HEADER LIGASE 06-APR-20 6YKN TITLE NEISSERIA GONORRHOEAE LEUCYL-TRNA SYNTHETASE IN COMPLEX WITH COMPOUND TITLE 2 11B COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LEUCYL-TRNA SYNTHETASE; COMPND 5 SYNONYM: LEUCYL-TRNA SYNTHETASE,LEURS; COMPND 6 EC: 6.1.1.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NEISSERIA GONORRHOEAE; SOURCE 3 ORGANISM_TAXID: 485; SOURCE 4 GENE: LEUS, VT05_02036, WHOO_00006, WHOO_00455; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 (DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETRUK KEYWDS PROTEIN-INHIBITOR COMPLEX, ROSSMANN FOLD, TRNA SYNTHETASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR L.PANG,S.V.STRELKOV,S.D.WEEKS REVDAT 4 24-JAN-24 6YKN 1 REMARK REVDAT 3 03-FEB-21 6YKN 1 JRNL REVDAT 2 09-DEC-20 6YKN 1 JRNL REVDAT 1 02-DEC-20 6YKN 0 JRNL AUTH D.DE RUYSSCHER,L.PANG,S.M.G.LENDERS,D.CAPPOEN,P.COS, JRNL AUTH 2 J.ROZENSKI,S.V.STRELKOV,S.D.WEEKS,A.VAN AERSCHOT JRNL TITL SYNTHESIS AND STRUCTURE-ACTIVITY STUDIES OF NOVEL JRNL TITL 2 ANHYDROHEXITOL-BASED LEUCYL-TRNA SYNTHETASE INHIBITORS. JRNL REF EUR.J.MED.CHEM. V. 211 13021 2021 JRNL REFN ISSN 0223-5234 JRNL PMID 33248851 JRNL DOI 10.1016/J.EJMECH.2020.113021 REMARK 2 REMARK 2 RESOLUTION. 2.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.88 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 28023 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 1363 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 76.8780 - 5.6582 0.99 2845 156 0.1910 0.2226 REMARK 3 2 5.6582 - 4.4912 1.00 2696 146 0.1768 0.2217 REMARK 3 3 4.4912 - 3.9235 1.00 2705 120 0.1651 0.2371 REMARK 3 4 3.9235 - 3.5648 1.00 2639 150 0.1795 0.2299 REMARK 3 5 3.5648 - 3.3093 1.00 2636 152 0.2112 0.2692 REMARK 3 6 3.3093 - 3.1142 1.00 2634 131 0.2292 0.3225 REMARK 3 7 3.1142 - 2.9582 1.00 2654 124 0.2341 0.3210 REMARK 3 8 2.9582 - 2.8294 1.00 2621 121 0.2492 0.3122 REMARK 3 9 2.8294 - 2.7205 1.00 2563 123 0.2512 0.3154 REMARK 3 10 2.7205 - 2.6300 1.00 2667 140 0.2504 0.3498 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.980 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.29 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 645 THROUGH 779 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.4101 -17.8770 -47.5313 REMARK 3 T TENSOR REMARK 3 T11: 0.3272 T22: 0.3108 REMARK 3 T33: 0.3640 T12: 0.0102 REMARK 3 T13: -0.0164 T23: -0.0166 REMARK 3 L TENSOR REMARK 3 L11: 1.8481 L22: 1.2929 REMARK 3 L33: 2.0432 L12: 0.6178 REMARK 3 L13: 0.8266 L23: 0.3740 REMARK 3 S TENSOR REMARK 3 S11: 0.0885 S12: -0.0007 S13: -0.0108 REMARK 3 S21: 0.0257 S22: 0.0155 S23: 0.2491 REMARK 3 S31: 0.1335 S32: -0.0233 S33: -0.1021 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 780 THROUGH 876 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.7310 -12.2475 -61.9742 REMARK 3 T TENSOR REMARK 3 T11: 0.4587 T22: 0.8099 REMARK 3 T33: 0.6345 T12: 0.0273 REMARK 3 T13: -0.0249 T23: -0.0093 REMARK 3 L TENSOR REMARK 3 L11: 1.9504 L22: 1.2286 REMARK 3 L33: 1.5400 L12: -0.8725 REMARK 3 L13: 1.3717 L23: -0.6273 REMARK 3 S TENSOR REMARK 3 S11: -0.0095 S12: 0.5687 S13: -0.3204 REMARK 3 S21: 0.1437 S22: 0.0575 S23: 0.5042 REMARK 3 S31: -0.1969 S32: -0.2059 S33: -0.0542 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 235 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1742 1.0504 -31.1869 REMARK 3 T TENSOR REMARK 3 T11: 0.3934 T22: 0.4666 REMARK 3 T33: 0.4309 T12: 0.0328 REMARK 3 T13: -0.0385 T23: 0.0100 REMARK 3 L TENSOR REMARK 3 L11: 0.3275 L22: 0.7266 REMARK 3 L33: 0.7145 L12: 0.3526 REMARK 3 L13: 0.3358 L23: 0.4096 REMARK 3 S TENSOR REMARK 3 S11: 0.0451 S12: 0.0102 S13: -0.0828 REMARK 3 S21: 0.0887 S22: 0.0498 S23: -0.0018 REMARK 3 S31: 0.1491 S32: 0.0490 S33: -0.1069 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 236 THROUGH 361 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3108 35.7333 -11.2499 REMARK 3 T TENSOR REMARK 3 T11: 0.5646 T22: 0.5052 REMARK 3 T33: 0.5427 T12: 0.0141 REMARK 3 T13: -0.0124 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 1.9410 L22: 1.2040 REMARK 3 L33: 2.5468 L12: 0.1336 REMARK 3 L13: -0.1468 L23: -0.8039 REMARK 3 S TENSOR REMARK 3 S11: 0.0411 S12: -0.2224 S13: 0.0566 REMARK 3 S21: 0.0328 S22: 0.0461 S23: -0.0527 REMARK 3 S31: -0.1667 S32: 0.2183 S33: -0.0659 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 362 THROUGH 644 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.7440 10.8197 -26.2173 REMARK 3 T TENSOR REMARK 3 T11: 0.4512 T22: 0.4663 REMARK 3 T33: 0.4124 T12: -0.0004 REMARK 3 T13: -0.0168 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.4889 L22: 0.4862 REMARK 3 L33: 0.6018 L12: 0.1227 REMARK 3 L13: 0.0410 L23: 0.1761 REMARK 3 S TENSOR REMARK 3 S11: 0.0357 S12: 0.0050 S13: -0.0259 REMARK 3 S21: 0.0582 S22: 0.0123 S23: 0.0497 REMARK 3 S31: 0.0393 S32: 0.0365 S33: -0.0488 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 6YKN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292106412. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28093 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.627 REMARK 200 RESOLUTION RANGE LOW (A) : 76.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : 0.13100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.77 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : 1.02600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: 6Q89 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HOLO PROTEIN AT 10 MG/ML IN 10 MM TRIS REMARK 280 PH 7, 100 MM NACL, 2.5 MM 2-MERCAPTOETHANOL WAS MIXED WITH 0.1 M REMARK 280 BIS-TRIS PROPANE PH 8.5, 0.1 M MGCL2, 20% W/V PEG 3350 AND A REMARK 280 CRYSTAL SEED STOCK IN A 0.75:1.0:0.25 (V/V) RATIO. THE SEED REMARK 280 STOCK WAS PREPARED IN THE SAME CRYSTALLIZATION BUFFER. SUITABLE REMARK 280 CRYSTALS WERE SOAKED WITH 2 MM SYNTHESIZED COMPOUND 11B IN AN REMARK 280 EQUILVALENT PRECIPITANT SOLUTION SUPPLEMENTED WITH 22% V/V REMARK 280 ETHYLENE GLYCOL., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 24.50200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 113.04950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.87450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 113.04950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.50200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.87450 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 KCAL/MOL 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 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 0 REMARK 465 PHE A 609 REMARK 465 ASP A 610 REMARK 465 ASP A 611 REMARK 465 LYS A 612 REMARK 465 GLY A 613 REMARK 465 ARG A 614 REMARK 465 ARG A 828 REMARK 465 GLY A 829 REMARK 465 LYS A 830 REMARK 465 ILE A 831 REMARK 465 THR A 832 REMARK 465 VAL A 833 REMARK 465 ALA A 834 REMARK 465 ALA A 835 REMARK 465 ASP A 836 REMARK 465 ALA A 837 REMARK 465 SER A 838 REMARK 465 LYS A 839 REMARK 465 GLU A 850 REMARK 465 GLY A 851 REMARK 465 ALA A 852 REMARK 465 VAL A 853 REMARK 465 LYS A 854 REMARK 465 PHE A 855 REMARK 465 MET A 856 REMARK 465 GLU A 857 REMARK 465 GLY A 858 REMARK 465 LYS A 859 REMARK 465 PRO A 860 REMARK 465 ALA A 861 REMARK 465 LYS A 862 REMARK 465 LYS A 863 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 GLN A 2 CD OE1 NE2 REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 LYS A 129 CE NZ REMARK 470 LYS A 142 CE NZ REMARK 470 GLU A 145 CD OE1 OE2 REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 214 CD OE1 OE2 REMARK 470 GLU A 245 CG CD OE1 OE2 REMARK 470 GLU A 293 CG CD OE1 OE2 REMARK 470 MET A 304 CG SD CE REMARK 470 THR A 306 OG1 CG2 REMARK 470 GLU A 308 CG CD OE1 OE2 REMARK 470 LYS A 310 CE NZ REMARK 470 VAL A 371 CG1 CG2 REMARK 470 ASP A 373 OD1 OD2 REMARK 470 ASP A 377 CG OD1 OD2 REMARK 470 ARG A 380 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 389 CG CD OE1 OE2 REMARK 470 LYS A 451 CG CD CE NZ REMARK 470 MET A 475 CG SD CE REMARK 470 SER A 477 OG REMARK 470 LYS A 481 CE NZ REMARK 470 LYS A 498 CD CE NZ REMARK 470 LYS A 521 CD CE NZ REMARK 470 LYS A 533 CD CE NZ REMARK 470 ARG A 590 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 594 CG CD CE NZ REMARK 470 ASP A 598 CG OD1 OD2 REMARK 470 GLU A 606 CG CD OE1 OE2 REMARK 470 LEU A 607 CG CD1 CD2 REMARK 470 VAL A 616 CG1 CG2 REMARK 470 SER A 617 OG REMARK 470 VAL A 619 CG1 CG2 REMARK 470 LEU A 620 CG CD1 CD2 REMARK 470 LYS A 621 CG CD CE NZ REMARK 470 ASP A 623 CG OD1 OD2 REMARK 470 LEU A 625 CG CD1 CD2 REMARK 470 VAL A 627 CG1 CG2 REMARK 470 LYS A 637 CG CD CE NZ REMARK 470 ARG A 690 CZ NH1 NH2 REMARK 470 LYS A 703 CE NZ REMARK 470 LYS A 714 CD CE NZ REMARK 470 GLU A 762 CD OE1 OE2 REMARK 470 VAL A 813 CG1 CG2 REMARK 470 LYS A 814 CG CD CE NZ REMARK 470 GLU A 816 CD OE1 OE2 REMARK 470 ILE A 817 CG1 CG2 CD1 REMARK 470 GLU A 818 CG CD OE1 OE2 REMARK 470 VAL A 819 CG1 CG2 REMARK 470 MET A 820 CG SD CE REMARK 470 GLN A 822 CD OE1 NE2 REMARK 470 VAL A 823 CG1 CG2 REMARK 470 ASN A 824 CG OD1 ND2 REMARK 470 LYS A 826 CE NZ REMARK 470 LEU A 827 CG CD1 CD2 REMARK 470 ASP A 841 CG OD1 OD2 REMARK 470 LEU A 842 CG CD1 CD2 REMARK 470 GLU A 843 CD OE1 OE2 REMARK 470 LEU A 847 CD1 CD2 REMARK 470 ILE A 864 CG1 CG2 CD1 REMARK 470 ILE A 865 CG1 CG2 CD1 REMARK 470 VAL A 866 CG1 CG2 REMARK 470 ARG A 870 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 875 CG1 CG2 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 PRO A 44 74.53 -67.64 REMARK 500 SER A 298 50.23 -140.33 REMARK 500 HIS A 350 12.49 -141.12 REMARK 500 MET A 475 56.88 -109.93 REMARK 500 ILE A 549 -68.57 -107.30 REMARK 500 VAL A 616 -116.09 -160.64 REMARK 500 SER A 630 -157.10 -119.72 REMARK 500 ARG A 736 -63.77 -109.57 REMARK 500 VAL A 875 95.87 -67.91 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 ZN A1006 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 449 SG REMARK 620 2 CYS A 452 SG 111.1 REMARK 620 3 CYS A 490 SG 113.1 104.0 REMARK 620 4 CYS A 493 SG 107.6 109.6 111.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OV8 A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1006 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6YKL RELATED DB: PDB DBREF1 6YKN A 1 876 UNP A0A5K1KQ39_NEIGO DBREF2 6YKN A A0A5K1KQ39 3 878 SEQADV 6YKN GLY A 0 UNP A0A5K1KQ3 EXPRESSION TAG SEQADV 6YKN ASN A 454 UNP A0A5K1KQ3 ASP 456 ENGINEERED MUTATION SEQADV 6YKN ILE A 508 UNP A0A5K1KQ3 MET 510 CONFLICT SEQRES 1 A 877 GLY MET GLN GLU HIS TYR GLN PRO ALA ALA ILE GLU PRO SEQRES 2 A 877 ALA ALA GLN LYS LYS TRP ASP ASP ALA ARG ILE SER ASN SEQRES 3 A 877 VAL SER GLU ASP ALA SER LYS PRO LYS TYR TYR CYS LEU SEQRES 4 A 877 SER MET PHE PRO TYR PRO SER GLY LYS LEU HIS MET GLY SEQRES 5 A 877 HIS VAL ARG ASN TYR THR ILE GLY ASP VAL LEU SER ARG SEQRES 6 A 877 PHE LYS LEU LEU ASN GLY PHE ASN VAL MET GLN PRO MET SEQRES 7 A 877 GLY TRP ASP ALA PHE GLY MET PRO ALA GLU ASN ALA ALA SEQRES 8 A 877 MET LYS ASN ASN VAL ALA PRO ALA ALA TRP THR TYR ASP SEQRES 9 A 877 ASN ILE GLU TYR MET LYS THR GLN LEU LYS SER LEU GLY SEQRES 10 A 877 PHE ALA VAL ASP TRP GLU ARG GLU VAL ALA THR CYS LYS SEQRES 11 A 877 PRO GLU TYR TYR ARG TRP GLU GLN TRP LEU PHE THR LYS SEQRES 12 A 877 LEU PHE GLU LYS GLY ILE VAL TYR ARG LYS ASN GLY THR SEQRES 13 A 877 VAL ASN TRP ASP PRO VAL ASP GLN THR VAL LEU ALA ASN SEQRES 14 A 877 GLU GLN VAL ILE ASP GLY ARG GLY TRP ARG SER GLY ALA SEQRES 15 A 877 LEU ILE GLU LYS ARG GLU ILE PRO MET TYR TYR PHE LYS SEQRES 16 A 877 ILE THR ASP TYR ALA GLU GLU LEU LEU ASN ASP LEU ASP SEQRES 17 A 877 LYS LEU GLU HIS TRP PRO GLU GLN VAL LYS THR MET GLN SEQRES 18 A 877 ARG ASN TRP ILE GLY LYS SER ARG GLY MET THR VAL ARG SEQRES 19 A 877 PHE ALA VAL SER ASP ASP SER LYS GLN GLY LEU GLU GLY SEQRES 20 A 877 ASP TYR ALA LYS PHE LEU GLN VAL TYR THR THR ARG PRO SEQRES 21 A 877 ASP THR LEU MET GLY ALA THR TYR VAL ALA VAL ALA ALA SEQRES 22 A 877 GLU HIS PRO LEU ALA THR ALA ALA ALA ALA ASP LYS PRO SEQRES 23 A 877 GLU LEU GLN ALA PHE ILE ALA GLU CYS LYS ALA GLY SER SEQRES 24 A 877 VAL ALA GLU ALA ASP MET ALA THR MET GLU LYS LYS GLY SEQRES 25 A 877 VAL PRO THR GLY ARG TYR VAL VAL ASN PRO LEU ASN GLY SEQRES 26 A 877 ASP LYS LEU GLU VAL TRP ILE ALA ASN TYR VAL LEU TRP SEQRES 27 A 877 GLY TYR GLY ASP GLY ALA VAL MET ALA VAL PRO ALA HIS SEQRES 28 A 877 ASP GLU ARG ASP PHE GLU PHE ALA ALA LYS TYR ASN LEU SEQRES 29 A 877 PRO LYS LYS GLN VAL ILE ALA VAL GLY ASP ASN ALA PHE SEQRES 30 A 877 ASP ALA ASN ARG TRP GLN GLU TRP TYR GLY ASP LYS GLU SEQRES 31 A 877 ASN GLY VAL LEU VAL ASN SER GLY ASP LEU ASP GLY LEU SEQRES 32 A 877 ASP PHE GLN THR ALA PHE ASP ALA VAL ALA ALA LYS LEU SEQRES 33 A 877 GLN SER GLN GLY ALA GLY GLU PRO LYS THR GLN TYR ARG SEQRES 34 A 877 LEU ARG ASP TRP GLY ILE SER ARG GLN ARG TYR TRP GLY SEQRES 35 A 877 CYS PRO ILE PRO ILE VAL HIS CYS GLU LYS CYS GLY ASN SEQRES 36 A 877 VAL PRO VAL PRO ALA ASP GLN LEU PRO VAL VAL LEU PRO SEQRES 37 A 877 GLU ASN VAL VAL PRO ASP GLY MET GLY SER PRO LEU ALA SEQRES 38 A 877 LYS MET PRO GLU PHE TYR GLU THR SER CYS PRO CYS CYS SEQRES 39 A 877 GLY GLY ALA ALA LYS ARG GLU THR ASP THR MET ASP THR SEQRES 40 A 877 PHE ILE GLU SER SER TRP TYR PHE PHE ARG TYR MET SER SEQRES 41 A 877 PRO LYS PHE SER ASP GLY MET VAL SER ALA GLU SER ALA SEQRES 42 A 877 LYS TYR TRP GLY ALA VAL ASP GLN TYR ILE GLY GLY ILE SEQRES 43 A 877 GLU HIS ALA ILE LEU HIS LEU LEU TYR ALA ARG PHE PHE SEQRES 44 A 877 THR LYS LEU MET ARG ASP GLU GLY LEU VAL ASN VAL ASP SEQRES 45 A 877 GLU PRO PHE GLU ARG LEU LEU THR GLN GLY MET VAL VAL SEQRES 46 A 877 CYS GLU THR TYR TYR ARG GLU ASN ASP LYS GLY GLY LYS SEQRES 47 A 877 ASP TRP ILE ASN PRO ALA ASP VAL GLU LEU THR PHE ASP SEQRES 48 A 877 ASP LYS GLY ARG PRO VAL SER ALA VAL LEU LYS ALA ASP SEQRES 49 A 877 GLY LEU PRO VAL VAL ILE SER GLY THR GLU LYS MET SER SEQRES 50 A 877 LYS SER LYS ASN ASN GLY VAL ASP PRO GLN GLU LEU ILE SEQRES 51 A 877 ASN ALA TYR GLY ALA ASP THR ALA ARG LEU PHE MET MET SEQRES 52 A 877 PHE ALA ALA PRO PRO GLU GLN SER LEU GLU TRP SER ASP SEQRES 53 A 877 SER GLY VAL GLU GLY ALA HIS ARG PHE LEU ARG ARG LEU SEQRES 54 A 877 TRP ARG THR VAL TYR GLU TYR LEU LYS GLN GLY GLY ALA SEQRES 55 A 877 VAL LYS ALA PHE ALA GLY ASN GLN ASP GLY LEU SER LYS SEQRES 56 A 877 GLU LEU LYS ASP LEU ARG HIS LYS LEU HIS SER THR THR SEQRES 57 A 877 ALA LYS VAL SER ASP ASP TYR GLY ARG ARG GLN GLN PHE SEQRES 58 A 877 ASN THR ALA ILE ALA ALA VAL MET GLU LEU LEU ASN GLN SEQRES 59 A 877 TYR ASP LYS THR ASP THR GLY SER GLU GLN GLY ARG ALA SEQRES 60 A 877 VAL ALA GLN GLU VAL LEU GLU ALA ALA VAL ARG LEU LEU SEQRES 61 A 877 TRP PRO ILE VAL PRO HIS ILE CYS GLU THR LEU TRP SER SEQRES 62 A 877 GLU LEU ASN GLY ALA LYS LEU TRP GLU ALA GLY TRP PRO SEQRES 63 A 877 THR VAL ASP GLU ALA ALA LEU VAL LYS SER GLU ILE GLU SEQRES 64 A 877 VAL MET VAL GLN VAL ASN GLY LYS LEU ARG GLY LYS ILE SEQRES 65 A 877 THR VAL ALA ALA ASP ALA SER LYS ALA ASP LEU GLU ALA SEQRES 66 A 877 ALA ALA LEU ALA ASN GLU GLY ALA VAL LYS PHE MET GLU SEQRES 67 A 877 GLY LYS PRO ALA LYS LYS ILE ILE VAL VAL PRO GLY ARG SEQRES 68 A 877 LEU VAL ASN ILE VAL VAL HET EDO A1001 4 HET OV8 A1002 64 HET EDO A1003 4 HET EDO A1004 4 HET MG A1005 1 HET ZN A1006 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM OV8 [(2~{R},3~{S},4~{S},5~{R})-5-[3-[4-(AMINOMETHYL)-1,2,3- HETNAM 2 OV8 TRIAZOL-1-YL]PROPYL]-3,4-BIS(OXIDANYL)OXAN-2-YL]METHYL HETNAM 3 OV8 ~{N}-[(2~{S})-2-AZANYL-4-METHYL-PENTANOYL]SULFAMATE HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 3(C2 H6 O2) FORMUL 3 OV8 C18 H34 N6 O7 S FORMUL 6 MG MG 2+ FORMUL 7 ZN ZN 2+ FORMUL 8 HOH *87(H2 O) HELIX 1 AA1 GLN A 6 ARG A 22 1 17 HELIX 2 AA2 HIS A 49 ASN A 69 1 21 HELIX 3 AA3 GLY A 83 ASN A 94 1 12 HELIX 4 AA4 ALA A 96 LEU A 115 1 20 HELIX 5 AA5 ASP A 120 GLU A 124 5 5 HELIX 6 AA6 LYS A 129 LYS A 146 1 18 HELIX 7 AA7 ALA A 167 GLU A 169 5 3 HELIX 8 AA8 ILE A 195 ASP A 197 5 3 HELIX 9 AA9 TYR A 198 ASP A 205 1 8 HELIX 10 AB1 LEU A 206 LEU A 209 5 4 HELIX 11 AB2 PRO A 213 GLY A 225 1 13 HELIX 12 AB3 ASP A 238 LYS A 241 5 4 HELIX 13 AB4 GLU A 245 ALA A 249 5 5 HELIX 14 AB5 ARG A 258 ALA A 265 5 8 HELIX 15 AB6 HIS A 274 ALA A 281 1 8 HELIX 16 AB7 LYS A 284 GLY A 297 1 14 HELIX 17 AB8 ALA A 300 MET A 304 5 5 HELIX 18 AB9 ASP A 351 ASN A 362 1 12 HELIX 19 AC1 GLN A 382 ASP A 387 5 6 HELIX 20 AC2 SER A 396 ASP A 400 5 5 HELIX 21 AC3 ASP A 403 GLN A 418 1 16 HELIX 22 AC4 PRO A 458 LEU A 462 5 5 HELIX 23 AC5 SER A 477 LYS A 481 5 5 HELIX 24 AC6 MET A 482 TYR A 486 1 5 HELIX 25 AC7 THR A 506 SER A 511 5 6 HELIX 26 AC8 TRP A 512 TYR A 517 1 6 HELIX 27 AC9 SER A 528 GLY A 536 1 9 HELIX 28 AD1 GLU A 546 ALA A 548 5 3 HELIX 29 AD2 ILE A 549 GLY A 566 1 18 HELIX 30 AD3 ASN A 601 ALA A 603 5 3 HELIX 31 AD4 ASP A 644 GLY A 653 1 10 HELIX 32 AD5 GLY A 653 ALA A 665 1 13 HELIX 33 AD6 SER A 674 LYS A 697 1 24 HELIX 34 AD7 SER A 713 ARG A 736 1 24 HELIX 35 AD8 GLN A 739 LYS A 756 1 18 HELIX 36 AD9 SER A 761 LEU A 779 1 19 HELIX 37 AE1 VAL A 783 ASN A 795 1 13 HELIX 38 AE2 LYS A 798 GLY A 803 1 6 HELIX 39 AE3 ASP A 808 VAL A 813 5 6 HELIX 40 AE4 ASP A 841 ALA A 848 1 8 SHEET 1 AA1 4 ASN A 72 MET A 74 0 SHEET 2 AA1 4 LYS A 34 SER A 39 1 N TYR A 35 O MET A 74 SHEET 3 AA1 4 VAL A 538 GLY A 544 1 O GLN A 540 N LEU A 38 SHEET 4 AA1 4 PHE A 574 GLN A 580 1 O LEU A 578 N TYR A 541 SHEET 1 AA2 2 GLY A 78 TRP A 79 0 SHEET 2 AA2 2 VAL A 125 ALA A 126 1 O VAL A 125 N TRP A 79 SHEET 1 AA3 4 THR A 164 LEU A 166 0 SHEET 2 AA3 4 VAL A 149 ASP A 159 -1 N ASN A 157 O LEU A 166 SHEET 3 AA3 4 GLU A 184 PHE A 193 -1 O ILE A 188 N GLY A 154 SHEET 4 AA3 4 TRP A 432 GLY A 433 -1 O TRP A 432 N PHE A 193 SHEET 1 AA4 2 VAL A 171 ILE A 172 0 SHEET 2 AA4 2 ARG A 175 GLY A 176 -1 O ARG A 175 N ILE A 172 SHEET 1 AA5 6 PHE A 251 THR A 256 0 SHEET 2 AA5 6 LYS A 226 VAL A 236 -1 N PHE A 234 O LEU A 252 SHEET 3 AA5 6 GLY A 311 VAL A 319 -1 O VAL A 319 N ALA A 235 SHEET 4 AA5 6 LYS A 326 ALA A 332 -1 O LEU A 327 N VAL A 318 SHEET 5 AA5 6 TYR A 267 VAL A 270 1 N VAL A 270 O TRP A 330 SHEET 6 AA5 6 ALA A 343 ALA A 346 -1 O VAL A 344 N ALA A 269 SHEET 1 AA6 3 PHE A 251 THR A 256 0 SHEET 2 AA6 3 LYS A 226 VAL A 236 -1 N PHE A 234 O LEU A 252 SHEET 3 AA6 3 GLY A 421 TYR A 427 -1 O GLU A 422 N THR A 231 SHEET 1 AA7 2 ILE A 369 ALA A 370 0 SHEET 2 AA7 2 VAL A 392 LEU A 393 -1 O VAL A 392 N ALA A 370 SHEET 1 AA8 2 SER A 435 ARG A 436 0 SHEET 2 AA8 2 THR A 503 MET A 504 -1 O THR A 503 N ARG A 436 SHEET 1 AA9 4 GLY A 453 PRO A 456 0 SHEET 2 AA9 4 ILE A 446 CYS A 449 -1 N VAL A 447 O VAL A 455 SHEET 3 AA9 4 ALA A 496 ARG A 499 -1 O LYS A 498 N HIS A 448 SHEET 4 AA9 4 GLU A 487 SER A 489 -1 N THR A 488 O ALA A 497 SHEET 1 AB1 5 LYS A 597 ILE A 600 0 SHEET 2 AB1 5 VAL A 583 GLU A 591 -1 N TYR A 588 O ILE A 600 SHEET 3 AB1 5 PRO A 626 LYS A 634 -1 O SER A 630 N THR A 587 SHEET 4 AB1 5 ALA A 618 LEU A 620 -1 N ALA A 618 O VAL A 627 SHEET 5 AB1 5 VAL A 605 LEU A 607 -1 N GLU A 606 O VAL A 619 SHEET 1 AB2 3 LYS A 597 ILE A 600 0 SHEET 2 AB2 3 VAL A 583 GLU A 591 -1 N TYR A 588 O ILE A 600 SHEET 3 AB2 3 LEU A 671 GLU A 672 1 O LEU A 671 N VAL A 584 SHEET 1 AB3 3 MET A 820 VAL A 823 0 SHEET 2 AB3 3 LEU A 871 ILE A 874 1 O VAL A 872 N MET A 820 SHEET 3 AB3 3 VAL A 866 VAL A 867 -1 N VAL A 867 O LEU A 871 LINK OE1 GLU A 210 MG MG A1005 1555 1555 2.90 LINK SG CYS A 449 ZN ZN A1006 1555 1555 2.46 LINK SG CYS A 452 ZN ZN A1006 1555 1555 2.39 LINK SG CYS A 490 ZN ZN A1006 1555 1555 2.31 LINK SG CYS A 493 ZN ZN A1006 1555 1555 2.42 CISPEP 1 LEU A 462 PRO A 463 0 2.20 SITE 1 AC1 3 GLU A 773 ARG A 777 ASN A 795 SITE 1 AC2 19 MET A 40 PHE A 41 PRO A 42 TYR A 43 SITE 2 AC2 19 HIS A 49 GLY A 51 HIS A 52 ASN A 55 SITE 3 AC2 19 TYR A 56 ASP A 80 GLY A 543 GLY A 544 SITE 4 AC2 19 GLU A 546 HIS A 547 HIS A 551 MET A 582 SITE 5 AC2 19 VAL A 583 LYS A 634 MET A 635 SITE 1 AC3 5 TRP A 223 GLU A 301 TYR A 339 ARG A 428 SITE 2 AC3 5 HOH A1121 SITE 1 AC4 7 TRP A 223 LEU A 429 ARG A 430 ASP A 431 SITE 2 AC4 7 TYR A 554 HOH A1121 HOH A1145 SITE 1 AC5 1 GLU A 210 SITE 1 AC6 4 CYS A 449 CYS A 452 CYS A 490 CYS A 493 CRYST1 49.004 81.749 226.099 90.00 90.00 90.00 P 21 21 21 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 0.020406 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004423 0.00000