HEADER HYDROLASE 27-JUN-22 8A8Z TITLE CRYSTAL STRUCTURE OF DANIO RERIO HDAC6 CD2 IN COMPLEX WITH IN SITU TITLE 2 ENZYMATICALLY HYDROLYZED DFMO-BASED ITF5924 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE DEACETYLASE 6; COMPND 3 CHAIN: A, B; 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 KEYWDS HISTONE DEACETYLASE, COMPLEX WITH HYDRAZIDE, HYDROLASE, NON- KEYWDS 2 HYDROXAMATE ZINC BINDING GROUP, MECHANISM-BASED INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR K.ZRUBEK,G.SANDRONE,C.D.CUKIER,A.STEVENAZZI REVDAT 2 07-FEB-24 8A8Z 1 REMARK REVDAT 1 25-JAN-23 8A8Z 0 JRNL AUTH E.CELLUPICA,G.CAPRINI,P.CORDELLA,C.CUKIER,G.FOSSATI, JRNL AUTH 2 M.MARCHINI,I.ROCCHIO,G.SANDRONE,M.A.VANONI,B.VERGANI, JRNL AUTH 3 K.ZRUBEK,A.STEVENAZZI,C.STEINKUHLER JRNL TITL DIFLUOROMETHYL-1,3,4-OXADIAZOLES ARE SLOW-BINDING SUBSTRATE JRNL TITL 2 ANALOG INHIBITORS OF HISTONE DEACETYLASE 6 WITH JRNL TITL 3 UNPRECEDENTED ISOTYPE SELECTIVITY. JRNL REF J.BIOL.CHEM. V. 299 02800 2022 JRNL REFN ESSN 1083-351X JRNL PMID 36528061 JRNL DOI 10.1016/J.JBC.2022.102800 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 87601 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4695 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6242 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.3150 REMARK 3 BIN FREE R VALUE SET COUNT : 347 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5580 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 62 REMARK 3 SOLVENT ATOMS : 686 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.05 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.67 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : 1.03000 REMARK 3 B33 (A**2) : -0.72000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.81000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.082 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.085 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.073 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.292 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5845 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5331 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7950 ; 1.609 ; 1.635 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12286 ; 1.479 ; 1.570 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 736 ; 6.408 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 318 ;31.953 ;20.943 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 932 ;12.912 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;16.361 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 750 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6742 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1394 ; 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): 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): 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 : 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 8A8Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1292123831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-21 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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.283 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 VERSION MAR 15, 2019 REMARK 200 BUILT=20191015 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92341 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 47.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.13300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 2.49400 REMARK 200 R SYM FOR SHELL (I) : 2.68300 REMARK 200 FOR SHELL : 0.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 5EEK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA-CITRATE PH 6.5, 20% (V/V) REMARK 280 PEG4000, 20% (V/V) ISOPROPANOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 59.46200 REMARK 290 SMTRY3 2 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 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 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 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 434 REMARK 465 SER A 435 REMARK 465 ASN A 436 REMARK 465 ALA A 437 REMARK 465 GLY A 438 REMARK 465 GLY A 439 REMARK 465 SER A 440 REMARK 465 SER A 441 REMARK 465 GLY B 434 REMARK 465 SER B 435 REMARK 465 ASN B 436 REMARK 465 ALA B 437 REMARK 465 GLY B 438 REMARK 465 GLY B 439 REMARK 465 SER B 440 REMARK 465 SER B 441 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 1160 O HOH A 1171 1.89 REMARK 500 O HOH A 1137 O HOH A 1191 1.96 REMARK 500 O HOH B 991 O HOH B 1073 1.98 REMARK 500 O HOH A 932 O HOH A 1121 2.01 REMARK 500 N PRO A 442 O HOH A 901 2.05 REMARK 500 O HOH B 1132 O HOH B 1163 2.11 REMARK 500 O HOH B 1126 O HOH B 1149 2.16 REMARK 500 O HOH A 1160 O HOH A 1252 2.18 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 1228 O HOH B 1130 2554 2.12 REMARK 500 O HOH A 934 O HOH B 1152 1656 2.15 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 B 788 CG - CD - NE ANGL. DEV. = -13.3 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 HIS A 463 133.88 -39.08 REMARK 500 SER A 531 62.82 60.88 REMARK 500 SER A 531 61.37 62.23 REMARK 500 THR A 600 -95.34 -125.76 REMARK 500 TYR A 637 -51.90 -121.98 REMARK 500 LEU A 685 -60.70 -127.93 REMARK 500 GLU A 742 -113.18 -110.04 REMARK 500 HIS A 771 39.49 74.13 REMARK 500 ILE B 443 -149.46 -119.94 REMARK 500 ASP B 460 79.36 -160.08 REMARK 500 SER B 531 60.02 63.56 REMARK 500 THR B 600 -100.33 -124.02 REMARK 500 TYR B 637 -50.17 -123.19 REMARK 500 LEU B 685 -63.30 -127.12 REMARK 500 GLU B 742 -111.18 -110.63 REMARK 500 LEU B 769 79.05 -108.61 REMARK 500 ASP B 770 -158.79 -77.51 REMARK 500 HIS B 771 42.94 38.96 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 B1224 DISTANCE = 6.68 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 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 71.2 REMARK 620 3 ASP A 612 O 100.6 97.5 REMARK 620 4 HIS A 614 O 164.8 93.8 78.2 REMARK 620 5 SER A 633 OG 85.5 112.0 150.2 103.1 REMARK 620 6 LEU A 634 O 77.9 144.0 70.2 115.3 82.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 802 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 110.7 99.6 REMARK 620 4 LDL A 801 N8 94.0 101.5 144.2 REMARK 620 5 LDL A 801 O1 163.1 86.8 83.3 69.4 REMARK 620 N 1 2 3 4 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 74.3 REMARK 620 3 VAL A 629 O 117.7 79.0 REMARK 620 4 TYR A 662 O 154.4 119.4 87.3 REMARK 620 5 HOH A1030 O 70.3 143.9 124.2 91.3 REMARK 620 6 HOH A1043 O 79.5 86.8 153.0 79.9 80.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 803 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 610 O REMARK 620 2 ASP B 610 OD1 70.7 REMARK 620 3 ASP B 612 O 99.5 94.9 REMARK 620 4 HIS B 614 O 164.2 93.6 79.8 REMARK 620 5 SER B 633 OG 85.3 112.8 151.8 102.8 REMARK 620 6 LEU B 634 O 78.9 143.8 70.7 115.2 83.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 612 OD1 REMARK 620 2 HIS B 614 ND1 100.9 REMARK 620 3 ASP B 705 OD2 108.9 96.3 REMARK 620 4 LDL B 801 N8 94.9 103.2 145.7 REMARK 620 5 LDL B 801 O1 165.5 84.7 83.5 70.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K B 804 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 623 O REMARK 620 2 ASP B 626 O 77.4 REMARK 620 3 VAL B 629 O 117.4 79.3 REMARK 620 4 TYR B 662 O 155.6 117.5 85.6 REMARK 620 5 HOH B1020 O 80.9 87.7 154.0 80.6 REMARK 620 6 HOH B1026 O 69.4 146.2 121.8 91.9 80.8 REMARK 620 N 1 2 3 4 5 DBREF 8A8Z A 440 798 UNP F8W4B7 F8W4B7_DANRE 440 798 DBREF 8A8Z B 440 798 UNP F8W4B7 F8W4B7_DANRE 440 798 SEQADV 8A8Z GLY A 434 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z SER A 435 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z ASN A 436 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z ALA A 437 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z GLY A 438 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z GLY A 439 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z GLY B 434 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z SER B 435 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z ASN B 436 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z ALA B 437 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z GLY B 438 UNP F8W4B7 CLONING ARTIFACT SEQADV 8A8Z GLY B 439 UNP F8W4B7 CLONING ARTIFACT SEQRES 1 A 365 GLY SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU SEQRES 2 A 365 VAL TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP SEQRES 3 A 365 ASP SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG SEQRES 4 A 365 ILE PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG SEQRES 5 A 365 CYS HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU SEQRES 6 A 365 LEU ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE SEQRES 7 A 365 LYS SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG SEQRES 8 A 365 LEU GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SEQRES 9 A 365 SER TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE SEQRES 10 A 365 ASN SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN SEQRES 11 A 365 ALA VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU SEQRES 12 A 365 LYS ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA SEQRES 13 A 365 ALA LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SEQRES 14 A 365 SER LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS SEQRES 15 A 365 GLY ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER SEQRES 16 A 365 VAL LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA SEQRES 17 A 365 PHE PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL SEQRES 18 A 365 GLY LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO SEQRES 19 A 365 TRP ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA SEQRES 20 A 365 ALA PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE SEQRES 21 A 365 ALA PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA SEQRES 22 A 365 ALA ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO SEQRES 23 A 365 GLU GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU SEQRES 24 A 365 ALA ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR SEQRES 25 A 365 ASN LEU THR SER ILE SER GLU SER MET SER MET CYS THR SEQRES 26 A 365 SER MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS SEQRES 27 A 365 LEU THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN SEQRES 28 A 365 ASN VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU SEQRES 29 A 365 ARG SEQRES 1 B 365 GLY SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU SEQRES 2 B 365 VAL TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP SEQRES 3 B 365 ASP SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG SEQRES 4 B 365 ILE PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG SEQRES 5 B 365 CYS HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU SEQRES 6 B 365 LEU ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE SEQRES 7 B 365 LYS SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG SEQRES 8 B 365 LEU GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SEQRES 9 B 365 SER TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE SEQRES 10 B 365 ASN SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN SEQRES 11 B 365 ALA VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU SEQRES 12 B 365 LYS ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA SEQRES 13 B 365 ALA LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SEQRES 14 B 365 SER LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS SEQRES 15 B 365 GLY ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER SEQRES 16 B 365 VAL LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA SEQRES 17 B 365 PHE PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL SEQRES 18 B 365 GLY LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO SEQRES 19 B 365 TRP ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA SEQRES 20 B 365 ALA PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE SEQRES 21 B 365 ALA PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA SEQRES 22 B 365 ALA ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO SEQRES 23 B 365 GLU GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU SEQRES 24 B 365 ALA ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR SEQRES 25 B 365 ASN LEU THR SER ILE SER GLU SER MET SER MET CYS THR SEQRES 26 B 365 SER MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS SEQRES 27 B 365 LEU THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN SEQRES 28 B 365 ASN VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU SEQRES 29 B 365 ARG HET LDL A 801 28 HET ZN A 802 1 HET K A 803 1 HET K A 804 1 HET LDL B 801 28 HET ZN B 802 1 HET K B 803 1 HET K B 804 1 HETNAM LDL 4-[[4-[4-(IMIDAZOLIDIN-2-YLIDENEAMINO)PHENYL]-1,2,3- HETNAM 2 LDL TRIAZOL-1-YL]METHYL]BENZOHYDRAZIDE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION FORMUL 3 LDL 2(C19 H20 N8 O) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 K 4(K 1+) FORMUL 11 HOH *686(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 GLU A 624 1 9 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 HELIX 21 AC3 ASP B 449 HIS B 455 5 7 HELIX 22 AC4 PRO B 467 LEU B 480 1 14 HELIX 23 AC5 LEU B 482 CYS B 486 5 5 HELIX 24 AC6 THR B 495 ALA B 500 1 6 HELIX 25 AC7 SER B 504 SER B 514 1 11 HELIX 26 AC8 GLU B 515 MET B 517 5 3 HELIX 27 AC9 LYS B 518 ASP B 527 1 10 HELIX 28 AD1 GLU B 537 THR B 558 1 22 HELIX 29 AD2 ASN B 587 ILE B 599 1 13 HELIX 30 AD3 GLY B 616 GLU B 624 1 9 HELIX 31 AD4 GLU B 638 ALA B 641 5 4 HELIX 32 AD5 SER B 646 ASN B 650 5 5 HELIX 33 AD6 LEU B 656 ARG B 660 5 5 HELIX 34 AD7 GLY B 674 LEU B 685 1 12 HELIX 35 AD8 LEU B 685 ALA B 694 1 10 HELIX 36 AD9 THR B 718 MET B 730 1 13 HELIX 37 AE1 SER B 731 GLY B 735 5 5 HELIX 38 AE2 ASN B 746 LEU B 762 1 17 HELIX 39 AE3 LYS B 776 ALA B 791 1 16 HELIX 40 AE4 TRP B 794 ARG B 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 LEU A 630 N ILE A 608 SHEET 8 AA1 8 ASN A 663 TRP A 668 1 O VAL A 664 N TYR A 631 SHEET 1 AA2 8 HIS B 487 ARG B 488 0 SHEET 2 AA2 8 THR B 444 VAL B 447 1 N THR B 444 O HIS B 487 SHEET 3 AA2 8 ASN B 563 ALA B 566 1 O ASN B 563 N GLY B 445 SHEET 4 AA2 8 VAL B 737 LEU B 741 1 O ILE B 739 N ALA B 566 SHEET 5 AA2 8 LEU B 697 ALA B 702 1 N VAL B 700 O ILE B 740 SHEET 6 AA2 8 VAL B 606 ASP B 610 1 N LEU B 607 O LEU B 699 SHEET 7 AA2 8 VAL B 629 ARG B 636 1 O ILE B 632 N ASP B 610 SHEET 8 AA2 8 ASN B 663 TRP B 668 1 O VAL B 664 N TYR B 631 LINK O ASP A 610 K K A 804 1555 1555 2.80 LINK OD1 ASP A 610 K K A 804 1555 1555 2.72 LINK OD1 ASP A 612 ZN ZN A 802 1555 1555 2.05 LINK O ASP A 612 K K A 804 1555 1555 2.54 LINK ND1 HIS A 614 ZN ZN A 802 1555 1555 2.08 LINK O HIS A 614 K K A 804 1555 1555 2.69 LINK O PHE A 623 K K A 803 1555 1555 2.67 LINK O ASP A 626 K K A 803 1555 1555 2.90 LINK O VAL A 629 K K A 803 1555 1555 2.61 LINK OG SER A 633 K K A 804 1555 1555 2.77 LINK O LEU A 634 K K A 804 1555 1555 2.65 LINK O TYR A 662 K K A 803 1555 1555 2.82 LINK OD2 ASP A 705 ZN ZN A 802 1555 1555 1.91 LINK N8 LDL A 801 ZN ZN A 802 1555 1555 2.11 LINK O1 LDL A 801 ZN ZN A 802 1555 1555 2.52 LINK K K A 803 O HOH A1030 1555 1555 3.01 LINK K K A 803 O HOH A1043 1555 1555 2.68 LINK O ASP B 610 K K B 803 1555 1555 2.77 LINK OD1 ASP B 610 K K B 803 1555 1555 2.70 LINK OD1 ASP B 612 ZN ZN B 802 1555 1555 2.01 LINK O ASP B 612 K K B 803 1555 1555 2.58 LINK ND1 HIS B 614 ZN ZN B 802 1555 1555 2.06 LINK O HIS B 614 K K B 803 1555 1555 2.77 LINK O PHE B 623 K K B 804 1555 1555 2.68 LINK O ASP B 626 K K B 804 1555 1555 2.86 LINK O VAL B 629 K K B 804 1555 1555 2.61 LINK OG SER B 633 K K B 803 1555 1555 2.71 LINK O LEU B 634 K K B 803 1555 1555 2.66 LINK O TYR B 662 K K B 804 1555 1555 2.79 LINK OD2 ASP B 705 ZN ZN B 802 1555 1555 2.00 LINK N8 LDL B 801 ZN ZN B 802 1555 1555 2.13 LINK O1 LDL B 801 ZN ZN B 802 1555 1555 2.43 LINK K K B 804 O HOH B1020 1555 1555 2.61 LINK K K B 804 O HOH B1026 1555 1555 3.02 CISPEP 1 ARG A 569 PRO A 570 0 0.16 CISPEP 2 PHE A 643 PRO A 644 0 4.83 CISPEP 3 ARG B 569 PRO B 570 0 -4.80 CISPEP 4 PHE B 643 PRO B 644 0 5.83 CRYST1 52.372 118.924 60.263 90.00 93.87 90.00 P 1 21 1 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 0.019094 0.000000 0.001292 0.00000 SCALE2 0.000000 0.008409 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016632 0.00000