HEADER VIRAL PROTEIN 29-MAR-16 5J1O TITLE EXCITED STATE (BOUND-LIKE) SAMPLED DURING RDC RESTRAINED REPLICA- TITLE 2 AVERAGED METADYNAMICS (RAM) SIMULATIONS OF THE HIV-1 TAR COMPLEXED TITLE 3 WITH CYCLIC PEPTIDE MIMETIC OF TAT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLIC PEPTIDE MIMETIC OF TAT; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: APICAL REGION (29MER) OF THE HIV-1 TAR ELEMENT; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: HIV-1 TAR RNA SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 4 ORGANISM_TAXID: 11676; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 7 ORGANISM_TAXID: 11676; SOURCE 8 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 9 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS TAR:TAT COMPLEX, RAM SIMULATIONS, RESIDUAL DIPOLAR COUPLINGS, EXCITED KEYWDS 2 STATE, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.N.BORKAR,M.F.BARDARO,G.VARANI,M.VENDRUSCOLO REVDAT 5 23-OCT-19 5J1O 1 REMARK REVDAT 4 01-FEB-17 5J1O 1 AUTHOR REVDAT 3 06-JUL-16 5J1O 1 JRNL REVDAT 2 22-JUN-16 5J1O 1 JRNL REVDAT 1 08-JUN-16 5J1O 0 JRNL AUTH A.N.BORKAR,M.F.BARDARO,C.CAMILLONI,F.A.APRILE,G.VARANI, JRNL AUTH 2 M.VENDRUSCOLO JRNL TITL STRUCTURE OF A LOW-POPULATION BINDING INTERMEDIATE IN JRNL TITL 2 PROTEIN-RNA RECOGNITION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 7171 2016 JRNL REFN ESSN 1091-6490 JRNL PMID 27286828 JRNL DOI 10.1073/PNAS.1521349113 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS AND PLUMED REMARK 3 AUTHORS : VENDRUSCOLO, CAMILLONI AND BORKAR REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RDC RESTRAINED RAM SIMULATIONS REMARK 4 REMARK 4 5J1O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219779. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.15 REMARK 210 PH : 6.6 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 UM [U-99% 13C; U-99% 15N] RNA REMARK 210 AND PEPTIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOT APPLICABLE REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 7790 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5970 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N ARG A 1 C PRO A 14 1.34 REMARK 500 N ARG A 1 O PRO A 14 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 1 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 ARG A 3 NH1 - CZ - NH2 ANGL. DEV. = -7.0 DEGREES REMARK 500 1 ARG A 3 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 1 ARG A 5 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 1 ARG A 8 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 1 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 1 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 G B 17 C5' - C4' - O4' ANGL. DEV. = 7.6 DEGREES REMARK 500 1 G B 17 O4' - C1' - N9 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 G B 17 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 1 G B 17 N1 - C6 - O6 ANGL. DEV. = -5.4 DEGREES REMARK 500 1 G B 18 C5' - C4' - O4' ANGL. DEV. = 5.7 DEGREES REMARK 500 1 G B 18 C6 - N1 - C2 ANGL. DEV. = -4.8 DEGREES REMARK 500 1 G B 18 C5 - C6 - N1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 G B 18 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 G B 18 C8 - N9 - C4 ANGL. DEV. = -3.4 DEGREES REMARK 500 1 G B 18 N9 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 1 G B 18 N1 - C6 - O6 ANGL. DEV. = -5.7 DEGREES REMARK 500 1 C B 19 O5' - C5' - C4' ANGL. DEV. = -5.3 DEGREES REMARK 500 1 C B 19 C6 - N1 - C2 ANGL. DEV. = -2.7 DEGREES REMARK 500 1 C B 19 N1 - C2 - N3 ANGL. DEV. = 5.0 DEGREES REMARK 500 1 C B 19 C4 - C5 - C6 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 C B 19 N1 - C2 - O2 ANGL. DEV. = 6.7 DEGREES REMARK 500 1 C B 19 N3 - C2 - O2 ANGL. DEV. = -11.8 DEGREES REMARK 500 1 A B 20 C5' - C4' - O4' ANGL. DEV. = 7.3 DEGREES REMARK 500 1 A B 20 N1 - C2 - N3 ANGL. DEV. = -3.1 DEGREES REMARK 500 1 A B 20 C2 - N3 - C4 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A B 20 N1 - C6 - N6 ANGL. DEV. = -9.7 DEGREES REMARK 500 1 A B 20 C5 - C6 - N6 ANGL. DEV. = 7.1 DEGREES REMARK 500 1 G B 21 C5' - C4' - O4' ANGL. DEV. = -9.4 DEGREES REMARK 500 1 G B 21 C1' - O4' - C4' ANGL. DEV. = -6.0 DEGREES REMARK 500 1 G B 21 C3' - C2' - C1' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 G B 21 O4' - C1' - C2' ANGL. DEV. = 6.4 DEGREES REMARK 500 1 G B 21 C2 - N3 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 A B 22 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 1 A B 22 C1' - O4' - C4' ANGL. DEV. = 5.8 DEGREES REMARK 500 1 A B 22 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 A B 22 C4 - C5 - C6 ANGL. DEV. = -3.0 DEGREES REMARK 500 1 A B 22 C5 - C6 - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 A B 22 N1 - C6 - N6 ANGL. DEV. = -7.4 DEGREES REMARK 500 1 U B 23 C3' - C2' - C1' ANGL. DEV. = 5.4 DEGREES REMARK 500 1 U B 23 N1 - C2 - N3 ANGL. DEV. = 6.4 DEGREES REMARK 500 1 U B 23 C2 - N3 - C4 ANGL. DEV. = -4.0 DEGREES REMARK 500 1 U B 23 C4 - C5 - C6 ANGL. DEV. = 6.9 DEGREES REMARK 500 1 U B 23 C5 - C6 - N1 ANGL. DEV. = -3.6 DEGREES REMARK 500 1 U B 23 N3 - C2 - O2 ANGL. DEV. = -6.3 DEGREES REMARK 500 1 U B 23 C5 - C4 - O4 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 C B 24 O4' - C1' - N1 ANGL. DEV. = 6.0 DEGREES REMARK 500 1 U B 25 O4' - C1' - N1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 U B 25 N3 - C4 - C5 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 1286 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL 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 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 3 LYS A 6 43.27 39.85 REMARK 500 7 LYS A 6 18.96 48.80 REMARK 500 REMARK 500 REMARK: NULL 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 ILE A 12 DPR A 13 3 -149.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 9 0.11 SIDE CHAIN REMARK 500 1 G B 17 0.08 SIDE CHAIN REMARK 500 1 C B 19 0.07 SIDE CHAIN REMARK 500 1 A B 20 0.07 SIDE CHAIN REMARK 500 1 G B 21 0.13 SIDE CHAIN REMARK 500 1 C B 24 0.07 SIDE CHAIN REMARK 500 1 G B 26 0.08 SIDE CHAIN REMARK 500 1 G B 28 0.12 SIDE CHAIN REMARK 500 1 C B 30 0.10 SIDE CHAIN REMARK 500 1 G B 33 0.10 SIDE CHAIN REMARK 500 1 A B 35 0.13 SIDE CHAIN REMARK 500 1 C B 37 0.11 SIDE CHAIN REMARK 500 1 U B 38 0.06 SIDE CHAIN REMARK 500 1 G B 43 0.10 SIDE CHAIN REMARK 500 1 C B 45 0.07 SIDE CHAIN REMARK 500 2 ARG A 9 0.10 SIDE CHAIN REMARK 500 2 A B 20 0.06 SIDE CHAIN REMARK 500 2 G B 21 0.11 SIDE CHAIN REMARK 500 2 U B 23 0.10 SIDE CHAIN REMARK 500 2 C B 24 0.06 SIDE CHAIN REMARK 500 2 U B 25 0.11 SIDE CHAIN REMARK 500 2 G B 26 0.09 SIDE CHAIN REMARK 500 2 A B 27 0.07 SIDE CHAIN REMARK 500 2 C B 29 0.09 SIDE CHAIN REMARK 500 2 G B 32 0.10 SIDE CHAIN REMARK 500 2 C B 39 0.08 SIDE CHAIN REMARK 500 2 C B 41 0.11 SIDE CHAIN REMARK 500 2 U B 42 0.08 SIDE CHAIN REMARK 500 2 G B 43 0.08 SIDE CHAIN REMARK 500 2 C B 44 0.10 SIDE CHAIN REMARK 500 3 ARG A 1 0.12 SIDE CHAIN REMARK 500 3 ARG A 3 0.09 SIDE CHAIN REMARK 500 3 G B 17 0.07 SIDE CHAIN REMARK 500 3 G B 18 0.11 SIDE CHAIN REMARK 500 3 A B 20 0.07 SIDE CHAIN REMARK 500 3 U B 23 0.08 SIDE CHAIN REMARK 500 3 C B 24 0.07 SIDE CHAIN REMARK 500 3 U B 25 0.11 SIDE CHAIN REMARK 500 3 A B 27 0.07 SIDE CHAIN REMARK 500 3 G B 28 0.10 SIDE CHAIN REMARK 500 3 G B 32 0.09 SIDE CHAIN REMARK 500 3 G B 33 0.12 SIDE CHAIN REMARK 500 3 G B 36 0.12 SIDE CHAIN REMARK 500 3 U B 38 0.08 SIDE CHAIN REMARK 500 3 C B 39 0.07 SIDE CHAIN REMARK 500 3 C B 44 0.09 SIDE CHAIN REMARK 500 4 G B 17 0.11 SIDE CHAIN REMARK 500 4 C B 19 0.07 SIDE CHAIN REMARK 500 4 A B 20 0.08 SIDE CHAIN REMARK 500 4 G B 21 0.09 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 162 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30049 RELATED DB: BMRB DBREF 5J1O A 1 14 PDB 5J1O 5J1O 1 14 DBREF 5J1O B 17 45 PDB 5J1O 5J1O 17 45 SEQRES 1 A 14 ARG VAL ARG THR ARG LYS GLY ARG ARG ILE ARG ILE DPR SEQRES 2 A 14 PRO SEQRES 1 B 29 G G C A G A U C U G A G C SEQRES 2 B 29 C U G G G A G C U C U C U SEQRES 3 B 29 G C C HET DPR A 13 14 HETNAM DPR D-PROLINE FORMUL 1 DPR C5 H9 N O2 SHEET 1 AA1 2 VAL A 2 ARG A 5 0 SHEET 2 AA1 2 ARG A 8 ARG A 11 -1 O ILE A 10 N ARG A 3 LINK C ILE A 12 N DPR A 13 1555 1555 1.34 LINK C DPR A 13 N PRO A 14 1555 1555 1.33 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 0.012803 -0.004526 0.007839 0.00000 SCALE2 0.000000 0.013579 -0.007839 0.00000 SCALE3 0.000000 0.000000 0.015680 0.00000 MODEL 1