HEADER HYDROLASE 27-JUN-18 6GXQ TITLE CRYSTAL STRUCTURE OF T. BRUCEI PDE-B1 CATALYTIC DOMAIN WITH INHIBITOR TITLE 2 NPD-1335 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHODIESTERASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.4.-; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES 565-918 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI; SOURCE 3 ORGANISM_TAXID: 5691; SOURCE 4 GENE: PDEB1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: CODON PLUS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PARASITIC PHOSPHODIESTERASE, HYDROLASE, AFRICAN TRYPANOSOMIASIS, KEYWDS 2 SLEEPING SICKNESS EXPDTA X-RAY DIFFRACTION AUTHOR A.K.SINGH,D.G.BROWN REVDAT 5 17-JAN-24 6GXQ 1 LINK REVDAT 4 04-SEP-19 6GXQ 1 JRNL REVDAT 3 14-AUG-19 6GXQ 1 JRNL REVDAT 2 24-JUL-19 6GXQ 1 JRNL REVDAT 1 10-JUL-19 6GXQ 0 JRNL AUTH E.DE HEUVEL,A.K.SINGH,P.BORONAT,A.J.KOOISTRA,T.VAN DER MEER, JRNL AUTH 2 P.SADEK,A.R.BLAAZER,N.C.SHANER,D.S.BINDELS,G.CALJON,L.MAES, JRNL AUTH 3 G.J.STERK,M.SIDERIUS,M.OBERHOLZER,I.J.P.DE ESCH,D.G.BROWN, JRNL AUTH 4 R.LEURS JRNL TITL ALKYNAMIDE PHTHALAZINONES AS A NEW CLASS OF TBRPDEB1 JRNL TITL 2 INHIBITORS (PART 2). JRNL REF BIOORG.MED.CHEM. V. 27 4013 2019 JRNL REFN ESSN 1464-3391 JRNL PMID 31378593 JRNL DOI 10.1016/J.BMC.2019.06.026 REMARK 2 REMARK 2 RESOLUTION. 1.96 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0222 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.28 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 55439 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2895 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3834 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.3950 REMARK 3 BIN FREE R VALUE SET COUNT : 188 REMARK 3 BIN FREE R VALUE : 0.4070 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5260 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 433 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.41000 REMARK 3 B22 (A**2) : -2.12000 REMARK 3 B33 (A**2) : -1.60000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.51000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.158 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.177 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.204 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5429 ; 0.008 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 4907 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7337 ; 1.247 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11443 ; 0.962 ; 1.642 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 663 ; 5.858 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 295 ;32.907 ;22.339 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 933 ;15.050 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;13.904 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 704 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6133 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1072 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2658 ; 2.795 ; 3.903 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2657 ; 2.791 ; 3.901 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3319 ; 4.135 ; 5.845 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3320 ; 4.135 ; 5.847 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2771 ; 3.333 ; 4.257 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2771 ; 3.333 ; 4.257 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4019 ; 5.134 ; 6.230 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6623 ; 6.768 ;47.623 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6623 ; 6.767 ;47.621 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 586 916 B 586 916 11266 0.08 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6GXQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010703. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91587 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59811 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 64.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.70400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 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: 4I15 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.4 M SODIUM FORMATE, REMARK 280 0.3 M GUANIDINE, 0.1 M MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 57.43800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 57.21200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.43800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 57.21200 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1181 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1344 LIES ON A SPECIAL POSITION. 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 559 REMARK 465 SER A 560 REMARK 465 HIS A 561 REMARK 465 MET A 562 REMARK 465 ALA A 563 REMARK 465 SER A 564 REMARK 465 GLU A 565 REMARK 465 LEU A 566 REMARK 465 ASN A 567 REMARK 465 GLU A 568 REMARK 465 HIS A 569 REMARK 465 ARG A 570 REMARK 465 ALA A 571 REMARK 465 THR A 572 REMARK 465 LEU A 573 REMARK 465 PHE A 574 REMARK 465 ASN A 575 REMARK 465 LYS A 576 REMARK 465 ASN A 577 REMARK 465 VAL A 578 REMARK 465 PRO A 579 REMARK 465 SER A 580 REMARK 465 ARG A 581 REMARK 465 ALA A 582 REMARK 465 VAL A 583 REMARK 465 LYS A 584 REMARK 465 ARG A 585 REMARK 465 GLY B 559 REMARK 465 SER B 560 REMARK 465 HIS B 561 REMARK 465 MET B 562 REMARK 465 ALA B 563 REMARK 465 SER B 564 REMARK 465 GLU B 565 REMARK 465 LEU B 566 REMARK 465 ASN B 567 REMARK 465 GLU B 568 REMARK 465 HIS B 569 REMARK 465 ARG B 570 REMARK 465 ALA B 571 REMARK 465 THR B 572 REMARK 465 LEU B 573 REMARK 465 PHE B 574 REMARK 465 ASN B 575 REMARK 465 LYS B 576 REMARK 465 ASN B 577 REMARK 465 VAL B 578 REMARK 465 PRO B 579 REMARK 465 SER B 580 REMARK 465 ARG B 581 REMARK 465 ALA B 582 REMARK 465 VAL B 583 REMARK 465 LYS B 584 REMARK 465 ARG B 585 REMARK 465 ARG B 918 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 B 1199 O HOH B 1237 1.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OG SER B 790 OE1 GLU B 793 2858 1.94 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 SER A 604 -2.72 90.89 REMARK 500 ASN A 670 -168.68 -118.78 REMARK 500 CYS A 893 -35.30 -171.14 REMARK 500 LEU A 894 61.57 -101.85 REMARK 500 TYR B 668 -59.35 -120.20 REMARK 500 ASN B 670 -168.98 -121.29 REMARK 500 ASP B 801 64.80 -108.84 REMARK 500 VAL B 881 -62.24 -121.37 REMARK 500 CYS B 893 -44.23 -178.16 REMARK 500 LEU B 894 58.47 -104.39 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 811 0.13 SIDE CHAIN REMARK 500 ARG A 834 0.13 SIDE CHAIN 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 A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 673 NE2 REMARK 620 2 HIS A 709 NE2 99.5 REMARK 620 3 ASP A 710 OD2 86.9 85.0 REMARK 620 4 ASP A 822 OD1 92.4 90.2 174.9 REMARK 620 5 HOH A1127 O 162.3 97.9 90.8 91.4 REMARK 620 6 HOH A1175 O 89.9 170.3 98.1 86.9 73.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 710 OD1 REMARK 620 2 HOH A1127 O 90.3 REMARK 620 3 HOH A1134 O 88.9 95.9 REMARK 620 4 HOH A1203 O 97.0 167.1 94.8 REMARK 620 5 HOH A1227 O 164.3 87.3 76.0 88.4 REMARK 620 6 HOH A1259 O 99.8 82.2 171.1 86.1 95.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1003 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 673 NE2 REMARK 620 2 HIS B 709 NE2 100.3 REMARK 620 3 ASP B 710 OD2 87.5 84.6 REMARK 620 4 ASP B 822 OD1 92.4 91.2 175.8 REMARK 620 5 HOH B1185 O 159.3 99.6 89.0 92.4 REMARK 620 6 HOH B1199 O 91.7 167.0 91.2 93.0 68.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B1002 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 710 OD1 REMARK 620 2 HOH B1112 O 95.5 REMARK 620 3 HOH B1154 O 168.2 73.0 REMARK 620 4 HOH B1170 O 96.8 88.1 80.2 REMARK 620 5 HOH B1185 O 94.1 99.1 90.7 166.2 REMARK 620 6 HOH B1242 O 103.0 161.5 88.4 89.1 80.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GAI A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GAI A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FFZ A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GAI A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GAI B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 1006 DBREF 6GXQ A 565 918 UNP Q8WQX9 Q8WQX9_9TRYP 565 918 DBREF 6GXQ B 565 918 UNP Q8WQX9 Q8WQX9_9TRYP 565 918 SEQADV 6GXQ GLY A 559 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ SER A 560 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ HIS A 561 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ MET A 562 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ ALA A 563 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ SER A 564 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ GLY B 559 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ SER B 560 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ HIS B 561 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ MET B 562 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ ALA B 563 UNP Q8WQX9 EXPRESSION TAG SEQADV 6GXQ SER B 564 UNP Q8WQX9 EXPRESSION TAG SEQRES 1 A 360 GLY SER HIS MET ALA SER GLU LEU ASN GLU HIS ARG ALA SEQRES 2 A 360 THR LEU PHE ASN LYS ASN VAL PRO SER ARG ALA VAL LYS SEQRES 3 A 360 ARG VAL THR ALA ILE THR LYS VAL GLU ARG GLU ALA VAL SEQRES 4 A 360 LEU VAL CYS GLU LEU PRO SER PHE ASP VAL THR ASP VAL SEQRES 5 A 360 GLU PHE ASP LEU PHE ARG ALA ARG GLU SER THR ASP LYS SEQRES 6 A 360 PRO LEU ASP VAL ALA ALA ALA ILE ALA TYR ARG LEU LEU SEQRES 7 A 360 LEU GLY SER GLY LEU PRO GLN LYS PHE GLY CYS SER ASP SEQRES 8 A 360 GLU VAL LEU LEU ASN PHE ILE LEU GLN CYS ARG LYS LYS SEQRES 9 A 360 TYR ARG ASN VAL PRO TYR HIS ASN PHE TYR HIS VAL VAL SEQRES 10 A 360 ASP VAL CYS GLN THR ILE HIS THR PHE LEU TYR ARG GLY SEQRES 11 A 360 ASN VAL TYR GLU LYS LEU THR GLU LEU GLU CYS PHE VAL SEQRES 12 A 360 LEU LEU ILE THR ALA LEU VAL HIS ASP LEU ASP HIS MET SEQRES 13 A 360 GLY LEU ASN ASN SER PHE TYR LEU LYS THR GLU SER PRO SEQRES 14 A 360 LEU GLY ILE LEU SER SER ALA SER GLY ASN THR SER VAL SEQRES 15 A 360 LEU GLU VAL HIS HIS CYS ASN LEU ALA VAL GLU ILE LEU SEQRES 16 A 360 SER ASP PRO GLU SER ASP VAL PHE ASP GLY LEU GLU GLY SEQRES 17 A 360 ALA GLU ARG THR LEU ALA PHE ARG SER MET ILE ASP CYS SEQRES 18 A 360 VAL LEU ALA THR ASP MET ALA LYS HIS GLY SER ALA LEU SEQRES 19 A 360 GLU ALA PHE LEU ALA SER ALA ALA ASP GLN SER SER ASP SEQRES 20 A 360 GLU ALA ALA PHE HIS ARG MET THR MET GLU ILE ILE LEU SEQRES 21 A 360 LYS ALA GLY ASP ILE SER ASN VAL THR LYS PRO PHE ASP SEQRES 22 A 360 ILE SER ARG GLN TRP ALA MET ALA VAL THR GLU GLU PHE SEQRES 23 A 360 TYR ARG GLN GLY ASP MET GLU LYS GLU ARG GLY VAL GLU SEQRES 24 A 360 VAL LEU PRO MET PHE ASP ARG SER LYS ASN MET GLU LEU SEQRES 25 A 360 ALA LYS GLY GLN ILE GLY PHE ILE ASP PHE VAL ALA ALA SEQRES 26 A 360 PRO PHE PHE GLN LYS ILE VAL ASP ALA CYS LEU GLN GLY SEQRES 27 A 360 MET GLN TRP THR VAL ASP ARG ILE LYS SER ASN ARG ALA SEQRES 28 A 360 GLN TRP GLU ARG VAL LEU GLU THR ARG SEQRES 1 B 360 GLY SER HIS MET ALA SER GLU LEU ASN GLU HIS ARG ALA SEQRES 2 B 360 THR LEU PHE ASN LYS ASN VAL PRO SER ARG ALA VAL LYS SEQRES 3 B 360 ARG VAL THR ALA ILE THR LYS VAL GLU ARG GLU ALA VAL SEQRES 4 B 360 LEU VAL CYS GLU LEU PRO SER PHE ASP VAL THR ASP VAL SEQRES 5 B 360 GLU PHE ASP LEU PHE ARG ALA ARG GLU SER THR ASP LYS SEQRES 6 B 360 PRO LEU ASP VAL ALA ALA ALA ILE ALA TYR ARG LEU LEU SEQRES 7 B 360 LEU GLY SER GLY LEU PRO GLN LYS PHE GLY CYS SER ASP SEQRES 8 B 360 GLU VAL LEU LEU ASN PHE ILE LEU GLN CYS ARG LYS LYS SEQRES 9 B 360 TYR ARG ASN VAL PRO TYR HIS ASN PHE TYR HIS VAL VAL SEQRES 10 B 360 ASP VAL CYS GLN THR ILE HIS THR PHE LEU TYR ARG GLY SEQRES 11 B 360 ASN VAL TYR GLU LYS LEU THR GLU LEU GLU CYS PHE VAL SEQRES 12 B 360 LEU LEU ILE THR ALA LEU VAL HIS ASP LEU ASP HIS MET SEQRES 13 B 360 GLY LEU ASN ASN SER PHE TYR LEU LYS THR GLU SER PRO SEQRES 14 B 360 LEU GLY ILE LEU SER SER ALA SER GLY ASN THR SER VAL SEQRES 15 B 360 LEU GLU VAL HIS HIS CYS ASN LEU ALA VAL GLU ILE LEU SEQRES 16 B 360 SER ASP PRO GLU SER ASP VAL PHE ASP GLY LEU GLU GLY SEQRES 17 B 360 ALA GLU ARG THR LEU ALA PHE ARG SER MET ILE ASP CYS SEQRES 18 B 360 VAL LEU ALA THR ASP MET ALA LYS HIS GLY SER ALA LEU SEQRES 19 B 360 GLU ALA PHE LEU ALA SER ALA ALA ASP GLN SER SER ASP SEQRES 20 B 360 GLU ALA ALA PHE HIS ARG MET THR MET GLU ILE ILE LEU SEQRES 21 B 360 LYS ALA GLY ASP ILE SER ASN VAL THR LYS PRO PHE ASP SEQRES 22 B 360 ILE SER ARG GLN TRP ALA MET ALA VAL THR GLU GLU PHE SEQRES 23 B 360 TYR ARG GLN GLY ASP MET GLU LYS GLU ARG GLY VAL GLU SEQRES 24 B 360 VAL LEU PRO MET PHE ASP ARG SER LYS ASN MET GLU LEU SEQRES 25 B 360 ALA LYS GLY GLN ILE GLY PHE ILE ASP PHE VAL ALA ALA SEQRES 26 B 360 PRO PHE PHE GLN LYS ILE VAL ASP ALA CYS LEU GLN GLY SEQRES 27 B 360 MET GLN TRP THR VAL ASP ARG ILE LYS SER ASN ARG ALA SEQRES 28 B 360 GLN TRP GLU ARG VAL LEU GLU THR ARG HET MG A1001 1 HET ZN A1002 1 HET GAI A1003 4 HET GAI A1004 4 HET FFZ A1005 34 HET GAI A1006 4 HET GOL A1007 6 HET GAI B1001 4 HET MG B1002 1 HET ZN B1003 1 HET GOL B1004 6 HET GAI B1005 4 HET GOL B1006 6 HETNAM MG MAGNESIUM ION HETNAM ZN ZINC ION HETNAM GAI GUANIDINE HETNAM FFZ 3-[5-[(4AR,8AS)-4-OXIDANYLIDENE-3-PROPAN-2-YL-4A,5,8, HETNAM 2 FFZ 8A-TETRAHYDROPHTHALAZIN-1-YL]-2-METHOXY-PHENYL]-N- HETNAM 3 FFZ (PHENYLMETHYL)PROP-2-YNAMIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 2(MG 2+) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 GAI 5(C H5 N3) FORMUL 7 FFZ C28 H29 N3 O3 FORMUL 9 GOL 3(C3 H8 O3) FORMUL 16 HOH *433(H2 O) HELIX 1 AA1 THR A 590 VAL A 599 1 10 HELIX 2 AA2 ASP A 613 SER A 620 1 8 HELIX 3 AA3 LYS A 623 GLY A 640 1 18 HELIX 4 AA4 GLY A 640 PHE A 645 1 6 HELIX 5 AA5 SER A 648 LYS A 662 1 15 HELIX 6 AA6 ASN A 670 ARG A 687 1 18 HELIX 7 AA7 ASN A 689 LEU A 694 5 6 HELIX 8 AA8 THR A 695 HIS A 709 1 15 HELIX 9 AA9 ASN A 717 THR A 724 1 8 HELIX 10 AB1 SER A 726 GLY A 736 1 11 HELIX 11 AB2 SER A 739 SER A 754 1 16 HELIX 12 AB3 ASP A 755 ASP A 759 5 5 HELIX 13 AB4 GLU A 765 THR A 783 1 19 HELIX 14 AB5 ASP A 784 ALA A 786 5 3 HELIX 15 AB6 LYS A 787 ASP A 801 1 15 HELIX 16 AB7 ASP A 805 ILE A 823 1 19 HELIX 17 AB8 SER A 824 LYS A 828 5 5 HELIX 18 AB9 PRO A 829 GLY A 855 1 27 HELIX 19 AC1 LEU A 859 ASN A 867 5 9 HELIX 20 AC2 GLU A 869 VAL A 881 1 13 HELIX 21 AC3 VAL A 881 CYS A 893 1 13 HELIX 22 AC4 LEU A 894 GLY A 896 5 3 HELIX 23 AC5 MET A 897 THR A 917 1 21 HELIX 24 AC6 THR B 590 VAL B 599 1 10 HELIX 25 AC7 ASP B 613 SER B 620 1 8 HELIX 26 AC8 LYS B 623 GLY B 640 1 18 HELIX 27 AC9 GLY B 640 PHE B 645 1 6 HELIX 28 AD1 SER B 648 LYS B 662 1 15 HELIX 29 AD2 ASN B 670 ARG B 687 1 18 HELIX 30 AD3 ASN B 689 LEU B 694 5 6 HELIX 31 AD4 THR B 695 HIS B 709 1 15 HELIX 32 AD5 ASN B 717 THR B 724 1 8 HELIX 33 AD6 SER B 726 GLY B 736 1 11 HELIX 34 AD7 SER B 739 SER B 754 1 16 HELIX 35 AD8 ASP B 755 ASP B 759 5 5 HELIX 36 AD9 GLU B 765 THR B 783 1 19 HELIX 37 AE1 ASP B 784 ALA B 786 5 3 HELIX 38 AE2 LYS B 787 ASP B 801 1 15 HELIX 39 AE3 ASP B 805 ILE B 823 1 19 HELIX 40 AE4 SER B 824 LYS B 828 5 5 HELIX 41 AE5 PRO B 829 GLY B 855 1 27 HELIX 42 AE6 LEU B 859 ASN B 867 5 9 HELIX 43 AE7 GLU B 869 VAL B 881 1 13 HELIX 44 AE8 VAL B 881 CYS B 893 1 13 HELIX 45 AE9 LEU B 894 GLY B 896 5 3 HELIX 46 AF1 MET B 897 THR B 917 1 21 LINK NE2 HIS A 673 ZN ZN A1002 1555 1555 2.12 LINK NE2 HIS A 709 ZN ZN A1002 1555 1555 2.25 LINK OD1 ASP A 710 MG MG A1001 1555 1555 2.00 LINK OD2 ASP A 710 ZN ZN A1002 1555 1555 2.21 LINK OD1 ASP A 822 ZN ZN A1002 1555 1555 2.16 LINK MG MG A1001 O HOH A1127 1555 1555 2.08 LINK MG MG A1001 O HOH A1134 1555 1555 2.05 LINK MG MG A1001 O HOH A1203 1555 1555 2.05 LINK MG MG A1001 O HOH A1227 1555 1555 2.12 LINK MG MG A1001 O HOH A1259 1555 1555 2.03 LINK ZN ZN A1002 O HOH A1127 1555 1555 2.13 LINK ZN ZN A1002 O HOH A1175 1555 1555 2.37 LINK NE2 HIS B 673 ZN ZN B1003 1555 1555 2.11 LINK NE2 HIS B 709 ZN ZN B1003 1555 1555 2.24 LINK OD1 ASP B 710 MG MG B1002 1555 1555 1.96 LINK OD2 ASP B 710 ZN ZN B1003 1555 1555 2.18 LINK OD1 ASP B 822 ZN ZN B1003 1555 1555 2.18 LINK MG MG B1002 O HOH B1112 1555 1555 2.10 LINK MG MG B1002 O HOH B1154 1555 1555 2.16 LINK MG MG B1002 O HOH B1170 1555 1555 2.00 LINK MG MG B1002 O HOH B1185 1555 1555 1.99 LINK MG MG B1002 O HOH B1242 1555 1555 1.99 LINK ZN ZN B1003 O HOH B1185 1555 1555 2.23 LINK ZN ZN B1003 O HOH B1199 1555 1555 1.82 SITE 1 AC1 6 ASP A 710 HOH A1127 HOH A1134 HOH A1203 SITE 2 AC1 6 HOH A1227 HOH A1259 SITE 1 AC2 6 HIS A 673 HIS A 709 ASP A 710 ASP A 822 SITE 2 AC2 6 HOH A1127 HOH A1175 SITE 1 AC3 2 LYS A 644 GLU A 768 SITE 1 AC4 8 LEU A 753 SER A 754 ASP A 759 ASP A 762 SITE 2 AC4 8 ARG A 769 LEU A 915 HOH A1111 HOH A1139 SITE 1 AC5 8 MET A 785 ASP A 822 ASN A 825 GLY A 873 SITE 2 AC5 8 GLN A 874 PHE A 877 HOH A1170 HOH A1198 SITE 1 AC6 1 GLU A 692 SITE 1 AC7 7 ASP A 613 PRO A 829 PHE A 830 ASP A 831 SITE 2 AC7 7 ILE A 832 ASP B 849 ARG B 864 SITE 1 AC8 2 TYR B 686 TYR B 691 SITE 1 AC9 6 ASP B 710 HOH B1112 HOH B1154 HOH B1170 SITE 2 AC9 6 HOH B1185 HOH B1242 SITE 1 AD1 6 HIS B 673 HIS B 709 ASP B 710 ASP B 822 SITE 2 AD1 6 HOH B1185 HOH B1199 SITE 1 AD2 5 GLY B 688 ASN B 689 LYS B 693 LEU B 894 SITE 2 AD2 5 GLY B 896 SITE 1 AD3 4 TYR B 691 LEU B 694 THR B 695 HOH B1122 CRYST1 114.876 114.424 68.232 90.00 108.36 90.00 C 1 2 1 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 0.008705 0.000000 0.002889 0.00000 SCALE2 0.000000 0.008739 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015442 0.00000