HEADER DE NOVO PROTEIN 07-DEC-22 8BWW TITLE TARGETING TOLL-LIKE RECEPTOR-DRIVEN SYSTEMIC INFLAMMATION BY TITLE 2 ENGINEERING AN INNATE STRUCTURAL FOLD INTO DRUGS COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; 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_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS HOST DEFENCE PEPTIDE, CD14, BACTERIAL LPS, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR C.DIEHL REVDAT 4 15-NOV-23 8BWW 1 ATOM REVDAT 3 11-OCT-23 8BWW 1 JRNL REVDAT 2 27-SEP-23 8BWW 1 TITLE JRNL REVDAT 1 06-SEP-23 8BWW 0 JRNL AUTH G.PETRUK,M.PUTHIA,F.SAMSUDIN,J.PETRLOVA,F.OLM, JRNL AUTH 2 M.MITTENDORFER,S.HYLLEN,D.EDSTROM,A.C.STROMDAHL,C.DIEHL, JRNL AUTH 3 S.EKSTROM,B.WALSE,S.KJELLSTROM,P.J.BOND,S.LINDSTEDT, JRNL AUTH 4 A.SCHMIDTCHEN JRNL TITL TARGETING TOLL-LIKE RECEPTOR-DRIVEN SYSTEMIC INFLAMMATION BY JRNL TITL 2 ENGINEERING AN INNATE STRUCTURAL FOLD INTO DRUGS. JRNL REF NAT COMMUN V. 14 6097 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37773180 JRNL DOI 10.1038/S41467-023-41702-Y REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMACS REMARK 3 AUTHORS : M.J. ABRAHAM, T. MURTOLA, R. SCHULZ, S. PALL, J.C. REMARK 3 SMITH, B. HESS, E. LINDAHL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BWW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1292126996. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.6 MM SHVF18, 50 % V/V TFE, 10 REMARK 210 % V/V D2O, 200 UM DSS, 0.02 % V/ REMARK 210 V SODIUM AZIDE, TRIFLUOROETHANOL/ REMARK 210 WATER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H TOCSY; 2D 1H-1H NOESY; REMARK 210 2D 1H-1H ROESY; 2D DQF-COSY; 2D REMARK 210 1H-13C HSQC ALIPHATIC; 2D 1H-15N REMARK 210 SOFAST-HMQC; 2D 1H-13C HSQC- REMARK 210 TOCSY; 2D 1H-13C HMBC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, CCPNMR ANALYSIS REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 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 PHE A 3 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 1 ILE A 9 CB - CA - C ANGL. DEV. = 12.2 DEGREES REMARK 500 1 PHE A 16 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 PHE A 3 CB - CG - CD2 ANGL. DEV. = 4.6 DEGREES REMARK 500 2 TRP A 8 CD1 - CG - CD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 2 TRP A 8 CB - CG - CD1 ANGL. DEV. = -12.2 DEGREES REMARK 500 2 TRP A 8 CE2 - CD2 - CG ANGL. DEV. = -5.6 DEGREES REMARK 500 2 TRP A 8 CG - CD2 - CE3 ANGL. DEV. = 6.2 DEGREES REMARK 500 2 ILE A 9 CA - C - N ANGL. DEV. = 19.3 DEGREES REMARK 500 2 ILE A 9 O - C - N ANGL. DEV. = -12.4 DEGREES REMARK 500 3 PHE A 3 CB - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 3 PHE A 3 CB - CG - CD1 ANGL. DEV. = -8.8 DEGREES REMARK 500 3 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 6.4 DEGREES REMARK 500 4 ILE A 9 CA - C - N ANGL. DEV. = 15.5 DEGREES REMARK 500 4 PHE A 16 CB - CG - CD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 5 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 5 ARG A 4 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 5 GLY A 17 CA - C - O ANGL. DEV. = -11.0 DEGREES REMARK 500 6 TRP A 8 CE2 - CD2 - CG ANGL. DEV. = -5.3 DEGREES REMARK 500 6 PHE A 16 CB - CG - CD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 8 LYS A 6 CA - CB - CG ANGL. DEV. = 13.8 DEGREES REMARK 500 8 TRP A 8 CB - CG - CD1 ANGL. DEV. = -9.0 DEGREES REMARK 500 8 ILE A 9 CA - C - N ANGL. DEV. = 13.6 DEGREES REMARK 500 8 ILE A 9 O - C - N ANGL. DEV. = -9.9 DEGREES REMARK 500 8 MK8 A 10 O - C - N ANGL. DEV. = -15.4 DEGREES REMARK 500 8 VAL A 12 C - N - CA ANGL. DEV. = 15.3 DEGREES REMARK 500 9 PHE A 3 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 9 ARG A 4 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 9 TRP A 8 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 9 TRP A 8 CG - CD1 - NE1 ANGL. DEV. = -6.4 DEGREES REMARK 500 9 TRP A 8 CG - CD2 - CE3 ANGL. DEV. = 5.6 DEGREES REMARK 500 10 VAL A 12 CG1 - CB - CG2 ANGL. DEV. = -10.4 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 MK8 A 10 -74.19 -108.59 REMARK 500 2 VAL A 12 -17.63 -41.58 REMARK 500 3 PHE A 3 -3.14 -57.72 REMARK 500 3 LEU A 5 2.29 -68.86 REMARK 500 3 ILE A 9 -72.02 -111.78 REMARK 500 3 MK8 A 10 -88.59 -106.46 REMARK 500 4 PHE A 3 -19.09 -46.84 REMARK 500 4 MK8 A 10 -82.00 -78.41 REMARK 500 5 ARG A 4 -19.41 -45.17 REMARK 500 5 LEU A 5 -18.19 -49.19 REMARK 500 5 ILE A 9 -61.01 -96.54 REMARK 500 5 MK8 A 10 -80.07 -104.44 REMARK 500 6 ILE A 9 -72.23 -95.63 REMARK 500 6 MK8 A 10 -70.03 -106.27 REMARK 500 7 ILE A 9 -64.36 -103.33 REMARK 500 7 MK8 A 10 -72.43 -105.66 REMARK 500 8 MK8 A 10 -60.98 -91.31 REMARK 500 9 ILE A 9 -71.55 -97.69 REMARK 500 9 MK8 A 10 -76.78 -102.38 REMARK 500 10 ILE A 9 -68.72 -100.32 REMARK 500 10 MK8 A 10 -76.83 -101.27 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 9 MK8 A 10 1 103.30 REMARK 500 MK8 A 10 LYS A 11 1 121.91 REMARK 500 LYS A 11 VAL A 12 1 -35.29 REMARK 500 MK8 A 10 LYS A 11 2 103.57 REMARK 500 LYS A 11 VAL A 12 2 -34.15 REMARK 500 ILE A 9 MK8 A 10 3 116.76 REMARK 500 MK8 A 10 LYS A 11 3 131.19 REMARK 500 LYS A 11 VAL A 12 3 -30.15 REMARK 500 ILE A 9 MK8 A 10 4 31.53 REMARK 500 MK8 A 10 LYS A 11 4 130.30 REMARK 500 LYS A 11 VAL A 12 4 -31.14 REMARK 500 LYS A 6 LYS A 7 5 -149.57 REMARK 500 ILE A 9 MK8 A 10 5 88.84 REMARK 500 MK8 A 10 LYS A 11 5 131.13 REMARK 500 LYS A 11 VAL A 12 5 -32.28 REMARK 500 ILE A 9 MK8 A 10 6 105.96 REMARK 500 MK8 A 10 LYS A 11 6 129.67 REMARK 500 ILE A 9 MK8 A 10 7 93.44 REMARK 500 MK8 A 10 LYS A 11 7 115.81 REMARK 500 ILE A 9 MK8 A 10 8 48.28 REMARK 500 MK8 A 10 LYS A 11 8 112.36 REMARK 500 LYS A 6 LYS A 7 9 -146.07 REMARK 500 ILE A 9 MK8 A 10 9 103.93 REMARK 500 MK8 A 10 LYS A 11 9 122.95 REMARK 500 LYS A 7 TRP A 8 10 -145.86 REMARK 500 ILE A 9 MK8 A 10 10 98.93 REMARK 500 MK8 A 10 LYS A 11 10 128.24 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 4 0.08 SIDE CHAIN 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 3 MK8 A 10 -11.17 REMARK 500 6 MK8 A 10 -12.01 REMARK 500 7 ARG A 4 -10.44 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34778 RELATED DB: BMRB REMARK 900 STAPLING A HOST DEFENSE PEPTIDE FOR BOOSTED DUAL TARGETING OF CD14 REMARK 900 AND BACTERIAL LPS DBREF 8BWW A 1 18 UNP P00734 THRB_HUMAN 605 622 SEQADV 8BWW MK8 A 10 UNP P00734 GLN 614 ENGINEERED MUTATION SEQADV 8BWW MK8 A 14 UNP P00734 ASP 618 ENGINEERED MUTATION SEQRES 1 A 18 HIS VAL PHE ARG LEU LYS LYS TRP ILE MK8 LYS VAL ILE SEQRES 2 A 18 MK8 GLN PHE GLY GLU HET MK8 A 10 20 HET MK8 A 14 20 HETNAM MK8 2-METHYL-L-NORLEUCINE FORMUL 1 MK8 2(C7 H15 N O2) HELIX 1 AA1 HIS A 1 LYS A 7 5 7 HELIX 2 AA2 VAL A 12 GLY A 17 5 6 LINK C ILE A 9 N MK8 A 10 1555 1555 1.34 LINK C MK8 A 10 N LYS A 11 1555 1555 1.34 LINK CE MK8 A 10 CE MK8 A 14 1555 1555 1.40 LINK C ILE A 13 N MK8 A 14 1555 1555 1.34 LINK C MK8 A 14 N GLN A 15 1555 1555 1.34 CISPEP 1 ILE A 9 MK8 A 10 2 26.70 CISPEP 2 LYS A 11 VAL A 12 6 -17.74 CISPEP 3 LYS A 11 VAL A 12 7 18.32 CISPEP 4 LYS A 11 VAL A 12 8 -18.79 CISPEP 5 LYS A 11 VAL A 12 9 -13.39 CISPEP 6 LYS A 11 VAL A 12 10 -18.28 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