HEADER HYDROLASE 27-JUL-20 6ZW1 TITLE X-RAY STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 (HDAC6) CD2 IN TITLE 2 COMPLEX WITH AN INHIBITOR SW101 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: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293T; SOURCE 10 EXPRESSION_SYSTEM_ORGAN: KIDNEY KEYWDS HISTONE DEACETYLASE, DEACETYLATION, INHIBITOR, DANIO RERIO, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.BARINKA,L.MOTLOVA,K.USTINOVA REVDAT 3 31-JAN-24 6ZW1 1 REMARK REVDAT 2 11-AUG-21 6ZW1 1 JRNL REVDAT 1 04-AUG-21 6ZW1 0 JRNL AUTH S.SHEN,C.PICCI,K.USTINOVA,V.BENOY,Z.KUTIL,G.ZHANG, JRNL AUTH 2 M.T.TAVARES,J.PAVLICEK,C.A.ZIMPRICH,M.B.ROBERS, JRNL AUTH 3 L.VAN DEN BOSCH,C.BARINKA,B.LANGLEY,A.P.KOZIKOWSKI JRNL TITL TETRAHYDROQUINOLINE-CAPPED HISTONE DEACETYLASE 6 INHIBITOR JRNL TITL 2 SW-101 AMELIORATES PATHOLOGICAL PHENOTYPES IN A JRNL TITL 3 CHARCOT-MARIE-TOOTH TYPE 2A MOUSE MODEL. JRNL REF J.MED.CHEM. V. 64 4810 2021 JRNL REFN ISSN 0022-2623 JRNL PMID 33830764 JRNL DOI 10.1021/ACS.JMEDCHEM.0C02210 REMARK 2 REMARK 2 RESOLUTION. 1.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 150734 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) : 0.140 REMARK 3 R VALUE (WORKING SET) : 0.140 REMARK 3 FREE R VALUE : 0.159 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2100 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) : 1.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 10837 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.08 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 151 REMARK 3 BIN FREE R VALUE : 0.2300 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 : 45 REMARK 3 SOLVENT ATOMS : 413 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.29000 REMARK 3 B22 (A**2) : 2.58000 REMARK 3 B33 (A**2) : -1.30000 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): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.397 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 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): 3093 ; 0.014 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2878 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4216 ; 1.748 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6641 ; 2.055 ; 2.993 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 400 ; 6.412 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 143 ;35.747 ;23.147 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 509 ;12.439 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;15.709 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3609 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 757 ; 0.010 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5970 ; 6.781 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 102 ;31.482 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6199 ; 9.953 ; 5.000 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 : BABINET MODEL WITH MASK 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 6ZW1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUL-20. REMARK 100 THE DEPOSITION ID IS D_1292110322. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JAN-19 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 152836 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.730 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: 6R0K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 3350 (SIGMA-ALDRICH), 0.2 M REMARK 280 KSCN (HAMPTON RESEARCH), 0.1 M BIS-TRIS (SIGMA-ALDRICH) AT PH REMARK 280 6.5., 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 41.96650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.07900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.96650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.07900 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: 950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 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 SER A 440 REMARK 465 SER A 441 REMARK 465 ASP A 770 REMARK 465 HIS A 771 REMARK 465 LEU A 772 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 2294 O HOH A 2397 2.14 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 O HOH A 2314 O HOH A 2412 4555 2.13 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 SER A 765 CA SER A 765 CB 0.158 REMARK 500 SER A 765 CA SER A 765 CB 0.100 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 PHE A 550 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 SER A 765 N - CA - CB ANGL. DEV. = 13.6 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 PHE A 583 -1.20 79.24 REMARK 500 THR A 600 -95.13 -133.32 REMARK 500 TYR A 637 -56.26 -124.68 REMARK 500 LEU A 685 -61.55 -123.41 REMARK 500 GLU A 742 -114.66 -111.62 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 K A2005 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 71.7 REMARK 620 3 ASP A 612 O 98.5 95.6 REMARK 620 4 HIS A 614 O 165.0 93.5 80.3 REMARK 620 5 SER A 633 OG 84.7 110.0 153.7 103.1 REMARK 620 6 LEU A 634 O 77.9 143.9 69.8 115.1 85.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A2001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 612 OD1 REMARK 620 2 HIS A 614 ND1 99.5 REMARK 620 3 ASP A 705 OD2 104.5 98.5 REMARK 620 4 QRB A2002 OAE 169.6 85.8 83.3 REMARK 620 5 QRB A2002 OAD 92.6 99.3 152.8 77.6 REMARK 620 6 QRB A2002 NAC 119.6 79.2 135.6 52.4 31.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A2006 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 623 O REMARK 620 2 ASP A 626 O 77.5 REMARK 620 3 VAL A 629 O 118.9 78.7 REMARK 620 4 TYR A 662 O 156.5 114.3 84.2 REMARK 620 5 HOH A2206 O 81.7 84.7 149.3 79.4 REMARK 620 6 HOH A2250 O 70.4 146.6 125.1 93.1 81.8 REMARK 620 N 1 2 3 4 5 DBREF 6ZW1 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 A2001 1 HET QRB A2002 24 HET GOL A2003 6 HET GOL A2004 6 HET K A2005 1 HET K A2006 1 HET SCN A2007 3 HET SCN A2008 3 HETNAM ZN ZINC ION HETNAM QRB 1-[[4-(OXIDANYLCARBAMOYL)PHENYL]METHYL]-3,4-DIHYDRO- HETNAM 2 QRB 2~{H}-QUINOLINE-6-CARBOXAMIDE HETNAM GOL GLYCEROL HETNAM K POTASSIUM ION HETNAM SCN THIOCYANATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ZN ZN 2+ FORMUL 3 QRB C18 H19 N3 O3 FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 K 2(K 1+) FORMUL 8 SCN 2(C N S 1-) FORMUL 10 HOH *413(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 GLU A 528 1 11 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 ILE A 740 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 A2005 1555 1555 2.81 LINK OD1 ASP A 610 K K A2005 1555 1555 2.70 LINK OD1 ASP A 612 ZN ZN A2001 1555 1555 2.05 LINK O ASP A 612 K K A2005 1555 1555 2.54 LINK ND1 HIS A 614 ZN ZN A2001 1555 1555 2.14 LINK O HIS A 614 K K A2005 1555 1555 2.66 LINK O PHE A 623 K K A2006 1555 1555 2.67 LINK O ASP A 626 K K A2006 1555 1555 2.94 LINK O VAL A 629 K K A2006 1555 1555 2.67 LINK OG SER A 633 K K A2005 1555 1555 2.69 LINK O LEU A 634 K K A2005 1555 1555 2.65 LINK O TYR A 662 K K A2006 1555 1555 2.78 LINK OD2 ASP A 705 ZN ZN A2001 1555 1555 1.96 LINK ZN ZN A2001 OAE QRB A2002 1555 1555 2.30 LINK ZN ZN A2001 OAD QRB A2002 1555 1555 1.93 LINK ZN ZN A2001 NAC QRB A2002 1555 1555 2.62 LINK K K A2006 O HOH A2206 1555 1555 2.69 LINK K K A2006 O HOH A2250 1555 1555 2.93 CISPEP 1 ARG A 569 PRO A 570 0 -7.06 CISPEP 2 PHE A 643 PRO A 644 0 9.13 CRYST1 83.933 94.158 51.487 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 0.011914 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010620 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019422 0.00000