HEADER HYDROLASE/HYDROLASE INHIBITOR 01-MAY-20 6WSJ TITLE CRYSTAL STRUCTURE OF DANIO RERIO HISTONE DEACETYLASE 6 CATALYTIC TITLE 2 DOMAIN 2 COMPLEXED WITH CYCLOPEPTIDE DES4.3.1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HDAC6 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HISTONE DEACETYLASE 6; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: CYCLOPEPTIDE DES4.3.1; COMPND 8 CHAIN: I; COMPND 9 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 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, HISTONE DEACETYLASE, INHIBITOR, METALLOHYDROLASE, KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.R.WATSON,D.W.CHRISTIANSON REVDAT 4 15-NOV-23 6WSJ 1 REMARK REVDAT 3 18-OCT-23 6WSJ 1 REMARK REVDAT 2 01-SEP-21 6WSJ 1 JRNL REVDAT 1 28-APR-21 6WSJ 0 JRNL AUTH P.HOSSEINZADEH,P.R.WATSON,T.W.CRAVEN,X.LI,S.RETTIE, JRNL AUTH 2 F.PARDO-AVILA,A.K.BERA,V.K.MULLIGAN,P.LU,A.S.FORD, JRNL AUTH 3 B.D.WEITZNER,L.J.STEWART,A.P.MOYER,M.DI PIAZZA,J.G.WHALEN, JRNL AUTH 4 P.J.GREISEN,D.W.CHRISTIANSON,D.BAKER JRNL TITL ANCHOR EXTENSION: A STRUCTURE-GUIDED APPROACH TO DESIGN JRNL TITL 2 CYCLIC PEPTIDES TARGETING ENZYME ACTIVE SITES. JRNL REF NAT COMMUN V. 12 3384 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34099674 JRNL DOI 10.1038/S41467-021-23609-8 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 45657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.155 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 2204 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 62.7600 - 4.2900 1.00 2877 169 0.1488 0.1525 REMARK 3 2 4.2900 - 3.4000 1.00 2810 128 0.1488 0.1617 REMARK 3 3 3.4000 - 2.9700 1.00 2750 145 0.1666 0.2004 REMARK 3 4 2.9700 - 2.7000 1.00 2717 151 0.1613 0.1809 REMARK 3 5 2.7000 - 2.5100 1.00 2721 143 0.1567 0.2031 REMARK 3 6 2.5100 - 2.3600 1.00 2702 144 0.0000 0.1478 REMARK 3 7 2.3600 - 2.2400 1.00 2656 160 0.1449 0.1696 REMARK 3 8 2.2400 - 2.1400 1.00 2691 131 0.1454 0.1646 REMARK 3 9 2.1400 - 2.0600 1.00 2694 140 0.1459 0.1780 REMARK 3 10 2.0600 - 1.9900 1.00 2706 136 0.1566 0.1759 REMARK 3 11 1.9900 - 1.9300 1.00 2697 132 0.1417 0.1677 REMARK 3 12 1.9300 - 1.8700 1.00 2700 125 0.1435 0.1803 REMARK 3 13 1.8700 - 1.8200 1.00 2685 121 0.1490 0.1985 REMARK 3 14 1.8200 - 1.7800 1.00 2677 122 0.1544 0.2078 REMARK 3 15 1.7800 - 1.7400 1.00 2693 145 0.1800 0.2125 REMARK 3 16 1.7400 - 1.7000 1.00 2677 112 0.1951 0.2480 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.162 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.339 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 2897 REMARK 3 ANGLE : 0.963 3929 REMARK 3 CHIRALITY : 0.057 429 REMARK 3 PLANARITY : 0.006 512 REMARK 3 DIHEDRAL : 8.319 2917 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6WSJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1000248942. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 45672 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 62.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.61900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.800 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: PDB ENTRY 5EEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML HDAC6 PROTEIN 0.2 M AMMONIUM REMARK 280 CHLORIDE AND 20% POLYETHYLENE GLYCOL (PEG) 3350 (W/V), VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.21000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.21000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, I 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE DES4.3.1 IS CYCLIC PEPTIDE, A MEMBER OF ENZYME INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: DES4.3.1 REMARK 400 CHAIN: I REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 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 LEU A 769 REMARK 465 ASP A 770 REMARK 465 HIS A 771 REMARK 465 LEU A 772 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 PRO A 442 N CA O CB CG CD REMARK 470 GLN A 450 CD OE1 NE2 REMARK 470 GLU A 497 CG CD OE1 OE2 REMARK 470 LYS A 518 CD CE NZ REMARK 470 GLN A 560 CD OE1 NE2 REMARK 470 GLU A 602 CD OE1 OE2 REMARK 470 LYS A 658 CD CE NZ REMARK 470 LYS A 672 CG CD CE NZ REMARK 470 SER A 768 OG 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 DAR I 4 NE DAR I 4 CZ 0.125 REMARK 500 DAR I 4 CZ DAR I 4 NH2 0.128 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 I 6 CB - CA - C ANGL. DEV. = -22.6 DEGREES REMARK 500 PHE I 6 CB - CG - CD2 ANGL. DEV. = -5.8 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 THR A 600 -71.63 -133.32 REMARK 500 TYR A 637 -51.59 -131.65 REMARK 500 LEU A 685 -62.79 -127.71 REMARK 500 GLN A 716 37.44 -142.36 REMARK 500 GLU A 742 -111.14 -112.31 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 A 802 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 610 O REMARK 620 2 ASP A 610 OD1 70.4 REMARK 620 3 ASP A 612 O 100.4 95.8 REMARK 620 4 HIS A 614 O 161.5 91.3 78.4 REMARK 620 5 SER A 633 OG 84.2 111.6 152.0 105.6 REMARK 620 6 LEU A 634 O 77.2 141.1 69.2 118.6 85.3 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 101.4 REMARK 620 3 ASP A 705 OD2 105.6 96.4 REMARK 620 4 U2M I 5 SH 117.1 116.8 116.7 REMARK 620 N 1 2 3 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 76.6 REMARK 620 3 VAL A 629 O 117.5 78.5 REMARK 620 4 TYR A 662 O 155.4 116.9 86.3 REMARK 620 5 HOH A 971 O 81.0 88.3 153.3 79.2 REMARK 620 6 HOH A1012 O 69.8 146.1 121.4 93.1 81.9 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 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 des4.3.1 chain I DBREF 6WSJ A 440 798 UNP A7YT55 A7YT55_DANRE 288 646 DBREF 6WSJ I 1 8 PDB 6WSJ 6WSJ 1 8 SEQADV 6WSJ SER A 435 UNP A7YT55 EXPRESSION TAG SEQADV 6WSJ ASN A 436 UNP A7YT55 EXPRESSION TAG SEQADV 6WSJ ALA A 437 UNP A7YT55 EXPRESSION TAG SEQADV 6WSJ GLY A 438 UNP A7YT55 EXPRESSION TAG SEQADV 6WSJ GLY A 439 UNP A7YT55 EXPRESSION TAG SEQRES 1 A 364 SER ASN ALA GLY GLY SER SER PRO ILE THR GLY LEU VAL SEQRES 2 A 364 TYR ASP GLN ARG MET MET LEU HIS HIS ASN MET TRP ASP SEQRES 3 A 364 SER HIS HIS PRO GLU LEU PRO GLN ARG ILE SER ARG ILE SEQRES 4 A 364 PHE SER ARG HIS GLU GLU LEU ARG LEU LEU SER ARG CYS SEQRES 5 A 364 HIS ARG ILE PRO ALA ARG LEU ALA THR GLU GLU GLU LEU SEQRES 6 A 364 ALA LEU CYS HIS SER SER LYS HIS ILE SER ILE ILE LYS SEQRES 7 A 364 SER SER GLU HIS MET LYS PRO ARG ASP LEU ASN ARG LEU SEQRES 8 A 364 GLY ASP GLU TYR ASN SER ILE PHE ILE SER ASN GLU SER SEQRES 9 A 364 TYR THR CYS ALA LEU LEU ALA ALA GLY SER CYS PHE ASN SEQRES 10 A 364 SER ALA GLN ALA ILE LEU THR GLY GLN VAL ARG ASN ALA SEQRES 11 A 364 VAL ALA ILE VAL ARG PRO PRO GLY HIS HIS ALA GLU LYS SEQRES 12 A 364 ASP THR ALA CYS GLY PHE CYS PHE PHE ASN THR ALA ALA SEQRES 13 A 364 LEU THR ALA ARG TYR ALA GLN SER ILE THR ARG GLU SER SEQRES 14 A 364 LEU ARG VAL LEU ILE VAL ASP TRP ASP VAL HIS HIS GLY SEQRES 15 A 364 ASN GLY THR GLN HIS ILE PHE GLU GLU ASP ASP SER VAL SEQRES 16 A 364 LEU TYR ILE SER LEU HIS ARG TYR GLU ASP GLY ALA PHE SEQRES 17 A 364 PHE PRO ASN SER GLU ASP ALA ASN TYR ASP LYS VAL GLY SEQRES 18 A 364 LEU GLY LYS GLY ARG GLY TYR ASN VAL ASN ILE PRO TRP SEQRES 19 A 364 ASN GLY GLY LYS MET GLY ASP PRO GLU TYR MET ALA ALA SEQRES 20 A 364 PHE HIS HIS LEU VAL MET PRO ILE ALA ARG GLU PHE ALA SEQRES 21 A 364 PRO GLU LEU VAL LEU VAL SER ALA GLY PHE ASP ALA ALA SEQRES 22 A 364 ARG GLY ASP PRO LEU GLY GLY PHE GLN VAL THR PRO GLU SEQRES 23 A 364 GLY TYR ALA HIS LEU THR HIS GLN LEU MET SER LEU ALA SEQRES 24 A 364 ALA GLY ARG VAL LEU ILE ILE LEU GLU GLY GLY TYR ASN SEQRES 25 A 364 LEU THR SER ILE SER GLU SER MET SER MET CYS THR SER SEQRES 26 A 364 MET LEU LEU GLY ASP SER PRO PRO SER LEU ASP HIS LEU SEQRES 27 A 364 THR PRO LEU LYS THR SER ALA THR VAL SER ILE ASN ASN SEQRES 28 A 364 VAL LEU ARG ALA HIS ALA PRO PHE TRP SER SER LEU ARG SEQRES 1 I 8 DAL DSN ASP DAR U2M PHE DNE LYS HET DAL I 1 5 HET DSN I 2 6 HET DAR I 4 11 HET U2M I 5 10 HET DNE I 7 8 HET ZN A 801 1 HET K A 802 1 HET K A 803 1 HET EDO A 804 4 HET EDO A 805 4 HETNAM DAL D-ALANINE HETNAM DSN D-SERINE HETNAM DAR D-ARGININE HETNAM U2M (2S)-2-AMINO-7-SULFANYLHEPTANOIC ACID HETNAM DNE D-NORLEUCINE HETNAM ZN ZINC ION HETNAM K POTASSIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 DAL C3 H7 N O2 FORMUL 2 DSN C3 H7 N O3 FORMUL 2 DAR C6 H15 N4 O2 1+ FORMUL 2 U2M C7 H15 N O2 S FORMUL 2 DNE C6 H13 N O2 FORMUL 3 ZN ZN 2+ FORMUL 4 K 2(K 1+) FORMUL 6 EDO 2(C2 H6 O2) FORMUL 8 HOH *239(H2 O) HELIX 1 AA1 GLN A 450 HIS A 455 5 6 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 TYR A 448 1 N THR A 444 O HIS A 487 SHEET 3 AA1 8 ASN A 563 ILE A 567 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 C DAL I 1 N DSN I 2 1555 1555 1.45 LINK N DAL I 1 C LYS I 8 1555 1555 1.45 LINK C DSN I 2 N ASP I 3 1555 1555 1.45 LINK C ASP I 3 N DAR I 4 1555 1555 1.44 LINK C DAR I 4 N U2M I 5 1555 1555 1.44 LINK C U2M I 5 N PHE I 6 1555 1555 1.44 LINK C PHE I 6 N DNE I 7 1555 1555 1.44 LINK C DNE I 7 N LYS I 8 1555 1555 1.45 LINK O ASP A 610 K K A 802 1555 1555 2.76 LINK OD1 ASP A 610 K K A 802 1555 1555 2.71 LINK OD1 ASP A 612 ZN ZN A 801 1555 1555 2.05 LINK O ASP A 612 K K A 802 1555 1555 2.54 LINK ND1 HIS A 614 ZN ZN A 801 1555 1555 2.09 LINK O HIS A 614 K K A 802 1555 1555 2.77 LINK O PHE A 623 K K A 803 1555 1555 2.68 LINK O ASP A 626 K K A 803 1555 1555 2.95 LINK O VAL A 629 K K A 803 1555 1555 2.64 LINK OG SER A 633 K K A 802 1555 1555 2.77 LINK O LEU A 634 K K A 802 1555 1555 2.69 LINK O TYR A 662 K K A 803 1555 1555 2.82 LINK OD2 ASP A 705 ZN ZN A 801 1555 1555 2.02 LINK ZN ZN A 801 SH U2M I 5 1555 1555 2.32 LINK K K A 803 O HOH A 971 1555 1555 2.67 LINK K K A 803 O HOH A1012 1555 1555 2.95 CISPEP 1 ARG A 569 PRO A 570 0 -3.78 CISPEP 2 PHE A 643 PRO A 644 0 8.98 SITE 1 AC1 4 ASP A 612 HIS A 614 ASP A 705 U2M I 5 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 971 HOH A1012 SITE 1 AC4 6 ALA A 641 PHE A 642 PHE A 643 ASN A 645 SITE 2 AC4 6 DAR I 4 HOH I 103 SITE 1 AC5 8 GLU A 624 ASP A 652 LYS A 653 VAL A 654 SITE 2 AC5 8 GLY A 655 LEU A 656 ARG A 660 HOH A1040 SITE 1 AC6 27 HIS A 463 PRO A 464 SER A 531 HIS A 573 SITE 2 AC6 27 HIS A 574 GLY A 582 PHE A 583 ARG A 601 SITE 3 AC6 27 LEU A 604 ASP A 612 HIS A 614 PHE A 643 SITE 4 AC6 27 ASN A 645 GLU A 696 ASP A 705 ARG A 736 SITE 5 AC6 27 GLY A 743 TYR A 745 ZN A 801 EDO A 804 SITE 6 AC6 27 HOH A 936 HOH A 992 HOH I 101 HOH I 102 SITE 7 AC6 27 HOH I 103 HOH I 104 HOH I 105 CRYST1 51.500 84.000 94.420 90.00 90.00 90.00 P 2 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.019417 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011905 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010591 0.00000