PDB Short entry for 1Q49 HEADER RIBONUCLEIC ACID 02-AUG-03 1Q49 TITLE THE INTERACTION BETWEEN MRNA AND TRNA (MODEL A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: P-SITE TRNA; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: A-SITE TRNA; COMPND 6 CHAIN: B; COMPND 7 MOL_ID: 3; COMPND 8 MOLECULE: SINGLE-STRANDED MRNA; COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 6 ORGANISM_COMMON: YEAST; SOURCE 7 MOL_ID: 3; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: SYNTHETIC CONSTRUCT KEYWDS INTERACTION, MRNA, TRNA EXPDTA THEORETICAL MODEL AUTHOR C.LIU,X.WANG,X.PAN REVDAT 2 09-SEP-03 1Q49 1 SEQADV REVDAT 1 26-AUG-03 1Q49 0 JRNL AUTH C.LIU,X.WANG,X.PAN JRNL TITL THE INTERACTION BETWEEN MRNA AND TRNA (MODEL A) JRNL REF TO BE PUBLISHED JRNL REFN 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: INSIGHTII REMARK 4 REMARK 4 1Q49 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-2003. REMARK 100 THE RCSB ID CODE IS RCSB019896. 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 ANTI- REMARK 220 CODONS OF 1EHZ WAS MODIFIED. TO HAVE A REASONABLE START REMARK 220 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: 1Q5S RELATED DB: PDB REMARK 900 THE INTERACTION BETWEEN MRNA AND TRNA (MODEL B) REMARK 999 REMARK 999 SEQUENCE REMARK 999 THESE RESIDUES ARE NATURALLY OCCURRING NUCLEOTIDES. REMARK 999 IN THE DATABASE SEQUENCE 1MFK_A, THE FIRST RESIDUE, N, REMARK 999 REPRESENTS C OR G OR T OR A. DBREF 1Q49 A 1 76 GB M10263 176479 1 76 DBREF 1Q49 B 1 76 GB M10263 176479 1 76 DBREF 1Q49 C 2 23 GB 1MFK_A 27065637 2 23 SEQADV 1Q49 2MG A 10 GB M10263 G 10 SEE REMARK 999 SEQADV 1Q49 H2U A 16 GB M10263 U 16 SEE REMARK 999 SEQADV 1Q49 H2U A 17 GB M10263 U 17 SEE REMARK 999 SEQADV 1Q49 M2G A 26 GB M10263 G 26 SEE REMARK 999 SEQADV 1Q49 OMC A 32 GB M10263 C 32 SEE REMARK 999 SEQADV 1Q49 A A 34 GB M10263 G 34 CONFLICT SEQADV 1Q49 C A 36 GB M10263 A 36 CONFLICT SEQADV 1Q49 YG A 37 GB M10263 G 37 SEE REMARK 999 SEQADV 1Q49 PSU A 39 GB M10263 U 39 SEE REMARK 999 SEQADV 1Q49 5MC A 40 GB M10263 C 40 SEE REMARK 999 SEQADV 1Q49 7MG A 46 GB M10263 G 46 SEE REMARK 999 SEQADV 1Q49 5MC A 49 GB M10263 C 49 SEE REMARK 999 SEQADV 1Q49 5MU A 54 GB M10263 U 54 SEE REMARK 999 SEQADV 1Q49 PSU A 55 GB M10263 U 55 SEE REMARK 999 SEQADV 1Q49 1MA A 58 GB M10263 A 58 SEE REMARK 999 SEQADV 1Q49 2MG B 10 GB M10263 G 10 SEE REMARK 999 SEQADV 1Q49 H2U B 16 GB M10263 U 16 SEE REMARK 999 SEQADV 1Q49 H2U B 17 GB M10263 U 17 SEE REMARK 999 SEQADV 1Q49 M2G B 26 GB M10263 G 26 SEE REMARK 999 SEQADV 1Q49 OMC B 32 GB M10263 C 32 SEE REMARK 999 SEQADV 1Q49 U B 34 GB M10263 G 34 CONFLICT SEQADV 1Q49 G B 35 GB M10263 A 35 CONFLICT SEQADV 1Q49 C B 36 GB M10263 A 36 CONFLICT SEQADV 1Q49 YG B 37 GB M10263 G 37 SEE REMARK 999 SEQADV 1Q49 PSU B 39 GB M10263 U 39 SEE REMARK 999 SEQADV 1Q49 5MC B 40 GB M10263 C 40 SEE REMARK 999 SEQADV 1Q49 7MG B 46 GB M10263 G 46 SEE REMARK 999 SEQADV 1Q49 5MC B 49 GB M10263 C 49 SEE REMARK 999 SEQADV 1Q49 5MU B 54 GB M10263 U 54 SEE REMARK 999 SEQADV 1Q49 PSU B 55 GB M10263 U 55 SEE REMARK 999 SEQADV 1Q49 1MA B 58 GB M10263 A 58 SEE REMARK 999 SEQADV 1Q49 G C 1 GB 1MFK_A SEE REMARK 999 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 A A 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 U G 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 1Q49 2MG A 10 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1Q49 H2U A 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 H2U A 17 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 M2G A 26 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1Q49 OMC A 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 1Q49 YG A 37 G WYBUTOSINE MODRES 1Q49 PSU A 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 5MC A 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1Q49 7MG A 46 G MODRES 1Q49 5MC A 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1Q49 5MU A 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1Q49 PSU A 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 1MA A 58 A MODRES 1Q49 2MG B 10 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1Q49 H2U B 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 H2U B 17 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 M2G B 26 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1Q49 OMC B 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 1Q49 YG B 37 G WYBUTOSINE MODRES 1Q49 PSU B 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 5MC B 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1Q49 7MG B 46 G MODRES 1Q49 5MC B 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1Q49 5MU B 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1Q49 PSU B 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1Q49 1MA B 58 A 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