HEADER HYDROLASE 21-NOV-19 6THV TITLE X-RAY STRUCTURE OF THE DANIO RERIO HISTONE DEACETYLASE 6 (HDAC6; TITLE 2 CATALYTIC DOMAIN 2) IN COMPLEX WITH TUBASTATIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 6; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: HDAC6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS HISTONE DEACETYLASE 6, TUBASTATIN A, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.BARINKA,L.MOTLOVA,M.SVOBODA REVDAT 3 24-JAN-24 6THV 1 REMARK REVDAT 2 27-JAN-21 6THV 1 JRNL LINK REVDAT 1 15-JUL-20 6THV 0 JRNL AUTH S.SHEN,M.SVOBODA,G.ZHANG,M.A.CAVASIN,L.MOTLOVA,T.A.MCKINSEY, JRNL AUTH 2 J.H.EUBANKS,C.BARINKA,A.P.KOZIKOWSKI JRNL TITL STRUCTURAL AND IN VIVO CHARACTERIZATION OF TUBASTATIN A, A JRNL TITL 2 WIDELY USED HISTONE DEACETYLASE 6 INHIBITOR. JRNL REF ACS MED.CHEM.LETT. V. 11 706 2020 JRNL REFN ISSN 1948-5875 JRNL PMID 32435374 JRNL DOI 10.1021/ACSMEDCHEMLETT.9B00560 REMARK 2 REMARK 2 RESOLUTION. 1.10 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) : 1.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 164453 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.300 REMARK 3 FREE R VALUE TEST SET COUNT : 2101 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.13 REMARK 3 REFLECTION IN BIN (WORKING SET) : 11680 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 149 REMARK 3 BIN FREE R VALUE : 0.3010 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 369 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : 0.94000 REMARK 3 B33 (A**2) : -0.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.027 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.027 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3130 ; 0.013 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 2714 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4253 ; 1.627 ; 1.767 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6392 ; 3.633 ; 1.753 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 402 ; 6.027 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;30.574 ;19.392 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 465 ;11.961 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;16.381 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 395 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3642 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 595 ; 0.009 ; 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): 1543 ; 1.129 ; 1.005 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1540 ; 1.001 ; 0.996 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1958 ; 1.466 ; 1.502 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 NUMBER OF DIFFERENT NCS GROUPS : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6THV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105472. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X13 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9796 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 166560 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.100 REMARK 200 RESOLUTION RANGE LOW (A) : 46.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.4500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.16 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.84400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.940 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 5EEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KSCN, 20 % PEG 3350, 0.1 M BIS REMARK 280 -TRIS, PH5.8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 42.13900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.85650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.13900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.85650 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 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 S SCN A 808 LIES ON A SPECIAL POSITION. REMARK 375 C SCN A 808 LIES ON A SPECIAL POSITION. REMARK 375 N SCN A 808 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 SER A 440 REMARK 465 SER A 441 REMARK 465 ASP A 770 REMARK 465 HIS A 771 REMARK 465 LEU A 772 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 672 CB 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 O HOH A 1180 O HOH A 1181 0.23 REMARK 500 O HIS A 684 O2 EDO A 804 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 672 CA LYS A 672 CB 0.191 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 469 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 460 88.09 -151.74 REMARK 500 PHE A 583 -1.59 79.69 REMARK 500 THR A 600 -90.23 -131.71 REMARK 500 TYR A 637 -53.21 -125.28 REMARK 500 LEU A 685 -63.48 -123.62 REMARK 500 GLU A 742 -114.93 -112.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1269 DISTANCE = 5.90 ANGSTROMS 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 K A 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 71.0 REMARK 620 3 ASP A 612 O 99.3 97.1 REMARK 620 4 HIS A 614 O 165.6 94.7 79.8 REMARK 620 5 SER A 633 OG 84.9 110.5 151.9 102.7 REMARK 620 6 LEU A 634 O 77.8 143.2 68.8 114.7 85.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 801 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 HIS A 614 ND1 101.1 REMARK 620 3 ASP A 705 OD2 103.6 96.6 REMARK 620 4 N9W A 813 N1 169.2 81.7 86.3 REMARK 620 5 N9W A 813 O1 143.7 114.9 76.9 33.9 REMARK 620 6 HOH A 903 O 88.9 102.6 154.7 80.3 80.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 77.8 REMARK 620 3 ASP A 626 O 77.1 9.0 REMARK 620 4 VAL A 629 O 119.0 74.4 82.3 REMARK 620 5 TYR A 662 O 155.7 116.0 113.2 84.9 REMARK 620 6 HOH A 985 O 81.7 89.5 80.5 149.0 78.6 REMARK 620 7 HOH A1030 O 69.9 147.4 144.4 125.4 93.2 81.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 810 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 972 O REMARK 620 2 HOH A1183 O 87.6 REMARK 620 3 HOH A1220 O 116.1 116.0 REMARK 620 4 HOH A1230 O 150.8 70.2 91.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 811 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 924 O REMARK 620 2 HOH A 948 O 99.4 REMARK 620 3 HOH A 984 O 100.4 105.3 REMARK 620 4 HOH A1245 O 108.4 129.6 109.7 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 ZN A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SCN A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 812 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N9W A 813 DBREF 6THV A 440 798 UNP F8W4B7 F8W4B7_DANRE 440 798 SEQRES 1 A 359 SER SER PRO ILE THR GLY LEU VAL TYR ASP GLN ARG MET SEQRES 2 A 359 MET LEU HIS HIS ASN MET TRP ASP SER HIS HIS PRO GLU SEQRES 3 A 359 LEU PRO GLN ARG ILE SER ARG ILE PHE SER ARG HIS GLU SEQRES 4 A 359 GLU LEU ARG LEU LEU SER ARG CYS HIS ARG ILE PRO ALA SEQRES 5 A 359 ARG LEU ALA THR GLU GLU GLU LEU ALA LEU CYS HIS SER SEQRES 6 A 359 SER LYS HIS ILE SER ILE ILE LYS SER SER GLU HIS MET SEQRES 7 A 359 LYS PRO ARG ASP LEU ASN ARG LEU GLY ASP GLU TYR ASN SEQRES 8 A 359 SER ILE PHE ILE SER ASN GLU SER TYR THR CYS ALA LEU SEQRES 9 A 359 LEU ALA ALA GLY SER CYS PHE ASN SER ALA GLN ALA ILE SEQRES 10 A 359 LEU THR GLY GLN VAL ARG ASN ALA VAL ALA ILE VAL ARG SEQRES 11 A 359 PRO PRO GLY HIS HIS ALA GLU LYS ASP THR ALA CYS GLY SEQRES 12 A 359 PHE CYS PHE PHE ASN THR ALA ALA LEU THR ALA ARG TYR SEQRES 13 A 359 ALA GLN SER ILE THR ARG GLU SER LEU ARG VAL LEU ILE SEQRES 14 A 359 VAL ASP TRP ASP VAL HIS HIS GLY ASN GLY THR GLN HIS SEQRES 15 A 359 ILE PHE GLU GLU ASP ASP SER VAL LEU TYR ILE SER LEU SEQRES 16 A 359 HIS ARG TYR GLU ASP GLY ALA PHE PHE PRO ASN SER GLU SEQRES 17 A 359 ASP ALA ASN TYR ASP LYS VAL GLY LEU GLY LYS GLY ARG SEQRES 18 A 359 GLY TYR ASN VAL ASN ILE PRO TRP ASN GLY GLY LYS MET SEQRES 19 A 359 GLY ASP PRO GLU TYR MET ALA ALA PHE HIS HIS LEU VAL SEQRES 20 A 359 MET PRO ILE ALA ARG GLU PHE ALA PRO GLU LEU VAL LEU SEQRES 21 A 359 VAL SER ALA GLY PHE ASP ALA ALA ARG GLY ASP PRO LEU SEQRES 22 A 359 GLY GLY PHE GLN VAL THR PRO GLU GLY TYR ALA HIS LEU SEQRES 23 A 359 THR HIS GLN LEU MET SER LEU ALA ALA GLY ARG VAL LEU SEQRES 24 A 359 ILE ILE LEU GLU GLY GLY TYR ASN LEU THR SER ILE SER SEQRES 25 A 359 GLU SER MET SER MET CYS THR SER MET LEU LEU GLY ASP SEQRES 26 A 359 SER PRO PRO SER LEU ASP HIS LEU THR PRO LEU LYS THR SEQRES 27 A 359 SER ALA THR VAL SER ILE ASN ASN VAL LEU ARG ALA HIS SEQRES 28 A 359 ALA PRO PHE TRP SER SER LEU ARG HET ZN A 801 1 HET K A 802 1 HET K A 803 1 HET EDO A 804 8 HET EDO A 805 4 HET PEG A 806 7 HET PEG A 807 7 HET SCN A 808 6 HET SCN A 809 6 HET NA A 810 1 HET K A 811 1 HET GOL A 812 6 HET N9W A 813 25 HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM SCN THIOCYANATE ION HETNAM NA SODIUM ION HETNAM GOL GLYCEROL HETNAM N9W 4-[(2-METHYL-3,4-DIHYDRO-1~{H}-PYRIDO[4,3-B]INDOL-5- HETNAM 2 N9W YL)METHYL]-~{N}-OXIDANYL-BENZAMIDE HETSYN EDO ETHYLENE GLYCOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 K 3(K 1+) FORMUL 5 EDO 2(C2 H6 O2) FORMUL 7 PEG 2(C4 H10 O3) FORMUL 9 SCN 2(C N S 1-) FORMUL 11 NA NA 1+ FORMUL 13 GOL C3 H8 O3 FORMUL 14 N9W C20 H21 N3 O2 FORMUL 15 HOH *369(H2 O) HELIX 1 AA1 ASP A 449 HIS A 455 5 7 HELIX 2 AA2 PRO A 467 LEU A 480 1 14 HELIX 3 AA3 LEU A 482 CYS A 486 5 5 HELIX 4 AA4 THR A 495 ALA A 500 1 6 HELIX 5 AA5 SER A 504 SER A 514 1 11 HELIX 6 AA6 GLU A 515 MET A 517 5 3 HELIX 7 AA7 LYS A 518 ASP A 527 1 10 HELIX 8 AA8 GLU A 537 THR A 558 1 22 HELIX 9 AA9 ASN A 587 ILE A 599 1 13 HELIX 10 AB1 GLY A 616 PHE A 623 1 8 HELIX 11 AB2 GLU A 638 ALA A 641 5 4 HELIX 12 AB3 SER A 646 ASN A 650 5 5 HELIX 13 AB4 LEU A 656 ARG A 660 5 5 HELIX 14 AB5 GLY A 674 LEU A 685 1 12 HELIX 15 AB6 LEU A 685 ALA A 694 1 10 HELIX 16 AB7 THR A 718 MET A 730 1 13 HELIX 17 AB8 SER A 731 GLY A 735 5 5 HELIX 18 AB9 ASN A 746 LEU A 762 1 17 HELIX 19 AC1 LYS A 776 ALA A 791 1 16 HELIX 20 AC2 TRP A 794 ARG A 798 5 5 SHEET 1 AA1 8 HIS A 487 ARG A 488 0 SHEET 2 AA1 8 THR A 444 VAL A 447 1 N THR A 444 O HIS A 487 SHEET 3 AA1 8 ASN A 563 ALA A 566 1 O ASN A 563 N GLY A 445 SHEET 4 AA1 8 VAL A 737 LEU A 741 1 O ILE A 739 N ALA A 566 SHEET 5 AA1 8 LEU A 697 ALA A 702 1 N VAL A 700 O LEU A 738 SHEET 6 AA1 8 VAL A 606 ASP A 610 1 N LEU A 607 O LEU A 699 SHEET 7 AA1 8 VAL A 629 ARG A 636 1 O ILE A 632 N ASP A 610 SHEET 8 AA1 8 ASN A 663 TRP A 668 1 O VAL A 664 N TYR A 631 LINK O ASP A 610 K K A 802 1555 1555 2.83 LINK OD1 ASP A 610 K K A 802 1555 1555 2.74 LINK OD1 ASP A 612 ZN ZN A 801 1555 1555 2.05 LINK O ASP A 612 K K A 802 1555 1555 2.59 LINK ND1 HIS A 614 ZN ZN A 801 1555 1555 2.11 LINK O HIS A 614 K K A 802 1555 1555 2.71 LINK O PHE A 623 K K A 803 1555 1555 2.68 LINK O AASP A 626 K K A 803 1555 1555 2.90 LINK O BASP A 626 K K A 803 1555 1555 2.98 LINK O VAL A 629 K K A 803 1555 1555 2.64 LINK OG SER A 633 K K A 802 1555 1555 2.75 LINK O LEU A 634 K K A 802 1555 1555 2.69 LINK O TYR A 662 K K A 803 1555 1555 2.79 LINK OD2 ASP A 705 ZN ZN A 801 1555 1555 2.02 LINK ZN ZN A 801 N1 N9W A 813 1555 1555 2.43 LINK ZN ZN A 801 O1 N9W A 813 1555 1555 1.78 LINK ZN ZN A 801 O HOH A 903 1555 1555 1.96 LINK K K A 803 O HOH A 985 1555 1555 2.68 LINK K K A 803 O HOH A1030 1555 1555 2.93 LINK NA NA A 810 O HOH A 972 1555 1555 2.32 LINK NA NA A 810 O HOH A1183 1555 1555 2.76 LINK NA NA A 810 O HOH A1220 1555 1555 2.58 LINK NA NA A 810 O HOH A1230 1555 1555 2.36 LINK K K A 811 O HOH A 924 1555 1554 2.86 LINK K K A 811 O HOH A 948 1555 1555 2.45 LINK K K A 811 O HOH A 984 1555 1555 2.50 LINK K K A 811 O HOH A1245 1555 1555 2.67 CISPEP 1 ARG A 569 PRO A 570 0 -6.17 CISPEP 2 PHE A 643 PRO A 644 0 11.69 SITE 1 AC1 5 ASP A 612 HIS A 614 ASP A 705 N9W A 813 SITE 2 AC1 5 HOH A 903 SITE 1 AC2 5 ASP A 610 ASP A 612 HIS A 614 SER A 633 SITE 2 AC2 5 LEU A 634 SITE 1 AC3 6 PHE A 623 ASP A 626 VAL A 629 TYR A 662 SITE 2 AC3 6 HOH A 985 HOH A1030 SITE 1 AC4 5 HIS A 684 LEU A 787 LEU A 797 PEG A 807 SITE 2 AC4 5 HOH A 905 SITE 1 AC5 8 SER A 509 HIS A 683 MET A 687 ARG A 691 SITE 2 AC5 8 GLN A 728 HOH A 909 HOH A1053 HOH A1160 SITE 1 AC6 6 ASN A 457 ASP A 460 HIS A 463 ARG A 520 SITE 2 AC6 6 SER A 531 PHE A 533 SITE 1 AC7 9 LYS A 512 SER A 513 PRO A 688 ARG A 691 SITE 2 AC7 9 SER A 796 EDO A 804 HOH A 905 HOH A 980 SITE 3 AC7 9 HOH A1106 SITE 1 AC8 2 TRP A 459 ASN A 523 SITE 1 AC9 7 GLN A 620 GLU A 624 LYS A 653 GLY A 655 SITE 2 AC9 7 ASN A 663 HOH A 981 HOH A1107 SITE 1 AD1 4 HOH A 972 HOH A1183 HOH A1220 HOH A1230 SITE 1 AD2 4 HOH A 924 HOH A 948 HOH A 984 HOH A1245 SITE 1 AD3 5 ARG A 660 TYR A 662 PHE A 793 TRP A 794 SITE 2 AD3 5 HOH A 920 SITE 1 AD4 13 SER A 531 HIS A 574 GLY A 582 PHE A 583 SITE 2 AD4 13 ARG A 601 ASP A 612 HIS A 614 PHE A 643 SITE 3 AD4 13 ASP A 705 GLY A 743 TYR A 745 ZN A 801 SITE 4 AD4 13 HOH A 903 CRYST1 84.278 93.713 51.574 90.00 90.00 90.00 P 21 21 2 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 0.011865 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019390 0.00000