HEADER DE NOVO PROTEIN 25-OCT-17 6BEQ TITLE SOLUTION STRUCTURE OF DE NOVO MACROCYCLE DESIGN10.1 CAVEAT 6BEQ DTH A 8 HAS WRONG CHIRALITY AT ATOM CB COMPND MOL_ID: 1; COMPND 2 MOLECULE: AAR(DVA)(DPR)R(DLE)(DTH)PE; 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 5 06-NOV-24 6BEQ 1 REMARK REVDAT 4 15-NOV-23 6BEQ 1 REMARK REVDAT 3 14-JUN-23 6BEQ 1 REMARK REVDAT 2 01-JAN-20 6BEQ 1 REMARK REVDAT 1 10-JAN-18 6BEQ 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 6BEQ 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_1000230779. 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 10.1, 5 % [U-2H] REMARK 210 GLYCEROL, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX 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 N ALA A 1 C GLU A 10 1.34 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 ALA A 2 N - CA - CB ANGL. DEV. = -9.0 DEGREES REMARK 500 1 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 1 ARG A 6 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 1 DLE A 7 CB - CG - CD1 ANGL. DEV. = 13.1 DEGREES REMARK 500 3 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 4 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 5 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 5 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 5 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 6.8 DEGREES REMARK 500 5 PRO A 9 N - CA - CB ANGL. DEV. = 7.3 DEGREES REMARK 500 6 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 7 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 8 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 8.4 DEGREES REMARK 500 8 DPR A 5 N - CD - CG ANGL. DEV. = 9.9 DEGREES REMARK 500 8 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 7.5 DEGREES REMARK 500 9 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 PRO A 9 C - N - CA ANGL. DEV. = 9.2 DEGREES REMARK 500 10 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -5.8 DEGREES REMARK 500 10 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 6.2 DEGREES REMARK 500 10 DPR A 5 C - N - CA ANGL. DEV. = 10.1 DEGREES REMARK 500 10 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 3 NH1 - CZ - NH2 ANGL. DEV. = -6.8 DEGREES REMARK 500 11 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 6.1 DEGREES REMARK 500 12 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 13 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 13 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 14 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -3.9 DEGREES REMARK 500 14 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 5.0 DEGREES REMARK 500 14 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 15 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 DPR A 5 N - CA - CB ANGL. DEV. = 9.0 DEGREES REMARK 500 16 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 16 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 6.2 DEGREES REMARK 500 16 ARG A 6 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 16 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 8.1 DEGREES REMARK 500 17 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 5.7 DEGREES REMARK 500 17 ARG A 6 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 17 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 7.4 DEGREES REMARK 500 18 ARG A 3 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ALA A 1 N - CA - CB ANGL. DEV. = -10.0 DEGREES REMARK 500 19 ARG A 3 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 19 ARG A 3 NE - CZ - NH2 ANGL. DEV. = 5.5 DEGREES REMARK 500 19 ARG A 6 NE - CZ - NH1 ANGL. DEV. = -6.8 DEGREES REMARK 500 19 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 4.3 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 2 PRO A 9 1.14 -60.12 REMARK 500 3 ARG A 3 -31.30 -133.11 REMARK 500 5 ARG A 3 -50.59 -121.07 REMARK 500 6 ARG A 3 -12.36 -140.68 REMARK 500 7 PRO A 9 -6.85 -49.18 REMARK 500 9 ARG A 3 -22.24 -141.00 REMARK 500 11 ARG A 3 -18.90 -141.03 REMARK 500 12 ARG A 3 -29.36 -145.54 REMARK 500 14 ARG A 3 -53.78 -127.41 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 DPR A 5 ARG A 6 11 143.13 REMARK 500 ARG A 3 DVA A 4 12 146.11 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 2 ARG A 3 0.10 SIDE CHAIN REMARK 500 9 ARG A 6 0.10 SIDE CHAIN REMARK 500 12 ARG A 6 0.12 SIDE CHAIN REMARK 500 18 ARG A 6 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30359 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF DE NOVO MACROCYCLE DESIGN10.1 DBREF 6BEQ A 1 10 PDB 6BEQ 6BEQ 1 10 SEQRES 1 A 10 ALA ALA ARG DVA DPR ARG DLE DTH PRO GLU HET DVA A 4 16 HET DPR A 5 14 HET DLE A 7 19 HET DTH A 8 14 HETNAM DVA D-VALINE HETNAM DPR D-PROLINE HETNAM DLE D-LEUCINE HETNAM DTH D-THREONINE FORMUL 1 DVA C5 H11 N O2 FORMUL 1 DPR C5 H9 N O2 FORMUL 1 DLE C6 H13 N O2 FORMUL 1 DTH C4 H9 N O3 LINK C ARG A 3 N DVA A 4 1555 1555 1.34 LINK C DVA A 4 N DPR A 5 1555 1555 1.33 LINK C DPR A 5 N ARG A 6 1555 1555 1.33 LINK C ARG A 6 N DLE A 7 1555 1555 1.33 LINK C DLE A 7 N DTH A 8 1555 1555 1.33 LINK C DTH A 8 N PRO A 9 1555 1555 1.34 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