HEADER SIGNALING PROTEIN/INHIBITOR 03-JUN-22 7XZQ TITLE CRYSTAL STRUCTURE OF TNIK-THIOPEPTIDE TP1 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRAF2 AND NCK-INTERACTING PROTEIN KINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.11.1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THIOPEPTIDE TP1; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TNIK, KIAA0551; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS RIPP, THIOPEPTIDE, KINASE INHIBITION, COMPLEX, SIGNALING PROTEIN, KEYWDS 2 SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.HAMADA,A.A.VINOGRADOV,Y.ZHANG,J.S.CHANG,H.NISHIMURA,Y.GOTO,H.ONAKA, AUTHOR 2 H.SUGA,K.OGATA,T.SENGOKU REVDAT 4 29-NOV-23 7XZQ 1 REMARK REVDAT 3 23-NOV-22 7XZQ 1 JRNL REVDAT 2 09-NOV-22 7XZQ 1 JRNL REVDAT 1 26-OCT-22 7XZQ 0 JRNL AUTH A.A.VINOGRADOV,Y.ZHANG,K.HAMADA,J.S.CHANG,C.OKADA, JRNL AUTH 2 H.NISHIMURA,N.TERASAKA,Y.GOTO,K.OGATA,T.SENGOKU,H.ONAKA, JRNL AUTH 3 H.SUGA JRNL TITL DE NOVO DISCOVERY OF THIOPEPTIDE PSEUDO-NATURAL PRODUCTS JRNL TITL 2 ACTING AS POTENT AND SELECTIVE TNIK KINASE INHIBITORS. JRNL REF J.AM.CHEM.SOC. V. 144 20332 2022 JRNL REFN ESSN 1520-5126 JRNL PMID 36282922 JRNL DOI 10.1021/JACS.2C07937 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.19.2_4158: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.48 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24372 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1915 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 49.4800 - 5.0400 1.00 1725 146 0.1668 0.2302 REMARK 3 2 5.0300 - 4.0000 1.00 1641 141 0.1491 0.2284 REMARK 3 3 4.0000 - 3.4900 1.00 1619 138 0.1734 0.2349 REMARK 3 4 3.4900 - 3.1700 1.00 1616 137 0.1936 0.2244 REMARK 3 5 3.1700 - 2.9500 1.00 1596 136 0.2060 0.2309 REMARK 3 6 2.9500 - 2.7700 1.00 1601 137 0.2015 0.2633 REMARK 3 7 2.7700 - 2.6300 1.00 1597 135 0.2081 0.2845 REMARK 3 8 2.6300 - 2.5200 1.00 1580 135 0.2086 0.2534 REMARK 3 9 2.5200 - 2.4200 1.00 1588 136 0.2206 0.2501 REMARK 3 10 2.4200 - 2.3400 1.00 1594 136 0.2330 0.3022 REMARK 3 11 2.3400 - 2.2700 1.00 1585 136 0.2617 0.3386 REMARK 3 12 2.2600 - 2.2000 1.00 1563 134 0.2826 0.3471 REMARK 3 13 2.2000 - 2.1400 1.00 1577 135 0.3349 0.3416 REMARK 3 14 2.1400 - 2.0900 1.00 1575 133 0.4039 0.4588 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.320 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 2617 REMARK 3 ANGLE : 0.973 3522 REMARK 3 CHIRALITY : 0.053 372 REMARK 3 PLANARITY : 0.011 450 REMARK 3 DIHEDRAL : 15.168 363 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 11 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.9945 23.8239 -14.9403 REMARK 3 T TENSOR REMARK 3 T11: 0.2303 T22: 0.3680 REMARK 3 T33: 0.3423 T12: -0.0208 REMARK 3 T13: -0.0626 T23: 0.0210 REMARK 3 L TENSOR REMARK 3 L11: 7.8989 L22: 3.6101 REMARK 3 L33: 8.5382 L12: 1.0213 REMARK 3 L13: -6.8119 L23: 0.5544 REMARK 3 S TENSOR REMARK 3 S11: -0.0794 S12: -0.1325 S13: -0.0328 REMARK 3 S21: -0.0688 S22: -0.0052 S23: 0.0831 REMARK 3 S31: -0.1441 S32: -0.1964 S33: 0.0737 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 126 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.6477 22.8728 -8.0890 REMARK 3 T TENSOR REMARK 3 T11: 0.2816 T22: 0.3018 REMARK 3 T33: 0.3620 T12: 0.0023 REMARK 3 T13: 0.0272 T23: -0.0192 REMARK 3 L TENSOR REMARK 3 L11: 4.9711 L22: 1.2825 REMARK 3 L33: 1.2809 L12: -0.4567 REMARK 3 L13: 0.5284 L23: -0.7926 REMARK 3 S TENSOR REMARK 3 S11: 0.1493 S12: 0.1622 S13: -0.0262 REMARK 3 S21: 0.0096 S22: -0.0650 S23: 0.2021 REMARK 3 S31: 0.0586 S32: -0.1943 S33: -0.0725 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 127 THROUGH 279 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.5818 19.6810 5.8914 REMARK 3 T TENSOR REMARK 3 T11: 0.2822 T22: 0.2953 REMARK 3 T33: 0.2397 T12: -0.0739 REMARK 3 T13: 0.0217 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 3.7401 L22: 3.5048 REMARK 3 L33: 1.9107 L12: 0.3308 REMARK 3 L13: -0.8341 L23: -0.5542 REMARK 3 S TENSOR REMARK 3 S11: 0.1814 S12: -0.4174 S13: 0.0313 REMARK 3 S21: 0.3931 S22: -0.1916 S23: -0.0143 REMARK 3 S31: -0.0952 S32: 0.0835 S33: 0.0145 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 280 THROUGH 310 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.2686 27.4675 -8.0596 REMARK 3 T TENSOR REMARK 3 T11: 0.3723 T22: 0.3921 REMARK 3 T33: 0.5362 T12: -0.0898 REMARK 3 T13: 0.0828 T23: 0.1172 REMARK 3 L TENSOR REMARK 3 L11: 4.9200 L22: 2.6559 REMARK 3 L33: 2.6377 L12: 0.1703 REMARK 3 L13: 0.5945 L23: 2.5609 REMARK 3 S TENSOR REMARK 3 S11: -0.0564 S12: 0.3725 S13: 0.6379 REMARK 3 S21: -0.2311 S22: -0.1207 S23: -0.1525 REMARK 3 S31: -0.4453 S32: 0.2147 S33: 0.1431 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7XZQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300029982. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-NOV-21 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.999990 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24396 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.090 REMARK 200 RESOLUTION RANGE LOW (A) : 49.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 29.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6RA7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES-NA, NACL, 1,4-BUTANEDIOL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 49.48000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 49.48000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 26.64500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 76.42000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.64500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 76.42000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.48000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.64500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 76.42000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.48000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.64500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 76.42000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE THIOPEPTIDE TP1 IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: THIOPEPTIDE TP1 REMARK 400 CHAIN: B REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 9 REMARK 465 PRO A 10 REMARK 465 LYS A 311 REMARK 465 LYS A 312 REMARK 465 ARG A 313 REMARK 465 GLY A 314 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 11 CG OD1 OD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 1614 O HOH A 1617 2.17 REMARK 500 OD2 ASP A 291 O HOH A 1501 2.17 REMARK 500 O HOH A 1606 O HOH A 1621 2.18 REMARK 500 O HOH A 1615 O HOH A 1619 2.19 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 LYS B 10 O - C - N ANGL. DEV. = -12.5 DEGREES REMARK 500 DHA B 16 CA - C - N ANGL. DEV. = 13.5 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 ALA A 22 -69.84 -29.21 REMARK 500 VAL A 28 -52.85 -125.95 REMARK 500 ARG A 152 -1.25 78.44 REMARK 500 ASP A 153 50.81 -142.82 REMARK 500 ASP A 171 81.98 78.02 REMARK 500 ASN A 186 15.17 -143.25 REMARK 500 ASP A 211 -152.84 -140.94 REMARK 500 LEU A 270 53.35 -96.32 REMARK 500 LYS B 7 -118.24 47.34 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 ARG A 80 0.09 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 LYS B 10 -10.85 REMARK 500 GLY B 13 15.27 REMARK 500 REMARK 500 REMARK: NULL DBREF 7XZQ A 11 314 UNP Q9UKE5 TNIK_HUMAN 11 314 DBREF 7XZQ B 1 18 PDB 7XZQ 7XZQ 1 18 SEQADV 7XZQ GLY A 9 UNP Q9UKE5 EXPRESSION TAG SEQADV 7XZQ PRO A 10 UNP Q9UKE5 EXPRESSION TAG SEQRES 1 A 306 GLY PRO ASP GLU ILE ASP LEU SER ALA LEU ARG ASP PRO SEQRES 2 A 306 ALA GLY ILE PHE GLU LEU VAL GLU LEU VAL GLY ASN GLY SEQRES 3 A 306 THR TYR GLY GLN VAL TYR LYS GLY ARG HIS VAL LYS THR SEQRES 4 A 306 GLY GLN LEU ALA ALA ILE LYS VAL MET ASP VAL THR GLY SEQRES 5 A 306 ASP GLU GLU GLU GLU ILE LYS GLN GLU ILE ASN MET LEU SEQRES 6 A 306 LYS LYS TYR SER HIS HIS ARG ASN ILE ALA THR TYR TYR SEQRES 7 A 306 GLY ALA PHE ILE LYS LYS ASN PRO PRO GLY MET ASP ASP SEQRES 8 A 306 GLN LEU TRP LEU VAL MET GLU PHE CYS GLY ALA GLY SER SEQRES 9 A 306 VAL THR ASP LEU ILE LYS ASN THR LYS GLY ASN THR LEU SEQRES 10 A 306 LYS GLU GLU TRP ILE ALA TYR ILE CYS ARG GLU ILE LEU SEQRES 11 A 306 ARG GLY LEU SER HIS LEU HIS GLN HIS LYS VAL ILE HIS SEQRES 12 A 306 ARG ASP ILE LYS GLY GLN ASN VAL LEU LEU THR GLU ASN SEQRES 13 A 306 ALA GLU VAL LYS LEU VAL ASP PHE GLY VAL SER ALA GLN SEQRES 14 A 306 LEU ASP ARG TPO VAL GLY ARG ARG ASN TPO PHE ILE GLY SEQRES 15 A 306 THR PRO TYR TRP MET ALA PRO GLU VAL ILE ALA CYS ASP SEQRES 16 A 306 GLU ASN PRO ASP ALA THR TYR ASP PHE LYS SER ASP LEU SEQRES 17 A 306 TRP SER LEU GLY ILE THR ALA ILE GLU MET ALA GLU GLY SEQRES 18 A 306 ALA PRO PRO LEU CYS ASP MET HIS PRO MET ARG ALA LEU SEQRES 19 A 306 PHE LEU ILE PRO ARG ASN PRO ALA PRO ARG LEU LYS SER SEQRES 20 A 306 LYS LYS TRP SER LYS LYS PHE GLN SER PHE ILE GLU SER SEQRES 21 A 306 CYS LEU VAL LYS ASN HIS SER GLN ARG PRO ALA THR GLU SEQRES 22 A 306 GLN LEU MET LYS HIS PRO PHE ILE ARG ASP GLN PRO ASN SEQRES 23 A 306 GLU ARG GLN VAL ARG ILE GLN LEU LYS ASP HIS ILE ASP SEQRES 24 A 306 ARG THR LYS LYS LYS ARG GLY SEQRES 1 B 18 DHA TRP GLY PHE ILE TYR LYS THR LEU LYS DHA DHA GLY SEQRES 2 B 18 DHA BB9 DHA BB9 MOH MODRES 7XZQ TPO A 181 THR MODIFIED RESIDUE MODRES 7XZQ TPO A 187 THR MODIFIED RESIDUE HET TPO A 181 11 HET TPO A 187 11 HET DHA B 1 4 HET DHA B 11 5 HET DHA B 12 5 HET DHA B 14 4 HET BB9 B 15 5 HET DHA B 16 4 HET BB9 B 17 6 HET MOH B 18 2 HET BU1 A1401 6 HET BU1 A1402 6 HET BU1 A1403 6 HET BU1 A1404 6 HET BU1 B 101 6 HETNAM TPO PHOSPHOTHREONINE HETNAM DHA 2-AMINO-ACRYLIC ACID HETNAM BB9 (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID HETNAM MOH METHANOL HETNAM BU1 1,4-BUTANEDIOL HETSYN TPO PHOSPHONOTHREONINE HETSYN DHA 2,3-DIDEHYDROALANINE FORMUL 1 TPO 2(C4 H10 N O6 P) FORMUL 2 DHA 5(C3 H5 N O2) FORMUL 2 BB9 2(C3 H5 N O2 S) FORMUL 2 MOH C H4 O FORMUL 3 BU1 5(C4 H10 O2) FORMUL 8 HOH *132(H2 O) HELIX 1 AA1 ASP A 14 LEU A 18 5 5 HELIX 2 AA2 THR A 59 ASP A 61 5 3 HELIX 3 AA3 GLU A 62 SER A 77 1 16 HELIX 4 AA4 VAL A 113 ASN A 119 1 7 HELIX 5 AA5 THR A 120 THR A 124 5 5 HELIX 6 AA6 LYS A 126 HIS A 147 1 22 HELIX 7 AA7 LYS A 155 GLN A 157 5 3 HELIX 8 AA8 THR A 191 MET A 195 5 5 HELIX 9 AA9 ALA A 196 ALA A 201 1 6 HELIX 10 AB1 PHE A 212 GLY A 229 1 18 HELIX 11 AB2 HIS A 237 ILE A 245 1 9 HELIX 12 AB3 SER A 259 LEU A 270 1 12 HELIX 13 AB4 ASN A 273 ARG A 277 5 5 HELIX 14 AB5 ALA A 279 LYS A 285 1 7 HELIX 15 AB6 HIS A 286 ASP A 291 1 6 HELIX 16 AB7 ASN A 294 THR A 309 1 16 SHEET 1 AA1 5 PHE A 25 GLY A 34 0 SHEET 2 AA1 5 GLY A 37 HIS A 44 -1 O LYS A 41 N GLU A 29 SHEET 3 AA1 5 LEU A 50 ASP A 57 -1 O ALA A 51 N GLY A 42 SHEET 4 AA1 5 GLN A 100 GLU A 106 -1 O LEU A 101 N MET A 56 SHEET 5 AA1 5 TYR A 85 LYS A 91 -1 N TYR A 86 O VAL A 104 SHEET 1 AA2 3 GLY A 111 SER A 112 0 SHEET 2 AA2 3 VAL A 159 LEU A 161 -1 O LEU A 161 N GLY A 111 SHEET 3 AA2 3 VAL A 167 LEU A 169 -1 O LYS A 168 N LEU A 160 SHEET 1 AA3 2 VAL A 149 ILE A 150 0 SHEET 2 AA3 2 ALA A 176 GLN A 177 -1 O ALA A 176 N ILE A 150 LINK C ARG A 180 N TPO A 181 1555 1555 1.33 LINK C TPO A 181 N VAL A 182 1555 1555 1.33 LINK C ASN A 186 N TPO A 187 1555 1555 1.33 LINK C TPO A 187 N PHE A 188 1555 1555 1.33 LINK C DHA B 1 N TRP B 2 1555 1555 1.34 LINK CA DHA B 1 C BB9 B 15 1555 1555 1.48 LINK CB DHA B 1 CB DHA B 16 1555 1555 1.40 LINK C LYS B 10 N DHA B 11 1555 1555 1.43 LINK C DHA B 11 N DHA B 12 1555 1555 1.34 LINK C DHA B 12 N GLY B 13 1555 1555 1.33 LINK C GLY B 13 N DHA B 14 1555 1555 1.33 LINK C DHA B 14 N BB9 B 15 1555 1555 1.32 LINK C DHA B 14 SG BB9 B 15 1555 1555 1.82 LINK C BB9 B 15 N DHA B 16 1555 1555 1.35 LINK C DHA B 16 N BB9 B 17 1555 1555 1.34 LINK C DHA B 16 SG BB9 B 17 1555 1555 1.82 LINK C BB9 B 17 O MOH B 18 1555 1555 1.41 CRYST1 53.290 152.840 98.960 90.00 90.00 90.00 C 2 2 21 8 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 0.018765 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006543 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010105 0.00000