HEADER LIGASE 15-OCT-20 7AP2 TITLE NEISSERIA GONORRHOEAE LEUCYL-TRNA SYNTHETASE IN COMPLEX WITH COMPOUND TITLE 2 LEUS7HMDDA 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_STRAIN: 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.DE GRAEF,S.V.STRELKOV,S.D.WEEKS REVDAT 2 31-JAN-24 7AP2 1 REMARK REVDAT 1 28-OCT-20 7AP2 0 JRNL AUTH B.ZHANG,L.PANG,M.NAUTIYAL,S.DE GRAEF,B.GADAKH,E.LESCRINIER, JRNL AUTH 2 J.ROZENSKI,S.V.STRELKOV,S.D.WEEKS,A.VAN AERSCHOT JRNL TITL SYNTHESIS AND BIOLOGICAL EVALUATION OF JRNL TITL 2 1,3-DIDEAZAPURINE-LIKE 7-AMINO-5-HYDROXYMETHYL-BENZIMIDAZOLE JRNL TITL 3 RIBONUCLEOSIDE ANALOGUES AS AMINOACYL-TRNA SYNTHETASE JRNL TITL 4 INHIBITORS. JRNL REF MOLECULES V. 25 2020 JRNL REFN ESSN 1420-3049 JRNL PMID 33081246 JRNL DOI 10.3390/MOLECULES25204751 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 43753 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.580 REMARK 3 FREE R VALUE TEST SET COUNT : 2006 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 56.2500 - 5.4200 1.00 3221 147 0.1745 0.2247 REMARK 3 2 5.4200 - 4.3000 1.00 3059 150 0.1576 0.1672 REMARK 3 3 4.3000 - 3.7600 1.00 3007 145 0.1536 0.1877 REMARK 3 4 3.7600 - 3.4200 1.00 3030 130 0.1698 0.2061 REMARK 3 5 3.4200 - 3.1700 1.00 2971 144 0.1925 0.2548 REMARK 3 6 3.1700 - 2.9800 1.00 2973 143 0.1984 0.2962 REMARK 3 7 2.9800 - 2.8300 1.00 2946 154 0.2156 0.2744 REMARK 3 8 2.8300 - 2.7100 1.00 2933 140 0.2133 0.2957 REMARK 3 9 2.7100 - 2.6100 1.00 2969 123 0.2185 0.2591 REMARK 3 10 2.6100 - 2.5200 1.00 2946 152 0.2211 0.2634 REMARK 3 11 2.5200 - 2.4400 1.00 2921 155 0.2368 0.3140 REMARK 3 12 2.4400 - 2.3700 1.00 2916 145 0.2478 0.3061 REMARK 3 13 2.3700 - 2.3100 1.00 2950 140 0.2639 0.3434 REMARK 3 14 2.3100 - 2.2500 1.00 2905 138 0.2888 0.3573 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.51 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 : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 235 ) REMARK 3 ORIGIN FOR THE GROUP (A): 1.1263 0.9378 -31.1350 REMARK 3 T TENSOR REMARK 3 T11: 0.3024 T22: 0.3724 REMARK 3 T33: 0.3659 T12: 0.0122 REMARK 3 T13: -0.0346 T23: -0.0161 REMARK 3 L TENSOR REMARK 3 L11: 0.2504 L22: 0.6540 REMARK 3 L33: 0.6303 L12: 0.1959 REMARK 3 L13: 0.2302 L23: 0.5275 REMARK 3 S TENSOR REMARK 3 S11: 0.0444 S12: 0.0707 S13: -0.0987 REMARK 3 S21: 0.0701 S22: 0.0418 S23: 0.0193 REMARK 3 S31: 0.1201 S32: 0.0875 S33: -0.0882 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 236 THROUGH 361 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.3702 35.3607 -11.1201 REMARK 3 T TENSOR REMARK 3 T11: 0.4396 T22: 0.2946 REMARK 3 T33: 0.4550 T12: 0.0052 REMARK 3 T13: 0.0037 T23: -0.0277 REMARK 3 L TENSOR REMARK 3 L11: 3.7780 L22: 0.4451 REMARK 3 L33: 4.2527 L12: -0.2021 REMARK 3 L13: 0.5131 L23: -0.7056 REMARK 3 S TENSOR REMARK 3 S11: 0.0610 S12: -0.0533 S13: -0.2331 REMARK 3 S21: 0.0580 S22: 0.0122 S23: 0.0192 REMARK 3 S31: -0.2099 S32: 0.2026 S33: -0.0641 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 362 THROUGH 564 ) REMARK 3 ORIGIN FOR THE GROUP (A): 2.4753 17.0177 -27.9684 REMARK 3 T TENSOR REMARK 3 T11: 0.2894 T22: 0.3237 REMARK 3 T33: 0.3410 T12: -0.0102 REMARK 3 T13: -0.0287 T23: 0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.2723 L22: 0.4525 REMARK 3 L33: 0.6479 L12: -0.0061 REMARK 3 L13: -0.1549 L23: 0.2086 REMARK 3 S TENSOR REMARK 3 S11: 0.0231 S12: 0.0156 S13: 0.0828 REMARK 3 S21: -0.0398 S22: 0.0100 S23: 0.0007 REMARK 3 S31: -0.0514 S32: 0.0471 S33: -0.0380 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 565 THROUGH 631 ) REMARK 3 ORIGIN FOR THE GROUP (A): -14.0323 -7.5833 -20.9750 REMARK 3 T TENSOR REMARK 3 T11: 0.5156 T22: 0.3640 REMARK 3 T33: 0.3582 T12: 0.0314 REMARK 3 T13: -0.0158 T23: -0.0702 REMARK 3 L TENSOR REMARK 3 L11: 3.3335 L22: 2.2576 REMARK 3 L33: 3.5920 L12: 1.0892 REMARK 3 L13: -1.4076 L23: -1.4886 REMARK 3 S TENSOR REMARK 3 S11: 0.0091 S12: -0.3608 S13: -0.1821 REMARK 3 S21: 0.5110 S22: 0.1527 S23: 0.1992 REMARK 3 S31: 0.2435 S32: -0.3328 S33: -0.0562 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 632 THROUGH 780 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.6044 -17.2248 -44.9641 REMARK 3 T TENSOR REMARK 3 T11: 0.2620 T22: 0.2520 REMARK 3 T33: 0.3528 T12: -0.0070 REMARK 3 T13: 0.0171 T23: -0.0377 REMARK 3 L TENSOR REMARK 3 L11: 1.4005 L22: 1.6182 REMARK 3 L33: 3.9764 L12: 0.4267 REMARK 3 L13: 1.1284 L23: 1.0036 REMARK 3 S TENSOR REMARK 3 S11: 0.1058 S12: -0.0659 S13: 0.0052 REMARK 3 S21: 0.0848 S22: -0.0454 S23: 0.2048 REMARK 3 S31: 0.0931 S32: -0.1567 S33: -0.0558 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 781 THROUGH 875 ) REMARK 3 ORIGIN FOR THE GROUP (A): -31.1479 -9.1981 -60.8346 REMARK 3 T TENSOR REMARK 3 T11: 0.5465 T22: 0.5291 REMARK 3 T33: 0.4698 T12: 0.0433 REMARK 3 T13: -0.1511 T23: 0.0002 REMARK 3 L TENSOR REMARK 3 L11: 3.1532 L22: 0.9801 REMARK 3 L33: 1.6540 L12: -0.2892 REMARK 3 L13: 1.0924 L23: -0.3578 REMARK 3 S TENSOR REMARK 3 S11: -0.1327 S12: 0.6939 S13: 0.2735 REMARK 3 S21: -0.2300 S22: -0.0294 S23: 0.2524 REMARK 3 S31: -0.4248 S32: -0.0064 S33: 0.0328 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 7AP2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1292111726. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-20 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 : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979997 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 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45493 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.220 REMARK 200 RESOLUTION RANGE LOW (A) : 112.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.90 REMARK 200 R MERGE (I) : 0.16800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 13.10 REMARK 200 R MERGE FOR SHELL (I) : 1.38700 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 (%): 46.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 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 LEUS7HMDDA REMARK 280 IN AN 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 24.61850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 112.49150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.49350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 112.49150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.61850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.49350 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 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 PRO A 615 REMARK 465 VAL A 616 REMARK 465 GLU A 818 REMARK 465 VAL A 819 REMARK 465 MET A 820 REMARK 465 VAL A 821 REMARK 465 GLN A 822 REMARK 465 VAL A 823 REMARK 465 ASN A 824 REMARK 465 GLY A 825 REMARK 465 LYS A 826 REMARK 465 LEU A 827 REMARK 465 ASN A 849 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 VAL A 876 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 SER A 31 OG REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 LYS A 129 CE NZ REMARK 470 LYS A 142 CD CE NZ REMARK 470 GLU A 145 CD OE1 OE2 REMARK 470 GLU A 169 CG CD OE1 OE2 REMARK 470 ASP A 173 CG OD1 OD2 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 ASP A 303 CG OD1 OD2 REMARK 470 MET A 304 CG SD CE REMARK 470 GLU A 308 CG CD OE1 OE2 REMARK 470 VAL A 371 CG1 CG2 REMARK 470 ASP A 373 OD1 OD2 REMARK 470 ARG A 380 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 383 CG CD OE1 OE2 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 LYS A 481 CE NZ REMARK 470 LYS A 521 CD CE NZ REMARK 470 GLU A 530 CD OE1 OE2 REMARK 470 LYS A 533 CG 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 GLU A 606 CG CD OE1 OE2 REMARK 470 LEU A 607 CG CD1 CD2 REMARK 470 SER A 617 OG REMARK 470 VAL A 619 CG1 CG2 REMARK 470 LEU A 620 CD1 CD2 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 LYS A 703 CE NZ REMARK 470 LYS A 714 CD CE NZ REMARK 470 VAL A 813 CG1 CG2 REMARK 470 LYS A 814 CG CD CE NZ REMARK 470 ARG A 828 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 830 CG CD CE NZ REMARK 470 VAL A 833 CG1 CG2 REMARK 470 ASP A 836 CG OD1 OD2 REMARK 470 LYS A 839 CG CD CE NZ REMARK 470 GLU A 843 CG CD OE1 OE2 REMARK 470 LYS A 863 CG CD CE NZ 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 CD NE CZ NH1 NH2 REMARK 470 LEU A 871 CG CD1 CD2 REMARK 470 VAL A 872 CG1 CG2 REMARK 470 ILE A 874 CG1 CG2 CD1 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 TYR A 132 -63.04 -90.03 REMARK 500 SER A 179 -37.21 -131.66 REMARK 500 ASN A 390 71.63 -106.18 REMARK 500 GLN A 437 58.63 -90.33 REMARK 500 TRP A 512 -0.36 -140.79 REMARK 500 SER A 519 73.98 -156.87 REMARK 500 ILE A 549 -70.51 -108.03 REMARK 500 ALA A 622 -89.35 -99.36 REMARK 500 SER A 630 -159.46 -123.61 REMARK 500 TYR A 652 -13.11 -143.36 REMARK 500 ARG A 736 -65.33 -95.84 REMARK 500 PRO A 868 97.82 -58.59 REMARK 500 ARG A 870 -40.29 -152.44 REMARK 500 LEU A 871 -163.62 -162.23 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 A1204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 449 SG REMARK 620 2 CYS A 452 SG 108.1 REMARK 620 3 CYS A 490 SG 113.2 106.8 REMARK 620 4 CYS A 493 SG 109.2 112.2 107.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1205 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A1310 O REMARK 620 2 HOH A1383 O 76.7 REMARK 620 3 HOH A1488 O 80.6 58.7 REMARK 620 4 HOH A1507 O 134.1 70.1 55.3 REMARK 620 5 HOH A1513 O 127.8 130.3 81.3 62.8 REMARK 620 N 1 2 3 4 DBREF1 7AP2 A 1 876 UNP A0A5K1KQ39_NEIGO DBREF2 7AP2 A A0A5K1KQ39 3 878 SEQADV 7AP2 GLY A 0 UNP A0A5K1KQ3 EXPRESSION TAG SEQADV 7AP2 ASN A 454 UNP A0A5K1KQ3 ASP 456 ENGINEERED MUTATION SEQADV 7AP2 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 A1201 4 HET EDO A1202 4 HET RRW A1203 33 HET ZN A1204 1 HET MG A1205 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM RRW [(2~{R},3~{S},4~{R},5~{R})-5-[7-AZANYL-5- HETNAM 2 RRW (HYDROXYMETHYL)BENZIMIDAZOL-1-YL]-3,4-BIS(OXIDANYL) HETNAM 3 RRW OXOLAN-2-YL]METHYL ~{N}-[(2~{S})-2-AZANYL-4-METHYL- HETNAM 4 RRW PENTANOYL]SULFAMATE HETNAM ZN ZINC ION HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO 2(C2 H6 O2) FORMUL 4 RRW C19 H29 N5 O8 S FORMUL 5 ZN ZN 2+ FORMUL 6 MG MG 2+ FORMUL 7 HOH *213(H2 O) HELIX 1 AA1 GLN A 6 ALA A 21 1 16 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 GLY A 246 LYS A 250 1 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 ASP A 351 ASN A 362 1 12 HELIX 18 AB9 GLN A 382 ASP A 387 5 6 HELIX 19 AC1 SER A 396 ASP A 400 5 5 HELIX 20 AC2 ASP A 403 GLN A 418 1 16 HELIX 21 AC3 PRO A 458 LEU A 462 5 5 HELIX 22 AC4 SER A 477 LYS A 481 5 5 HELIX 23 AC5 MET A 482 TYR A 486 1 5 HELIX 24 AC6 ILE A 508 SER A 511 5 4 HELIX 25 AC7 TRP A 512 TYR A 517 1 6 HELIX 26 AC8 SER A 528 GLY A 536 1 9 HELIX 27 AC9 GLU A 546 ALA A 548 5 3 HELIX 28 AD1 ILE A 549 GLU A 565 1 17 HELIX 29 AD2 ASN A 601 ALA A 603 5 3 HELIX 30 AD3 ASP A 644 GLY A 653 1 10 HELIX 31 AD4 GLY A 653 ALA A 665 1 13 HELIX 32 AD5 SER A 674 GLY A 700 1 27 HELIX 33 AD6 SER A 713 ARG A 736 1 24 HELIX 34 AD7 GLN A 739 LYS A 756 1 18 HELIX 35 AD8 SER A 761 TRP A 780 1 20 HELIX 36 AD9 VAL A 783 ASN A 795 1 13 HELIX 37 AE1 LYS A 798 GLY A 803 1 6 HELIX 38 AE2 ASP A 808 VAL A 813 5 6 HELIX 39 AE3 SER A 838 LEU A 847 1 10 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 GLU A 184 N TRP A 158 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 CYS A 449 O GLY A 453 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 3 LYS A 597 ILE A 600 0 SHEET 2 AB1 3 VAL A 583 GLU A 591 -1 N ARG A 590 O ASP A 598 SHEET 3 AB1 3 VAL A 628 LYS A 634 -1 O VAL A 628 N TYR A 589 SHEET 1 AB2 3 LYS A 597 ILE A 600 0 SHEET 2 AB2 3 VAL A 583 GLU A 591 -1 N ARG A 590 O ASP A 598 SHEET 3 AB2 3 LEU A 671 GLU A 672 1 O LEU A 671 N VAL A 584 SHEET 1 AB3 2 VAL A 605 GLU A 606 0 SHEET 2 AB3 2 VAL A 619 LEU A 620 -1 O VAL A 619 N GLU A 606 SHEET 1 AB4 2 ILE A 865 VAL A 867 0 SHEET 2 AB4 2 LEU A 871 ASN A 873 -1 O LEU A 871 N VAL A 867 LINK SG CYS A 449 ZN ZN A1204 1555 1555 2.34 LINK SG CYS A 452 ZN ZN A1204 1555 1555 2.21 LINK SG CYS A 490 ZN ZN A1204 1555 1555 2.33 LINK SG CYS A 493 ZN ZN A1204 1555 1555 2.44 LINK MG MG A1205 O HOH A1310 1555 1555 2.13 LINK MG MG A1205 O HOH A1383 1555 1555 2.46 LINK MG MG A1205 O HOH A1488 1555 1555 2.61 LINK MG MG A1205 O HOH A1507 1555 3454 2.47 LINK MG MG A1205 O HOH A1513 1555 3454 1.89 CISPEP 1 LEU A 462 PRO A 463 0 2.13 CRYST1 49.237 80.987 224.983 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 0.020310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012348 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004445 0.00000