HEADER DE NOVO PROTEIN 25-OCT-17 6BES TITLE SOLUTION STRUCTURE OF DE NOVO MACROCYCLE DESIGN11_SS COMPND MOL_ID: 1; COMPND 2 MOLECULE: (DAL)Q(DPR)(DCY)(DLY)DS(DTY)(DCY)P(DSN); 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 6BES 1 LINK REVDAT 2 01-JAN-20 6BES 1 REMARK REVDAT 1 27-DEC-17 6BES 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 6BES 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_1000230785. 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 11_SS, 5 % V/V [U REMARK 210 -99% 2H] GLYCEROL, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY 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 1 DCY A 4 CA - CB - SG ANGL. DEV. = 12.3 DEGREES REMARK 500 2 DPR A 3 C - N - CA ANGL. DEV. = 9.7 DEGREES REMARK 500 2 ASP A 6 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 3 DPR A 3 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 4 DCY A 4 CA - CB - SG ANGL. DEV. = 8.8 DEGREES REMARK 500 4 ASP A 6 CB - CG - OD1 ANGL. DEV. = 10.2 DEGREES REMARK 500 4 DTY A 8 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 ASP A 6 CB - CG - OD2 ANGL. DEV. = 7.5 DEGREES REMARK 500 5 DTY A 8 CB - CG - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 5 PRO A 10 C - N - CA ANGL. DEV. = 10.2 DEGREES REMARK 500 7 DCY A 4 CA - CB - SG ANGL. DEV. = 16.7 DEGREES REMARK 500 7 PRO A 10 N - CA - CB ANGL. DEV. = 7.7 DEGREES REMARK 500 8 DPR A 3 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 8 DPR A 3 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 8 DTY A 8 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 9 DTY A 8 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 10 DAL A 1 N - CA - CB ANGL. DEV. = -8.8 DEGREES REMARK 500 10 DPR A 3 C - N - CA ANGL. DEV. = 9.3 DEGREES REMARK 500 10 ASP A 6 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 11 ASP A 6 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 12 DCY A 9 CA - CB - SG ANGL. DEV. = 13.5 DEGREES REMARK 500 13 DAL A 1 N - CA - CB ANGL. DEV. = -9.6 DEGREES REMARK 500 14 DTY A 8 CB - CG - CD2 ANGL. DEV. = 3.6 DEGREES REMARK 500 15 ASP A 6 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 18 DAL A 1 N - CA - CB ANGL. DEV. = -9.1 DEGREES REMARK 500 18 DPR A 3 N - CA - CB ANGL. DEV. = 9.3 DEGREES REMARK 500 19 ASP A 6 CB - CG - OD1 ANGL. DEV. = 13.9 DEGREES REMARK 500 19 DTY A 8 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 20 DTY A 8 CB - CG - CD2 ANGL. DEV. = -4.7 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 5 DLY A 5 -104.41 54.13 REMARK 500 5 DCY A 9 -76.25 112.92 REMARK 500 8 DCY A 9 -72.88 115.51 REMARK 500 10 DLY A 5 -107.75 58.96 REMARK 500 11 DLY A 5 -104.78 46.90 REMARK 500 20 DLY A 5 -88.90 51.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30361 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF DE NOVO MACROCYCLE DESIGN11_SS DBREF 6BES A 1 11 PDB 6BES 6BES 1 11 SEQRES 1 A 11 DAL GLN DPR DCY DLY ASP SER DTY DCY PRO DSN HET DAL A 1 10 HET DPR A 3 14 HET DCY A 4 10 HET DLY A 5 22 HET DTY A 8 21 HET DCY A 9 10 HET DSN A 11 11 HETNAM DAL D-ALANINE HETNAM DPR D-PROLINE HETNAM DCY D-CYSTEINE HETNAM DLY D-LYSINE HETNAM DTY D-TYROSINE HETNAM DSN D-SERINE FORMUL 1 DAL C3 H7 N O2 FORMUL 1 DPR C5 H9 N O2 FORMUL 1 DCY 2(C3 H7 N O2 S) FORMUL 1 DLY C6 H14 N2 O2 FORMUL 1 DTY C9 H11 N O3 FORMUL 1 DSN C3 H7 N O3 SHEET 1 AA1 2 GLN A 2 DCY A 4 0 SHEET 2 AA1 2 SER A 7 DCY A 9 -1 O SER A 7 N DCY A 4 SSBOND 1 DCY A 4 DCY A 9 1555 1555 2.03 LINK C DAL A 1 N GLN A 2 1555 1555 1.33 LINK N DAL A 1 C DSN A 11 1555 1555 1.34 LINK C GLN A 2 N DPR A 3 1555 1555 1.33 LINK C DPR A 3 N DCY A 4 1555 1555 1.34 LINK C DCY A 4 N DLY A 5 1555 1555 1.33 LINK C DLY A 5 N ASP A 6 1555 1555 1.34 LINK C SER A 7 N DTY A 8 1555 1555 1.33 LINK C DTY A 8 N DCY A 9 1555 1555 1.34 LINK C DCY A 9 N PRO A 10 1555 1555 1.34 LINK C PRO A 10 N DSN A 11 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 HETATM 1 N DAL A 1 31.130 36.710 12.730 1.00 0.00 N HETATM 2 CA DAL A 1 31.770 36.340 11.490 1.00 0.00 C HETATM 3 CB DAL A 1 31.460 34.860 11.270 1.00 0.00 C HETATM 4 C DAL A 1 33.260 36.680 11.460 1.00 0.00 C HETATM 5 O DAL A 1 33.840 36.870 10.390 1.00 0.00 O HETATM 6 H1 DAL A 1 30.830 35.990 13.370 1.00 0.00 H HETATM 7 HA DAL A 1 31.290 36.920 10.700 1.00 0.00 H HETATM 8 HB1 DAL A 1 31.950 34.560 10.350 1.00 0.00 H HETATM 9 HB2 DAL A 1 30.410 34.560 11.330 1.00 0.00 H HETATM 10 HB3 DAL A 1 32.070 34.260 11.940 1.00 0.00 H