HEADER DE NOVO PROTEIN 25-OCT-17 6BET TITLE SOLUTION STRUCTURE OF DE NOVO MACROCYCLE DESIGN12_SS COMPND MOL_ID: 1; COMPND 2 MOLECULE: H(DPR)(DVA)CIP(DPR)E(DLY)VC(DGL); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS MACROCYCLE, DE NOVO, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.D.SHORTRIDGE,P.HOSSEINZADEH,F.PARDO-AVILA,G.VARANI,D.BAKER REVDAT 3 14-JUN-23 6BET 1 LINK REVDAT 2 01-JAN-20 6BET 1 REMARK REVDAT 1 27-DEC-17 6BET 0 JRNL AUTH P.HOSSEINZADEH,G.BHARDWAJ,V.K.MULLIGAN,M.D.SHORTRIDGE, JRNL AUTH 2 T.W.CRAVEN,F.PARDO-AVILA,S.A.RETTIE,D.E.KIM,D.A.SILVA, JRNL AUTH 3 Y.M.IBRAHIM,I.K.WEBB,J.R.CORT,J.N.ADKINS,G.VARANI,D.BAKER JRNL TITL COMPREHENSIVE COMPUTATIONAL DESIGN OF ORDERED PEPTIDE JRNL TITL 2 MACROCYCLES. JRNL REF SCIENCE V. 358 1461 2017 JRNL REFN ESSN 1095-9203 JRNL PMID 29242347 JRNL DOI 10.1126/SCIENCE.AAP7577 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS 2016.1 REMARK 3 AUTHORS : ABRAHAM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6BET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1000230786. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 278 REMARK 210 PH : 5.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 5 MG/ML DESIGN 12_SS, 5 % V/V [U REMARK 210 -2H] GLYCEROL, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR NIH, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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: 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 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 3 CYS A 11 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 7 DVA A 3 CA - CB - CG2 ANGL. DEV. = 9.2 DEGREES REMARK 500 7 CYS A 4 CA - CB - SG ANGL. DEV. = 10.4 DEGREES REMARK 500 9 PRO A 6 N - CA - CB ANGL. DEV. = 7.2 DEGREES REMARK 500 10 DPR A 7 N - CA - CB ANGL. DEV. = 7.9 DEGREES REMARK 500 11 CYS A 11 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 12 DVA A 3 CG1 - CB - CG2 ANGL. DEV. = -10.4 DEGREES REMARK 500 13 CYS A 4 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 15 DGL A 12 OE1 - CD - OE2 ANGL. DEV. = -7.3 DEGREES REMARK 500 18 GLU A 8 CB - CA - C ANGL. DEV. = 12.4 DEGREES REMARK 500 19 DPR A 7 C - N - CA ANGL. DEV. = 10.1 DEGREES REMARK 500 20 DVA A 3 CG1 - CB - CG2 ANGL. DEV. = -11.1 DEGREES REMARK 500 20 CYS A 11 CA - CB - SG ANGL. DEV. = 7.6 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 4 DPR A 2 -0.98 67.25 REMARK 500 8 DPR A 7 -49.78 78.89 REMARK 500 10 CYS A 4 144.54 -170.79 REMARK 500 12 GLU A 8 97.19 -54.03 REMARK 500 14 GLU A 8 96.04 -55.09 REMARK 500 17 DPR A 7 -2.96 65.94 REMARK 500 18 DPR A 7 -13.38 59.29 REMARK 500 19 DPR A 7 -47.80 76.83 REMARK 500 19 GLU A 8 31.80 -75.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 19 GLU A 8 -10.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30362 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF DE NOVO MACROCYCLE DESIGN12_SS DBREF 6BET A 1 12 PDB 6BET 6BET 1 12 SEQRES 1 A 12 HIS DPR DVA CYS ILE PRO DPR GLU DLY VAL CYS DGL HET DPR A 2 14 HET DVA A 3 16 HET DPR A 7 14 HET DLY A 9 22 HET DGL A 12 15 HETNAM DPR D-PROLINE HETNAM DVA D-VALINE HETNAM DLY D-LYSINE HETNAM DGL D-GLUTAMIC ACID FORMUL 1 DPR 2(C5 H9 N O2) FORMUL 1 DVA C5 H11 N O2 FORMUL 1 DLY C6 H14 N2 O2 FORMUL 1 DGL C5 H9 N O4 SHEET 1 AA1 2 DVA A 3 CYS A 4 0 SHEET 2 AA1 2 CYS A 11 DGL A 12 -1 O DGL A 12 N DVA A 3 SSBOND 1 CYS A 4 CYS A 11 1555 1555 2.04 LINK C HIS A 1 N DPR A 2 1555 1555 1.34 LINK N HIS A 1 C DGL A 12 1555 1555 1.34 LINK C DPR A 2 N DVA A 3 1555 1555 1.34 LINK C DVA A 3 N CYS A 4 1555 1555 1.33 LINK C PRO A 6 N DPR A 7 1555 1555 1.33 LINK C DPR A 7 N GLU A 8 1555 1555 1.34 LINK C GLU A 8 N DLY A 9 1555 1555 1.34 LINK C DLY A 9 N VAL A 10 1555 1555 1.34 LINK C CYS A 11 N DGL A 12 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 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