PDB Short entry for 1RD0 HEADER RIBONUCLEIC ACID 05-NOV-03 1RD0 TITLE THE INTERACTION BETWEEN MRNA AND TRNA (MODEL B2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: P-SITE TRNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: A-SITE TRNA; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: SINGLE-STRANDED MRNA; COMPND 11 CHAIN: C; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES KEYWDS INTERACTION, MRNA, TRNA EXPDTA THEORETICAL MODEL AUTHOR C.LIU,X.WANG REVDAT 1 18-NOV-03 1RD0 0 JRNL AUTH C.LIU,X.WANG JRNL TITL THE INTERACTION BETWEEN MRNA AND TRNA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : INSIGHTII 2000 REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RD0 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-NOV-2003. REMARK 100 THE RCSB ID CODE IS RCSB020657. REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: MD SIMULATION: FIRST, 1MFK WAS CHOSEN AS MRNA AND REMARK 220 UNFOLDED USING DYNAMICS SIMULATION. SECOND, THE REMARK 220 ANTICODONS OF 1EHZ WAS MODIFIED. TO HAVE A REASONABLE REMARK 220 START OF SIMULATION, 1EHZ WAS CHOSEN BECAUSE IT HAS HIGH REMARK 220 RESOLUTION. THIRD, AMBER FORCEFIELD WAS CHOSEN AND REMARK 220 SODIUMS WERE TREATED AS COUNTER IONS, THEN, SOAKED IN REMARK 220 WATER AND FURTHER SIMULATIONS WERE PERFORMED. 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RCZ RELATED DB: PDB REMARK 900 THE SAME STRUCTURE, MODEL A2 REMARK 900 RELATED ID: 1RD1 RELATED DB: PDB REMARK 900 THE SAME STRUCTURE, MODEL C2 REMARK 900 RELATED ID: 1RD2 RELATED DB: PDB REMARK 900 THE SAME STRUCTURE, MODEL D2 SEQRES 1 A 76 G C G G A U U U A 2MG C U C SEQRES 2 A 76 A G H2U H2U G G G A G A G C M2G SEQRES 3 A 76 C C A G A OMC U U G C YG A PSU SEQRES 4 A 76 5MC U G G A G 7MG U C 5MC U G U SEQRES 5 A 76 G 5MU PSU C G 1MA U C C A C A G SEQRES 6 A 76 A A U U C G C A C C A SEQRES 1 B 76 G C G G A U U U A 2MG C U C SEQRES 2 B 76 A G H2U H2U G G G A G A G C M2G SEQRES 3 B 76 C C A G A OMC U G C C YG A PSU SEQRES 4 B 76 5MC U G G A G 7MG U C 5MC U G U SEQRES 5 B 76 G 5MU PSU C G 1MA U C C A C A G SEQRES 6 B 76 A A U U C G C A C C A SEQRES 1 C 23 G G C G G U U G C A G G U SEQRES 2 C 23 C U G C A C C G C C MODRES 1RD0 2MG A 10 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1RD0 H2U A 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1RD0 H2U A 17 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1RD0 M2G A 26 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1RD0 OMC A 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 1RD0 YG A 37 G WYBUTOSINE MODRES 1RD0 5MC A 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1RD0 7MG A 46 G MODRES 1RD0 5MC A 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1RD0 5MU A 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1RD0 1MA A 58 A MODRES 1RD0 2MG B 10 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1RD0 H2U B 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1RD0 H2U B 17 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1RD0 M2G B 26 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1RD0 OMC B 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 1RD0 YG B 37 G WYBUTOSINE MODRES 1RD0 5MC B 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1RD0 7MG B 46 G MODRES 1RD0 5MC B 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1RD0 5MU B 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1RD0 1MA B 58 A MODRES 1RD0 PSU A 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1RD0 PSU A 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1RD0 PSU B 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1RD0 PSU B 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE HET 2MG A 10 36 HET H2U A 16 31 HET H2U A 17 31 HET M2G A 26 39 HET OMC A 32 34 HET YG A 37 64 HET PSU A 39 27 HET 5MC A 40 33 HET 7MG A 46 37 HET 5MC A 49 33 HET 5MU A 54 31 HET PSU A 55 27 HET 1MA A 58 36 HET 2MG B 10 36 HET H2U B 16 31 HET H2U B 17 31 HET M2G B 26 39 HET OMC B 32 34 HET YG B 37 64 HET PSU B 39 27 HET 5MC B 40 33 HET 7MG B 46 37 HET 5MC B 49 33 HET 5MU B 54 31 HET PSU B 55 27 HET 1MA B 58 36 HETNAM 2MG 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM H2U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE HETNAM M2G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM YG WYBUTOSINE HETNAM PSU PSEUDOURIDINE-5'-MONOPHOSPHATE HETNAM 5MC 5-METHYLCYTIDINE-5'-MONOPHOSPHATE HETNAM 7MG 7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE HETNAM 5MU 5-METHYLURIDINE 5'-MONOPHOSPHATE HETNAM 1MA 6-HYDRO-1-METHYLADENOSINE-5'-MONOPHOSPHATE HETSYN YG Y-BASE; 1H-IMIDAZO(1,2-ALPHA)PURINE-7-BUTANOIC ACID,4, HETSYN 2 YG 9-DIHYDRO-ALPHA-((METHOXYCARBONYL)AMINO)-4,6-DIMETHYL- HETSYN 3 YG 9-OXO-METHYL ESTER FORMUL 1 2MG 2(C11 H16 N5 O8 P) FORMUL 1 H2U 4(C9 H15 N2 O9 P) FORMUL 1 M2G 2(C12 H18 N5 O8 P) FORMUL 1 OMC 2(C10 H16 N3 O8 P) FORMUL 1 YG 2(C21 H29 N6 O12 P) FORMUL 1 PSU 4(C9 H13 N2 O9 P) FORMUL 1 5MC 4(C10 H16 N3 O8 P) FORMUL 1 7MG 2(C11 H18 N5 O8 P) FORMUL 1 5MU 2(C10 H15 N2 O9 P) FORMUL 1 1MA 2(C11 H18 N5 O7 P) LINK O3* A A 9 P 2MG A 10 LINK O3* 2MG A 10 P C A 11 LINK O3* G A 15 P H2U A 16 LINK O3* H2U A 16 P H2U A 17 LINK O3* H2U A 17 P G A 18 LINK O3* C A 25 P M2G A 26 LINK O3* M2G A 26 P C A 27 LINK O3* A A 31 P OMC A 32 LINK O3* OMC A 32 P U A 33 LINK O3* C A 36 P YG A 37 LINK O3* YG A 37 P A A 38 LINK O3* A A 38 P PSU A 39 LINK O3* PSU A 39 P 5MC A 40 LINK O3* 5MC A 40 P U A 41 LINK O3* G A 45 P 7MG A 46 LINK O3* 7MG A 46 P U A 47 LINK O3* C A 48 P 5MC A 49 LINK O3* 5MC A 49 P U A 50 LINK O3* G A 53 P 5MU A 54 LINK O3* 5MU A 54 P PSU A 55 LINK O3* PSU A 55 P C A 56 LINK O3* G A 57 P 1MA A 58 LINK O3* 1MA A 58 P U A 59 LINK O3* A B 9 P 2MG B 10 LINK O3* 2MG B 10 P C B 11 LINK O3* G B 15 P H2U B 16 LINK O3* H2U B 16 P H2U B 17 LINK O3* H2U B 17 P G B 18 LINK O3* C B 25 P M2G B 26 LINK O3* M2G B 26 P C B 27 LINK O3* A B 31 P OMC B 32 LINK O3* OMC B 32 P U B 33 LINK O3* C B 36 P YG B 37 LINK O3* YG B 37 P A B 38 LINK O3* A B 38 P PSU B 39 LINK O3* PSU B 39 P 5MC B 40 LINK O3* 5MC B 40 P U B 41 LINK O3* G B 45 P 7MG B 46 LINK O3* 7MG B 46 P U B 47 LINK O3* C B 48 P 5MC B 49 LINK O3* 5MC B 49 P U B 50 LINK O3* G B 53 P 5MU B 54 LINK O3* 5MU B 54 P PSU B 55 LINK O3* PSU B 55 P C B 56 LINK O3* G B 57 P 1MA B 58 LINK O3* 1MA B 58 P U B 59 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