PDB Short entry for 1A9A HEADER EXTRACELLULAR MATRIX 03-APR-98 1A9A TITLE MOLECULAR FEATURES OF THE COLLAGEN V HEPARIN BINDING SITE, TITLE 2 THEORETICAL MODEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: HETEROTRIMER COLLAGEN [ALPHA 1(V)]; COMPND 3 CHAIN: A, C; COMPND 4 FRAGMENT: HEPARIN BINDING DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: HETEROTRIMER COLLAGEN [ALPHA 2(V)]; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: HEPARIN BINDING DOMAIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_PLASMID: PT7-7; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7-7 KEYWDS HETEROTRIMER COLLAGEN [ALPHA (1)V]2 [ALPHA (2)V], HEPARIN KEYWDS 2 BINDING SITE, EXTRACELLULAR MATRIX EXPDTA THEORETICAL MODEL AUTHOR F.DELACOUX,A.FICHARD,C.GEOURJON,R.GARRONE,F.RUGGIERO REVDAT 2 18-NOV-98 1A9A 3 ATOM COMPND REMARK TITLE REVDAT 2 2 3 JRNL KEYWDS HEADER REVDAT 1 21-OCT-98 1A9A 0 JRNL AUTH F.DELACOUX,A.FICHARD,C.GEOURJON,R.GARRONE, JRNL AUTH 2 F.RUGGIERO JRNL TITL MOLECULAR FEATURES OF THE COLLAGEN V HEPARIN JRNL TITL 2 BINDING SITE. JRNL REF J.BIOL.CHEM. V. 273 15069 1998 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 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: A TEMPLATE STRUCTURE WITH RANDOMIZED REMARK 3 COORDINATES AND IDEAL GEOMETRY WAS GENERATED (PROTOCOL " REMARK 3 GENERATE_TEMPLATE.INP", USING THE ALL-HYDROGEN FORCE FIELDS " REMARK 3 TOPALLHDG" AND "PARALLHDG"). THEN A SUBSTRUCTURE DISTANCE REMARK 3 GEOMETRY PROTOCOL WAS APPLIED ("DG_SUB_EMBED.INP"), REMARK 3 INTRODUCING THE NOE-DERIVED DISTANCE CONSTRAINTS TO GENERATE REMARK 3 UNREGULARIZED STRUCTURES WITH A PARTIAL SET OF COORDINATES. REMARK 3 THE COORDINATES OF THESE STRUCTURES WERE THEN REGULARIZED BY REMARK 3 SIMULATED ANNEALING USING THE "DGSA.INP" PROTOCOL CONSISTING REMARK 3 OF 9 PS OF HEAT PROCEDURE UP TO 2000 K BY INCREASING STEPS OF REMARK 3 50 K. THE CONTRIBUTION OF THE VAN DER WAALS TERMS WAS REDUCED REMARK 3 DURING THIS STAGE TO ALLOW A MAXIMAL EXPLORATION OF THE REMARK 3 CONFORMATIONAL SPACE. THE SYSTEM WAS COOLED DOWN TO 250 K BY REMARK 3 STEPS OF 25 K IN 10 PS WITH A CONCOMITANT INCREASE OF THE VAN REMARK 3 DER WAALS INTERACTIONS. IN A FOLLOWING STEP, THE STRUCTURE REMARK 3 WERE REFINED BY THE APPLICATION OF THE PROTOCOL "REFINE.INP", REMARK 3 CONSISTING OF SIMULATED ANNEALING AND FINAL ENERGY REMARK 3 MINIMISATION. IN THIS STEP, THE DURATION OF THE HIGH REMARK 3 TEMPERATURE STAGE WAS 50 PS, AND THE TEMPERATURE WAS DECREASED REMARK 3 FROM 1000 K DOWN TO 250 K BY STEPS OF 25 K. EACH STRUCTURE WAS REMARK 3 THEN SUBMITTED TO 5000 CYCLES OF POWELL ENERGY MINIMISATION. A REMARK 3 FINAL MINIMISATION STEP WAS APPLIED WITH THE STANDARD FORCE REMARK 3 FIELD PARAMETERS EXCEPT THAT KBONDS AND KANGLES WERE FIXED TO REMARK 3 600 KCAL.MOL-1=C5-2 AND 90 KCAL.MOL-1.RAD-2 RESPECTIVELY. REMARK 4 REMARK 4 1A9A COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THE COORDINATES OF THE PDB ENTRY 1CAG WERE USED TO REMARK 220 CALCULATE INTERPROTON DISTANCES. IN THIS WAY, 683 REMARK 220 CONSTRAINTS WERE INTRODUCED FOR THE TRIPLE HELICAL REMARK 220 REGION. IN ADDITION, AVERAGE DIHEDRAL ANGLES DEDUCED REMARK 220 FROM THE CRYSTAL STRUCTURE WERE ALSO INTRODUCED. THREE- REMARK 220 DIMENSIONAL STRUCTURES WERE GENERATED FROM THE SET OF REMARK 220 CONSTRAINTS WITH THE X-PLOR 3.8.5 PROGRAM USING THE REMARK 220 DEFAULT PARAMETER SET, EXCEPT FOR SOME MINOR REMARK 220 MODIFICATIONS TO INCREASE THE DURATION OF THE MOLECULAR REMARK 220 DYNAMIC SIMULATIONS AND THE NUMBER OF ENERGY REMARK 220 MINIMISATION STEPS. 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 860 REMARK 860 CORRECTION AFTER RELEASE REMARK 860 DATE: 18-NOV-98 REMARK 860 MODID: 1A9AA REMARK 860 MODIFIED BY: PDB REMARK 860 DESCRIPTION: CONVERTED FROM LAYER 1 OR NDB TO LAYER 2 REMARK 999 REMARK 999 SEQUENCE REMARK 999 1A9A A SWS P20908 1 - 903 NOT IN ATOMS LIST REMARK 999 1A9A A SWS P20908 925 - 1838 NOT IN ATOMS LIST REMARK 999 1A9A B SWS P05997 1 - 557 NOT IN ATOMS LIST REMARK 999 1A9A B SWS P05997 579 - 1496 NOT IN ATOMS LIST REMARK 999 1A9A C SWS P20908 1 - 903 NOT IN ATOMS LIST REMARK 999 1A9A C SWS P20908 925 - 1838 NOT IN ATOMS LIST DBREF 1A9A A 1 21 UNP P20908 CA15_HUMAN 904 924 DBREF 1A9A B 22 42 UNP P05997 CA25_HUMAN 558 578 DBREF 1A9A C 43 63 UNP P20908 CA15_HUMAN 904 924 SEQRES 1 A 21 GLY LYS PRO GLY PRO ARG GLY GLN ARG GLY PRO THR GLY SEQRES 2 A 21 PRO ARG GLY GLU ARG GLY PRO ARG SEQRES 1 B 21 GLY ARG PRO GLY GLU PRO GLY LEU PRO GLY ALA ARG GLY SEQRES 2 B 21 LEU THR GLY ASN PRO GLY VAL GLN SEQRES 1 C 21 GLY LYS PRO GLY PRO ARG GLY GLN ARG GLY PRO THR GLY SEQRES 2 C 21 PRO ARG GLY GLU ARG GLY PRO ARG 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