HEADER SIGNALING PROTEIN/INHIBITOR 03-JUN-22 7XZR TITLE CRYSTAL STRUCTURE OF TNIK-AMPPNP-THIOPEPTIDE TP15 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRAF2 AND NCK-INTERACTING PROTEIN KINASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.7.11.1; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THIOPEPTIDE TP15; COMPND 8 CHAIN: C, D; 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 5 20-MAR-24 7XZR 1 SOURCE REVDAT 4 29-NOV-23 7XZR 1 REMARK REVDAT 3 23-NOV-22 7XZR 1 JRNL REVDAT 2 09-NOV-22 7XZR 1 JRNL REVDAT 1 26-OCT-22 7XZR 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. 2.26 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) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 41541 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 1957 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 43.3400 - 5.4400 1.00 2854 145 0.1525 0.1646 REMARK 3 2 5.4400 - 4.3200 1.00 2850 142 0.1361 0.1899 REMARK 3 3 4.3200 - 3.7800 1.00 2814 135 0.1413 0.1813 REMARK 3 4 3.7800 - 3.4300 1.00 2851 141 0.1652 0.2101 REMARK 3 5 3.4300 - 3.1900 1.00 2829 133 0.1961 0.2426 REMARK 3 6 3.1900 - 3.0000 1.00 2811 139 0.1983 0.2577 REMARK 3 7 3.0000 - 2.8500 1.00 2831 140 0.2097 0.2634 REMARK 3 8 2.8500 - 2.7200 1.00 2825 142 0.2243 0.2971 REMARK 3 9 2.7200 - 2.6200 1.00 2816 136 0.2287 0.2773 REMARK 3 10 2.6200 - 2.5300 1.00 2806 145 0.2256 0.3049 REMARK 3 11 2.5300 - 2.4500 1.00 2847 139 0.2345 0.2741 REMARK 3 12 2.4500 - 2.3800 1.00 2816 143 0.2632 0.2999 REMARK 3 13 2.3800 - 2.3200 1.00 2795 135 0.3001 0.3611 REMARK 3 14 2.3200 - 2.2600 1.00 2839 142 0.3520 0.3817 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.770 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 5266 REMARK 3 ANGLE : 1.022 7143 REMARK 3 CHIRALITY : 0.057 764 REMARK 3 PLANARITY : 0.009 904 REMARK 3 DIHEDRAL : 13.703 720 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 12 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.2402 28.1101 -2.0332 REMARK 3 T TENSOR REMARK 3 T11: 0.3593 T22: 0.2756 REMARK 3 T33: 0.5141 T12: 0.0083 REMARK 3 T13: 0.0780 T23: -0.0959 REMARK 3 L TENSOR REMARK 3 L11: 3.6844 L22: 2.9073 REMARK 3 L33: 3.8554 L12: -0.1795 REMARK 3 L13: 2.3997 L23: -0.6187 REMARK 3 S TENSOR REMARK 3 S11: -0.0726 S12: -0.1186 S13: -0.0599 REMARK 3 S21: -0.0645 S22: 0.0196 S23: 0.3708 REMARK 3 S31: 0.1043 S32: -0.2739 S33: 0.0227 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 100 THROUGH 166 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.1569 24.7726 1.0829 REMARK 3 T TENSOR REMARK 3 T11: 0.2957 T22: 0.2789 REMARK 3 T33: 0.4478 T12: -0.0167 REMARK 3 T13: 0.0541 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 3.1759 L22: 2.0695 REMARK 3 L33: 2.3002 L12: -0.0633 REMARK 3 L13: 0.0478 L23: 0.1888 REMARK 3 S TENSOR REMARK 3 S11: -0.0487 S12: 0.1478 S13: 0.1443 REMARK 3 S21: -0.1053 S22: -0.0612 S23: -0.2468 REMARK 3 S31: -0.1062 S32: 0.3307 S33: 0.1242 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 167 THROUGH 279 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.6845 11.2581 10.3008 REMARK 3 T TENSOR REMARK 3 T11: 0.3163 T22: 0.3128 REMARK 3 T33: 0.2832 T12: 0.0119 REMARK 3 T13: -0.0237 T23: -0.0306 REMARK 3 L TENSOR REMARK 3 L11: 4.6915 L22: 3.8883 REMARK 3 L33: 1.8637 L12: 1.6076 REMARK 3 L13: -0.8710 L23: -0.6534 REMARK 3 S TENSOR REMARK 3 S11: -0.0365 S12: -0.2741 S13: -0.2164 REMARK 3 S21: 0.3780 S22: -0.0862 S23: -0.1799 REMARK 3 S31: 0.1550 S32: 0.1542 S33: 0.1203 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 280 THROUGH 310 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.4402 29.2672 2.8193 REMARK 3 T TENSOR REMARK 3 T11: 0.4023 T22: 0.4242 REMARK 3 T33: 0.7154 T12: 0.0070 REMARK 3 T13: -0.0038 T23: -0.0906 REMARK 3 L TENSOR REMARK 3 L11: 4.9442 L22: 6.1581 REMARK 3 L33: 7.7102 L12: 0.0825 REMARK 3 L13: 1.2134 L23: -5.6202 REMARK 3 S TENSOR REMARK 3 S11: 0.0559 S12: 0.0742 S13: 0.9111 REMARK 3 S21: 0.5895 S22: -0.2933 S23: -0.8654 REMARK 3 S31: -1.3252 S32: 1.0419 S33: 0.2268 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 12 THROUGH 99 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.6857 -13.9907 11.8339 REMARK 3 T TENSOR REMARK 3 T11: 0.6403 T22: 0.3731 REMARK 3 T33: 0.4105 T12: 0.0019 REMARK 3 T13: 0.1083 T23: -0.0427 REMARK 3 L TENSOR REMARK 3 L11: 2.9149 L22: 2.3306 REMARK 3 L33: 1.7156 L12: 0.3298 REMARK 3 L13: -0.6380 L23: -0.3583 REMARK 3 S TENSOR REMARK 3 S11: -0.0993 S12: -0.1925 S13: -0.2593 REMARK 3 S21: 0.1985 S22: -0.0228 S23: 0.0287 REMARK 3 S31: 0.3724 S32: -0.0285 S33: 0.1206 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 100 THROUGH 312 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.2863 -23.2874 -5.8776 REMARK 3 T TENSOR REMARK 3 T11: 0.3956 T22: 0.2706 REMARK 3 T33: 0.4269 T12: 0.0057 REMARK 3 T13: 0.0772 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.9333 L22: 2.4421 REMARK 3 L33: 2.3572 L12: -0.0480 REMARK 3 L13: -0.1351 L23: -0.3959 REMARK 3 S TENSOR REMARK 3 S11: 0.0557 S12: 0.0638 S13: 0.0801 REMARK 3 S21: -0.1012 S22: -0.0850 S23: -0.4930 REMARK 3 S31: -0.0829 S32: 0.1164 S33: 0.0197 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 7XZR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1300029990. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-DEC-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) : 0.99999 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41561 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 43.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 45.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 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 (%): 59.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM ACETATE, MGSO4, HEPES-NA, PEG REMARK 280 SMEAR MEDIUM, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 83.82500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 3400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 2870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 TP15 IS CYCLIC PEPTIDE, A MEMBER OF INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: THIOPEPTIDE TP15 REMARK 400 CHAIN: C, D 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 ASP A 11 REMARK 465 LYS A 311 REMARK 465 LYS A 312 REMARK 465 ARG A 313 REMARK 465 GLY A 314 REMARK 465 GLY B 9 REMARK 465 PRO B 10 REMARK 465 ASP B 11 REMARK 465 ARG B 313 REMARK 465 GLY B 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 GLU A 12 CG CD OE1 OE2 REMARK 470 ARG A 180 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 310 CG CD CE NZ REMARK 470 GLU B 12 CG CD OE1 OE2 REMARK 470 TYR B 36 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 180 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 310 CG CD CE NZ REMARK 470 LYS B 311 CG CD CE NZ REMARK 470 LYS B 312 CG CD CE NZ 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 O3G ANP A 1401 O HOH A 1501 1.93 REMARK 500 O3G ANP A 1401 O HOH A 1502 2.07 REMARK 500 O2' ANP B 1401 O HOH B 1501 2.14 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 -134.97 40.18 REMARK 500 MET A 97 130.65 -173.92 REMARK 500 ASP A 153 48.04 -140.85 REMARK 500 ASP A 171 87.23 74.52 REMARK 500 ASN A 186 24.31 -141.67 REMARK 500 ASP A 211 -152.22 -142.06 REMARK 500 LEU A 270 49.54 -102.09 REMARK 500 ASN A 273 99.13 -69.70 REMARK 500 TYR B 36 70.68 60.12 REMARK 500 PRO B 95 -18.64 -48.20 REMARK 500 ASP B 171 83.31 70.33 REMARK 500 ASP B 211 -152.07 -145.37 REMARK 500 LEU B 270 64.30 -103.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 158 OD1 REMARK 620 2 ASP A 171 OD2 82.7 REMARK 620 3 ANP A1401 O1B 163.8 89.9 REMARK 620 4 ANP A1401 O2A 78.6 88.6 86.9 REMARK 620 5 HOH A1560 O 84.2 166.3 101.7 84.7 REMARK 620 6 HOH A1561 O 98.6 87.2 95.4 175.2 98.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN B 158 OD1 REMARK 620 2 ASP B 171 OD2 74.5 REMARK 620 3 ANP B1401 O1G 128.4 65.6 REMARK 620 4 ANP B1401 O1B 68.0 73.1 70.0 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7XZQ RELATED DB: PDB DBREF 7XZR A 11 314 UNP Q9UKE5 TNIK_HUMAN 11 314 DBREF 7XZR B 11 314 UNP Q9UKE5 TNIK_HUMAN 11 314 DBREF 7XZR C 1 18 PDB 7XZR 7XZR 1 18 DBREF 7XZR D 1 18 PDB 7XZR 7XZR 1 18 SEQADV 7XZR GLY A 9 UNP Q9UKE5 EXPRESSION TAG SEQADV 7XZR PRO A 10 UNP Q9UKE5 EXPRESSION TAG SEQADV 7XZR GLY B 9 UNP Q9UKE5 EXPRESSION TAG SEQADV 7XZR PRO B 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 306 GLY PRO ASP GLU ILE ASP LEU SER ALA LEU ARG ASP PRO SEQRES 2 B 306 ALA GLY ILE PHE GLU LEU VAL GLU LEU VAL GLY ASN GLY SEQRES 3 B 306 THR TYR GLY GLN VAL TYR LYS GLY ARG HIS VAL LYS THR SEQRES 4 B 306 GLY GLN LEU ALA ALA ILE LYS VAL MET ASP VAL THR GLY SEQRES 5 B 306 ASP GLU GLU GLU GLU ILE LYS GLN GLU ILE ASN MET LEU SEQRES 6 B 306 LYS LYS TYR SER HIS HIS ARG ASN ILE ALA THR TYR TYR SEQRES 7 B 306 GLY ALA PHE ILE LYS LYS ASN PRO PRO GLY MET ASP ASP SEQRES 8 B 306 GLN LEU TRP LEU VAL MET GLU PHE CYS GLY ALA GLY SER SEQRES 9 B 306 VAL THR ASP LEU ILE LYS ASN THR LYS GLY ASN THR LEU SEQRES 10 B 306 LYS GLU GLU TRP ILE ALA TYR ILE CYS ARG GLU ILE LEU SEQRES 11 B 306 ARG GLY LEU SER HIS LEU HIS GLN HIS LYS VAL ILE HIS SEQRES 12 B 306 ARG ASP ILE LYS GLY GLN ASN VAL LEU LEU THR GLU ASN SEQRES 13 B 306 ALA GLU VAL LYS LEU VAL ASP PHE GLY VAL SER ALA GLN SEQRES 14 B 306 LEU ASP ARG TPO VAL GLY ARG ARG ASN TPO PHE ILE GLY SEQRES 15 B 306 THR PRO TYR TRP MET ALA PRO GLU VAL ILE ALA CYS ASP SEQRES 16 B 306 GLU ASN PRO ASP ALA THR TYR ASP PHE LYS SER ASP LEU SEQRES 17 B 306 TRP SER LEU GLY ILE THR ALA ILE GLU MET ALA GLU GLY SEQRES 18 B 306 ALA PRO PRO LEU CYS ASP MET HIS PRO MET ARG ALA LEU SEQRES 19 B 306 PHE LEU ILE PRO ARG ASN PRO ALA PRO ARG LEU LYS SER SEQRES 20 B 306 LYS LYS TRP SER LYS LYS PHE GLN SER PHE ILE GLU SER SEQRES 21 B 306 CYS LEU VAL LYS ASN HIS SER GLN ARG PRO ALA THR GLU SEQRES 22 B 306 GLN LEU MET LYS HIS PRO PHE ILE ARG ASP GLN PRO ASN SEQRES 23 B 306 GLU ARG GLN VAL ARG ILE GLN LEU LYS ASP HIS ILE ASP SEQRES 24 B 306 ARG THR LYS LYS LYS ARG GLY SEQRES 1 C 18 DHA TRP THR ILE ARG THR ARG GLY ARG ILE ALA THR BB9 SEQRES 2 C 18 DHA BB9 DHA BB9 MOH SEQRES 1 D 18 DHA TRP THR ILE ARG THR ARG GLY ARG ILE ALA THR BB9 SEQRES 2 D 18 DHA BB9 DHA BB9 MOH MODRES 7XZR TPO A 181 THR MODIFIED RESIDUE MODRES 7XZR TPO A 187 THR MODIFIED RESIDUE MODRES 7XZR TPO B 181 THR MODIFIED RESIDUE MODRES 7XZR TPO B 187 THR MODIFIED RESIDUE HET TPO A 181 11 HET TPO A 187 11 HET TPO B 181 11 HET TPO B 187 11 HET DHA C 1 4 HET BB9 C 13 6 HET DHA C 14 4 HET BB9 C 15 5 HET DHA C 16 4 HET BB9 C 17 6 HET MOH C 18 2 HET DHA D 1 4 HET BB9 D 13 6 HET DHA D 14 4 HET BB9 D 15 5 HET DHA D 16 4 HET BB9 D 17 6 HET MOH D 18 2 HET ANP A1401 31 HET MG A1402 1 HET SO4 A1403 5 HET SO4 A1404 5 HET PGE A1405 10 HET ANP B1401 31 HET MG B1402 1 HET SO4 B1403 5 HETNAM TPO PHOSPHOTHREONINE HETNAM DHA 2-AMINO-ACRYLIC ACID HETNAM BB9 (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID HETNAM MOH METHANOL HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM SO4 SULFATE ION HETNAM PGE TRIETHYLENE GLYCOL HETSYN TPO PHOSPHONOTHREONINE HETSYN DHA 2,3-DIDEHYDROALANINE FORMUL 1 TPO 4(C4 H10 N O6 P) FORMUL 3 DHA 6(C3 H5 N O2) FORMUL 3 BB9 6(C3 H5 N O2 S) FORMUL 3 MOH 2(C H4 O) FORMUL 5 ANP 2(C10 H17 N6 O12 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 SO4 3(O4 S 2-) FORMUL 9 PGE C6 H14 O4 FORMUL 13 HOH *186(H2 O) HELIX 1 AA1 ASP A 14 LEU A 18 5 5 HELIX 2 AA2 GLU A 62 SER A 77 1 16 HELIX 3 AA3 SER A 112 THR A 120 1 9 HELIX 4 AA4 LYS A 121 THR A 124 5 4 HELIX 5 AA5 LYS A 126 HIS A 147 1 22 HELIX 6 AA6 LYS A 155 GLN A 157 5 3 HELIX 7 AA7 THR A 191 MET A 195 5 5 HELIX 8 AA8 ALA A 196 ALA A 201 1 6 HELIX 9 AA9 PHE A 212 GLY A 229 1 18 HELIX 10 AB1 HIS A 237 ILE A 245 1 9 HELIX 11 AB2 SER A 259 LEU A 270 1 12 HELIX 12 AB3 ALA A 279 LYS A 285 1 7 HELIX 13 AB4 HIS A 286 ASP A 291 1 6 HELIX 14 AB5 ASN A 294 THR A 309 1 16 HELIX 15 AB6 THR B 59 ASP B 61 5 3 HELIX 16 AB7 GLU B 62 SER B 77 1 16 HELIX 17 AB8 VAL B 113 THR B 120 1 8 HELIX 18 AB9 LYS B 121 THR B 124 5 4 HELIX 19 AC1 LYS B 126 HIS B 147 1 22 HELIX 20 AC2 LYS B 155 GLN B 157 5 3 HELIX 21 AC3 THR B 191 MET B 195 5 5 HELIX 22 AC4 ALA B 196 ASN B 205 1 10 HELIX 23 AC5 LYS B 213 GLY B 229 1 17 HELIX 24 AC6 HIS B 237 ILE B 245 1 9 HELIX 25 AC7 SER B 259 LEU B 270 1 12 HELIX 26 AC8 ASN B 273 ARG B 277 5 5 HELIX 27 AC9 ALA B 279 LYS B 285 1 7 HELIX 28 AD1 HIS B 286 ASP B 291 1 6 HELIX 29 AD2 ASN B 294 LYS B 312 1 19 HELIX 30 AD3 THR C 6 GLY C 8 5 3 HELIX 31 AD4 THR D 6 GLY D 8 5 3 SHEET 1 AA1 5 PHE A 25 ASN A 33 0 SHEET 2 AA1 5 GLN A 38 HIS A 44 -1 O LYS A 41 N VAL A 28 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 MET A 105 -1 O LEU A 103 N LYS A 54 SHEET 5 AA1 5 TYR A 85 LYS A 91 -1 N GLY A 87 O VAL A 104 SHEET 1 AA2 2 VAL A 149 ILE A 150 0 SHEET 2 AA2 2 ALA A 176 GLN A 177 -1 O ALA A 176 N ILE A 150 SHEET 1 AA3 2 VAL A 159 LEU A 161 0 SHEET 2 AA3 2 VAL A 167 LEU A 169 -1 O LYS A 168 N LEU A 160 SHEET 1 AA4 5 PHE B 25 GLY B 34 0 SHEET 2 AA4 5 GLY B 37 HIS B 44 -1 O VAL B 39 N GLY B 32 SHEET 3 AA4 5 LEU B 50 ASP B 57 -1 O ALA B 51 N GLY B 42 SHEET 4 AA4 5 GLN B 100 MET B 105 -1 O MET B 105 N ALA B 52 SHEET 5 AA4 5 TYR B 85 LYS B 91 -1 N LYS B 91 O GLN B 100 SHEET 1 AA5 3 GLY B 111 SER B 112 0 SHEET 2 AA5 3 VAL B 159 LEU B 161 -1 O LEU B 161 N GLY B 111 SHEET 3 AA5 3 VAL B 167 LEU B 169 -1 O LYS B 168 N LEU B 160 SHEET 1 AA6 2 VAL B 149 ILE B 150 0 SHEET 2 AA6 2 ALA B 176 GLN B 177 -1 O ALA B 176 N ILE B 150 SHEET 1 AA7 2 THR C 3 ILE C 4 0 SHEET 2 AA7 2 ILE C 10 ALA C 11 -1 O ALA C 11 N THR C 3 SHEET 1 AA8 2 THR D 3 ILE D 4 0 SHEET 2 AA8 2 ILE D 10 ALA D 11 -1 O ALA D 11 N THR D 3 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 ARG B 180 N TPO B 181 1555 1555 1.33 LINK C TPO B 181 N VAL B 182 1555 1555 1.33 LINK C ASN B 186 N TPO B 187 1555 1555 1.33 LINK C TPO B 187 N PHE B 188 1555 1555 1.33 LINK C DHA C 1 N TRP C 2 1555 1555 1.33 LINK CA DHA C 1 C BB9 C 15 1555 1555 1.43 LINK CB DHA C 1 CB DHA C 16 1555 1555 1.39 LINK C THR C 12 SG BB9 C 13 1555 1555 1.72 LINK C THR C 12 N BB9 C 13 1555 1555 1.33 LINK C BB9 C 13 N DHA C 14 1555 1555 1.36 LINK C DHA C 14 N BB9 C 15 1555 1555 1.32 LINK C DHA C 14 SG BB9 C 15 1555 1555 1.76 LINK C BB9 C 15 N DHA C 16 1555 1555 1.32 LINK C DHA C 16 N BB9 C 17 1555 1555 1.30 LINK C DHA C 16 SG BB9 C 17 1555 1555 1.78 LINK C BB9 C 17 O MOH C 18 1555 1555 1.37 LINK C DHA D 1 N TRP D 2 1555 1555 1.34 LINK CA DHA D 1 C BB9 D 15 1555 1555 1.45 LINK CB DHA D 1 CB DHA D 16 1555 1555 1.39 LINK C THR D 12 N BB9 D 13 1555 1555 1.31 LINK C THR D 12 SG BB9 D 13 1555 1555 1.73 LINK C BB9 D 13 N DHA D 14 1555 1555 1.38 LINK C DHA D 14 N BB9 D 15 1555 1555 1.31 LINK C DHA D 14 SG BB9 D 15 1555 1555 1.76 LINK C BB9 D 15 N DHA D 16 1555 1555 1.37 LINK C DHA D 16 N BB9 D 17 1555 1555 1.31 LINK C DHA D 16 SG BB9 D 17 1555 1555 1.79 LINK C BB9 D 17 O MOH D 18 1555 1555 1.40 LINK OD1 ASN A 158 MG MG A1402 1555 1555 2.32 LINK OD2 ASP A 171 MG MG A1402 1555 1555 2.17 LINK O1B ANP A1401 MG MG A1402 1555 1555 2.02 LINK O2A ANP A1401 MG MG A1402 1555 1555 2.32 LINK MG MG A1402 O HOH A1560 1555 1555 2.17 LINK MG MG A1402 O HOH A1561 1555 1555 2.13 LINK OD1 ASN B 158 MG MG B1402 1555 1555 2.59 LINK OD2 ASP B 171 MG MG B1402 1555 1555 2.87 LINK O1G ANP B1401 MG MG B1402 1555 1555 2.33 LINK O1B ANP B1401 MG MG B1402 1555 1555 2.76 CRYST1 53.110 167.650 53.710 90.00 108.50 90.00 P 1 21 1 4 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 0.018829 0.000000 0.006299 0.00000 SCALE2 0.000000 0.005965 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019633 0.00000