRES 10 A 169 ALA HIS GLU ILE GLY HIS SER LEU GLY LEU PHE HIS SER SEQRES 11 A 169 ALA ASN THR GLU ALA LEU MET TYR PRO LEU TYR HIS SER SEQRES 12 A 169 LEU THR ASP LEU THR ARG PHE ARG LEU SER GLN ASP ASP SEQRES 13 A 169 ILE ASN GLY ILE GLN SER LEU TYR GLY PRO PRO PRO ASP SEQRES 1 B 8 GLY PRO LEU ALA THR CYS VAL PRO
HET ZN A 1 1 HET ZN A 2 1 HET CA A 3 1 HET CA A 4 1 HET CA A 5 1
HETNAM ZN ZINC ION HETNAM CA CALCIUM ION
FORMUL 3 ZN 2(ZN 2+) FORMUL 5 CA 3(CA 2+)
HELIX 1 1 PRO A 42 GLU A 59 1 18 HELIX 2 2 LEU A 128 LEU A 140 1 13 HELIX 3 3 ASP A 161 PHE A 165 5 5 HELIX 4 4 SER A 168 GLY A 180 1 13
SHEET 1 A 6 THR A 64 ARG A 67 0 SHEET 2 A 6 HIS A 29 ILE A 34 1 N LEU A 30 O THR A 64 SHEET 3 A 6 ILE A 75 ALA A 80 1 O ILE A 77 N ARG A 33 SHEET 4 A 6 ALA A 111 ASP A 114 1 O PHE A 113 N ALA A 80 SHEET 5 A 6 VAL A 96 TYR A 101 -1 N HIS A 99 O HIS A 112 SHEET 6 A 6 PRO B 186 CYS B 190 -1 O THR B 189 N ALA A 98 SHEET 1 B 2 TRP A 119 THR A 120 0 SHEET 2 B 2 THR A 126 ASN A 127 1 O THR A 126 N THR A 120
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