HEADER RIBONUCLEIC ACID 10-JAN-02 1KS1 TITLE A MODEL FOR A FIVE-PRIME STACKED TRNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHENYLALANINE TRANSFER RNA; COMPND 3 CHAIN: B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST KEYWDS FIVE-PRIME STACK, TRNA EXPDTA THEORETICAL MODEL AUTHOR A.B.SIMONSON,J.A.LAKE REVDAT 1 22-MAR-02 1KS1 0 JRNL AUTH A.B.SIMONSON,J.A.LAKE JRNL TITL THE TRANSORIENTATION HYPOTHESIS FOR CODON JRNL TITL 2 RECOGNITION DURING PROTEIN SYNTHESIS JRNL REF NATURE V. 416 281 2002 JRNL REFN ASTM NATUAS UK ISSN 0028-0836 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.JOVINE,S.DJORDEVIC,D.RHODES REMARK 1 TITL THE CRYSTAL STRUCTURE OF YEAST PHENYLALANINE TRNA REMARK 1 TITL 2 AT 2.0 A RESOLUTION: PARTIAL CLEAVAGE BY MG2+ IN REMARK 1 TITL 3 15 YEAR OLD CRYSTALS REMARK 1 REF J.MOL.BIOL. V. 301 401 2000 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 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 1KS1 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-2002. REMARK 100 THE RCSB ID CODE IS RCSB015281. 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: THIS MODEL SHOWS A YEAST PHENYLALANYL TRNA ADOPTING A REMARK 220 5'-STACKED CONFORMATION IN THE ANTICODON LOOP. IT IS REMARK 220 BASED ON THE CRYSTAL STRUCTURE OF YEAST PHENYLALANYL- REMARK 220 TRNA, PDB ID 1EVV. THE PROGRAM O WAS USED TO BUILD THIS REMARK 220 STRUCTURE. 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: 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 YG B 37 O3* - P - O5* ANGL. DEV. = 13.1 DEGREES REMARK 500 YG B 37 C3* - O3* - P ANGL. DEV. = 13.3 DEGREES REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1L1U RELATED DB: PDB REMARK 900 THEORETICAL MODEL FOR INITIAL BINDING TO THE SMALL REMARK 900 RIBOSOMAL SUBUNIT OF TERNARY COMPLEX DURING THE ELONGATION REMARK 900 PHASE OF PROTEIN SYNTHESIS 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 OMG A A 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 MODRES 1KS1 2MG B 10 G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1KS1 H2U B 16 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1KS1 H2U B 17 U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE MODRES 1KS1 M2G B 26 G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1KS1 OMC B 32 C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE MODRES 1KS1 OMG B 34 G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE MODRES 1KS1 YG B 37 G WYBUTOSINE MODRES 1KS1 PSU B 39 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1KS1 5MC B 40 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1KS1 7MG B 46 G MODRES 1KS1 5MC B 49 C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE MODRES 1KS1 5MU B 54 U 5-METHYLURIDINE 5'-MONOPHOSPHATE MODRES 1KS1 PSU B 55 U PSEUDOURIDINE-5'-MONOPHOSPHATE MODRES 1KS1 1MA B 58 A HET 2MG B 10 24 HET H2U B 16 20 HET H2U B 17 20 HET M2G B 26 25 HET OMC B 32 21 HET OMG B 34 24 HET YG B 37 39 HET PSU B 39 20 HET 5MC B 40 21 HET 7MG B 46 24 HET 5MC B 49 21 HET 5MU B 54 21 HET PSU B 55 20 HET 1MA B 58 23 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 OMG O2'-METHYLGUANOSINE-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 C11 H16 N5 O8 P FORMUL 1 H2U 2(C9 H15 N2 O9 P) FORMUL 1 M2G C12 H18 N5 O8 P FORMUL 1 OMC C10 H16 N3 O8 P FORMUL 1 OMG C11 H16 N5 O8 P FORMUL 1 YG C21 H29 N6 O12 P FORMUL 1 PSU 2(C9 H13 N2 O9 P) FORMUL 1 5MC 2(C10 H16 N3 O8 P) FORMUL 1 7MG C11 H18 N5 O8 P FORMUL 1 5MU C10 H15 N2 O9 P FORMUL 1 1MA C11 H18 N5 O7 P 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* U B 33 P OMG B 34 LINK O3* OMG B 34 P A B 35 LINK O3* A 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 -0.000026 -0.000026 0.00000 SCALE2 0.000000 1.000000 -0.000026 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MASTER 64 0 14 0 0 0 0 6 0 0 0 6 END