HEADER HORMONE RECEPTOR 06-MAY-15 2N2F TITLE SOLUTION NMR STRUCTURE OF DYNORPHIN 1-13 BOUND TO KAPPA OPIOID TITLE 2 RECEPTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: DYNORPHIN A(1-13); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 207-219; COMPND 5 SYNONYM: PROENKEPHALIN-B, BETA-NEOENDORPHIN-DYNORPHIN, COMPND 6 PREPRODYNORPHIN; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: SYNTHESIS OF THE PEPTIDE WAS PERFORMED BY A SOLID SOURCE 7 PHASE METHOD USING FMOC CHEMISTRY. KEYWDS GPCR, HORMONE RECEPTOR EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR C.O'CONNOR,K.WHITE,N.DONCESCU,T.DIDENKO,B.L.ROTH,G.CZAPLICKI, AUTHOR 2 R.C.STEVENS,K.WUTHRICH,A.MILON REVDAT 3 14-JUN-23 2N2F 1 REMARK REVDAT 2 14-OCT-15 2N2F 1 JRNL REVDAT 1 09-SEP-15 2N2F 0 JRNL AUTH C.O'CONNOR,K.L.WHITE,N.DONCESCU,T.DIDENKO,B.L.ROTH, JRNL AUTH 2 G.CZAPLICKI,R.C.STEVENS,K.WUTHRICH,A.MILON JRNL TITL NMR STRUCTURE AND DYNAMICS OF THE AGONIST DYNORPHIN PEPTIDE JRNL TITL 2 BOUND TO THE HUMAN KAPPA OPIOID RECEPTOR. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 11852 2015 JRNL REFN ISSN 0027-8424 JRNL PMID 26372966 JRNL DOI 10.1073/PNAS.1510117112 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 3.2, AMBER 14 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, AND KOLLMAN REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N2F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1000104336. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 280 REMARK 210 PH : 6.1 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N-GFLI] DYNORPHIN 1, REMARK 210 150 MM POTASSIUM CHLORIDE, 40 MM REMARK 210 [U-2H] MES, 100 UM DSS, 10 UM REMARK 210 KOR, 8 MM DDM, 1.6 MM CHS, 90% REMARK 210 H2O/10% D2O; 1 MM [U-15N-GFLIR; REMARK 210 U-13C-R] DYNORPHIN 1, 150 MM REMARK 210 POTASSIUM CHLORIDE, 40 MM [U-2H] REMARK 210 MES, 100 UM DSS, 10 UM KOR, 8 MM REMARK 210 DDM, 1.6 MM CHS, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D HNCACB; 15N T1 T2 HETNOE; 15N REMARK 210 T2 REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 700 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 3.2, AMBER 14 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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 6 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 1 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 7 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 7 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES 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 1 ARG A 9 72.27 60.29 REMARK 500 1 PRO A 10 22.47 -75.66 REMARK 500 2 ARG A 6 -15.65 -41.36 REMARK 500 2 ARG A 7 -18.31 -46.37 REMARK 500 2 PRO A 10 40.98 -74.24 REMARK 500 2 LYS A 11 26.99 -165.86 REMARK 500 2 LEU A 12 37.09 -157.42 REMARK 500 3 ARG A 7 28.90 -55.71 REMARK 500 3 ARG A 9 60.73 -115.26 REMARK 500 4 ARG A 6 -16.16 -49.50 REMARK 500 4 ILE A 8 113.42 -169.76 REMARK 500 4 ARG A 9 83.44 57.04 REMARK 500 4 PRO A 10 1.52 -69.26 REMARK 500 4 LEU A 12 -29.72 78.93 REMARK 500 5 ARG A 6 5.66 -59.41 REMARK 500 5 ARG A 7 40.72 -75.92 REMARK 500 5 ILE A 8 72.37 51.19 REMARK 500 5 ARG A 9 66.10 78.92 REMARK 500 6 ARG A 6 1.48 -68.91 REMARK 500 6 ILE A 8 118.34 154.38 REMARK 500 6 ARG A 9 64.17 74.91 REMARK 500 7 LEU A 5 3.16 -67.82 REMARK 500 7 ARG A 6 34.80 -66.25 REMARK 500 7 ILE A 8 123.98 175.11 REMARK 500 7 ARG A 9 49.94 32.16 REMARK 500 8 ARG A 6 26.80 -70.32 REMARK 500 8 ARG A 7 44.98 -76.82 REMARK 500 8 ILE A 8 82.27 51.28 REMARK 500 8 ARG A 9 70.15 83.48 REMARK 500 8 LYS A 11 37.15 -140.68 REMARK 500 9 ARG A 6 -13.98 -49.70 REMARK 500 9 ARG A 9 82.12 74.71 REMARK 500 9 PRO A 10 31.84 -75.46 REMARK 500 9 LYS A 11 8.52 59.93 REMARK 500 9 LEU A 12 46.52 -155.02 REMARK 500 10 PRO A 10 40.47 -82.80 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 ARG A 7 ILE A 8 2 149.92 REMARK 500 ARG A 7 ILE A 8 6 140.68 REMARK 500 ARG A 7 ILE A 8 9 146.83 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 3 ARG A 9 0.09 SIDE CHAIN REMARK 500 7 TYR A 1 0.07 SIDE CHAIN REMARK 500 9 ARG A 6 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25597 RELATED DB: BMRB DBREF 2N2F A 1 13 UNP P01213 PDYN_HUMAN 207 219 SEQRES 1 A 13 TYR GLY GLY PHE LEU ARG ARG ILE ARG PRO LYS LEU LYS HELIX 1 1 PHE A 4 ILE A 8 5 5 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 MODEL 1