HEADER LIGASE 23-MAY-18 6GLC TITLE STRUCTURE OF PHOSPHO-PARKIN BOUND TO PHOSPHO-UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PARKIN,PARKIN RBR E3 UBIQUITIN-PROTEIN LIGASE,PARKINSON COMPND 5 JUVENILE DISEASE PROTEIN 2,PARKINSON DISEASE PROTEIN 2; COMPND 6 EC: 2.3.2.31; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: POLYUBIQUITIN-B; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRKN, PARK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: UBB; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN, PARKIN, PHOSPHO-UBIQUITIN, PARKINSON'S DISEASE, E3 LIGASE, KEYWDS 2 RBR DOMAIN, MITOPHAGY, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR C.GLADKOVA,S.L.MASLEN,J.M.SKEHEL,D.KOMANDER REVDAT 4 17-JAN-24 6GLC 1 REMARK REVDAT 3 01-AUG-18 6GLC 1 JRNL REVDAT 2 18-JUL-18 6GLC 1 JRNL REVDAT 1 13-JUN-18 6GLC 0 JRNL AUTH C.GLADKOVA,S.L.MASLEN,J.M.SKEHEL,D.KOMANDER JRNL TITL MECHANISM OF PARKIN ACTIVATION BY PINK1. JRNL REF NATURE V. 559 410 2018 JRNL REFN ESSN 1476-4687 JRNL PMID 29995846 JRNL DOI 10.1038/S41586-018-0224-X REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.460 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 40229 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2020 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 59.8188 - 4.3379 1.00 2885 171 0.1562 0.1581 REMARK 3 2 4.3379 - 3.4432 1.00 2790 140 0.1493 0.1733 REMARK 3 3 3.4432 - 3.0080 1.00 2776 126 0.1816 0.1939 REMARK 3 4 3.0080 - 2.7330 1.00 2746 128 0.1968 0.2281 REMARK 3 5 2.7330 - 2.5371 1.00 2720 138 0.1892 0.2433 REMARK 3 6 2.5371 - 2.3875 1.00 2693 165 0.2002 0.2615 REMARK 3 7 2.3875 - 2.2679 1.00 2711 141 0.1890 0.2209 REMARK 3 8 2.2679 - 2.1692 1.00 2740 132 0.1883 0.2338 REMARK 3 9 2.1692 - 2.0857 1.00 2708 143 0.2026 0.2513 REMARK 3 10 2.0857 - 2.0137 1.00 2658 156 0.2111 0.2750 REMARK 3 11 2.0137 - 1.9507 1.00 2657 148 0.2132 0.2487 REMARK 3 12 1.9507 - 1.8950 1.00 2734 141 0.2318 0.2649 REMARK 3 13 1.8950 - 1.8451 1.00 2708 149 0.2625 0.2949 REMARK 3 14 1.8451 - 1.8001 1.00 2683 142 0.2805 0.2958 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.140 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.007 3135 REMARK 3 ANGLE : 0.863 4255 REMARK 3 CHIRALITY : 0.056 483 REMARK 3 PLANARITY : 0.005 550 REMARK 3 DIHEDRAL : 9.941 2600 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -6.6329 -26.8647 -16.2338 REMARK 3 T TENSOR REMARK 3 T11: 0.1784 T22: 0.2594 REMARK 3 T33: 0.2549 T12: -0.0097 REMARK 3 T13: 0.0429 T23: 0.0543 REMARK 3 L TENSOR REMARK 3 L11: 0.8967 L22: 1.1407 REMARK 3 L33: 2.0369 L12: -0.1595 REMARK 3 L13: 0.6828 L23: 0.2808 REMARK 3 S TENSOR REMARK 3 S11: 0.0639 S12: 0.2440 S13: 0.1220 REMARK 3 S21: -0.0855 S22: -0.0894 S23: -0.1474 REMARK 3 S31: -0.2512 S32: 0.1791 S33: 0.0308 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 6GLC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1200010172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96859 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 72.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.77300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 5N2W, 5C1Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% (W/V) PEG 1000, 12.5% (W/V) PEG REMARK 280 3350, 12.5% (V/V) MPD, 0.03 M OF EACH SODIUM NITRATE, DISODIUM REMARK 280 HYDROGEN PHOSPHATE, AMMONIUM SULPHATE, 0.1 M MOPS/HEPES-NA (PH REMARK 280 7.5), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.07933 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.03967 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.03967 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 70.07933 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: 4160 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -42.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B 228 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 231 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 233 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 PRO A 73 REMARK 465 TRP A 74 REMARK 465 ARG A 75 REMARK 465 LYS A 76 REMARK 465 GLY A 77 REMARK 465 GLN A 78 REMARK 465 GLU A 79 REMARK 465 MET A 80 REMARK 465 ASN A 81 REMARK 465 ALA A 82 REMARK 465 THR A 83 REMARK 465 GLY A 84 REMARK 465 GLY A 85 REMARK 465 ASP A 86 REMARK 465 ASP A 87 REMARK 465 PRO A 88 REMARK 465 ARG A 89 REMARK 465 ASN A 90 REMARK 465 ALA A 91 REMARK 465 ALA A 92 REMARK 465 GLY A 93 REMARK 465 GLY A 94 REMARK 465 CYS A 95 REMARK 465 GLU A 96 REMARK 465 ARG A 97 REMARK 465 GLU A 98 REMARK 465 PRO A 99 REMARK 465 SER A 109 REMARK 465 SER A 110 REMARK 465 VAL A 111 REMARK 465 LEU A 112 REMARK 465 PRO A 113 REMARK 465 GLY A 114 REMARK 465 ASP A 115 REMARK 465 SER A 116 REMARK 465 VAL A 117 REMARK 465 GLY A 118 REMARK 465 LEU A 119 REMARK 465 ALA A 120 REMARK 465 VAL A 121 REMARK 465 ILE A 122 REMARK 465 LEU A 123 REMARK 465 HIS A 124 REMARK 465 THR A 125 REMARK 465 ASP A 126 REMARK 465 SER A 127 REMARK 465 ARG A 128 REMARK 465 LYS A 129 REMARK 465 ASP A 130 REMARK 465 SER A 131 REMARK 465 PRO A 132 REMARK 465 PRO A 133 REMARK 465 ALA A 134 REMARK 465 GLY A 135 REMARK 465 SER A 136 REMARK 465 PRO A 137 REMARK 465 ALA A 138 REMARK 465 GLY A 139 REMARK 465 ARG A 140 REMARK 465 SER A 141 REMARK 465 ILE A 142 REMARK 465 GLY A 354 REMARK 465 GLY A 355 REMARK 465 ALA A 379 REMARK 465 VAL A 380 REMARK 465 PHE A 381 REMARK 465 GLU A 382 REMARK 465 ASN A 383 REMARK 465 LEU A 384 REMARK 465 TYR A 385 REMARK 465 PHE A 386 REMARK 465 GLN A 387 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 GLN A 40 CD OE1 NE2 REMARK 470 ARG A 42 CZ NH1 NH2 REMARK 470 LYS A 48 CD CE NZ REMARK 470 ARG A 51 CD NE CZ NH1 NH2 REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 100 CG CD OE1 NE2 REMARK 470 ASP A 106 CG OD1 OD2 REMARK 470 GLN A 178 CG CD OE1 NE2 REMARK 470 HIS A 200 CG ND1 CD2 CE1 NE2 REMARK 470 GLN A 282 CG CD OE1 NE2 REMARK 470 GLU A 310 CG CD OE1 OE2 REMARK 470 ARG A 334 CZ NH1 NH2 REMARK 470 GLU A 353 CG CD OE1 OE2 REMARK 470 ASN A 356 CG OD1 ND2 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 ARG B 54 CZ NH1 NH2 REMARK 470 LYS B 63 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 CYS A 201 O HOH A 601 2.12 REMARK 500 O LEU A 358 O HOH A 602 2.17 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 ASN A 144 78.02 57.79 REMARK 500 CYS A 337 -97.79 -108.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 506 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 154 SG 110.0 REMARK 620 3 CYS A 212 SG 111.6 114.7 REMARK 620 4 HIS A 215 NE2 111.9 104.5 103.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 166 SG REMARK 620 2 CYS A 169 SG 109.4 REMARK 620 3 CYS A 196 SG 106.1 109.8 REMARK 620 4 CYS A 201 SG 100.4 122.1 107.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 CYS A 241 SG 105.2 REMARK 620 3 CYS A 260 SG 113.2 116.5 REMARK 620 4 CYS A 263 SG 112.4 107.6 102.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 253 SG REMARK 620 2 HIS A 257 ND1 108.9 REMARK 620 3 CYS A 289 SG 116.1 100.1 REMARK 620 4 CYS A 293 SG 114.0 102.4 113.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 505 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 332 SG REMARK 620 2 CYS A 337 SG 112.0 REMARK 620 3 CYS A 352 SG 111.7 104.0 REMARK 620 4 CYS A 360 SG 106.8 112.8 109.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 365 SG REMARK 620 2 CYS A 368 SG 108.1 REMARK 620 3 HIS A 373 NE2 112.4 104.2 REMARK 620 4 CYS A 377 SG 107.1 115.7 109.4 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 508 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 509 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 510 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 DBREF 6GLC A 1 382 UNP O60260 PRKN_HUMAN 1 382 DBREF 6GLC B 1 76 UNP P0CG47 UBB_HUMAN 1 76 SEQADV 6GLC GLY A -1 UNP O60260 EXPRESSION TAG SEQADV 6GLC PRO A 0 UNP O60260 EXPRESSION TAG SEQADV 6GLC CYS A 347 UNP O60260 GLN 347 ENGINEERED MUTATION SEQADV 6GLC ASN A 383 UNP O60260 EXPRESSION TAG SEQADV 6GLC LEU A 384 UNP O60260 EXPRESSION TAG SEQADV 6GLC TYR A 385 UNP O60260 EXPRESSION TAG SEQADV 6GLC PHE A 386 UNP O60260 EXPRESSION TAG SEQADV 6GLC GLN A 387 UNP O60260 EXPRESSION TAG SEQADV 6GLC 3CN B 76 UNP P0CG47 GLY 76 ENGINEERED MUTATION SEQRES 1 A 389 GLY PRO MET ILE VAL PHE VAL ARG PHE ASN SER SER HIS SEQRES 2 A 389 GLY PHE PRO VAL GLU VAL ASP SER ASP THR SER ILE PHE SEQRES 3 A 389 GLN LEU LYS GLU VAL VAL ALA LYS ARG GLN GLY VAL PRO SEQRES 4 A 389 ALA ASP GLN LEU ARG VAL ILE PHE ALA GLY LYS GLU LEU SEQRES 5 A 389 ARG ASN ASP TRP THR VAL GLN ASN CYS ASP LEU ASP GLN SEQRES 6 A 389 GLN SEP ILE VAL HIS ILE VAL GLN ARG PRO TRP ARG LYS SEQRES 7 A 389 GLY GLN GLU MET ASN ALA THR GLY GLY ASP ASP PRO ARG SEQRES 8 A 389 ASN ALA ALA GLY GLY CYS GLU ARG GLU PRO GLN SER LEU SEQRES 9 A 389 THR ARG VAL ASP LEU SER SER SER VAL LEU PRO GLY ASP SEQRES 10 A 389 SER VAL GLY LEU ALA VAL ILE LEU HIS THR ASP SER ARG SEQRES 11 A 389 LYS ASP SER PRO PRO ALA GLY SER PRO ALA GLY ARG SER SEQRES 12 A 389 ILE TYR ASN SER PHE TYR VAL TYR CYS LYS GLY PRO CYS SEQRES 13 A 389 GLN ARG VAL GLN PRO GLY LYS LEU ARG VAL GLN CYS SER SEQRES 14 A 389 THR CYS ARG GLN ALA THR LEU THR LEU THR GLN GLY PRO SEQRES 15 A 389 SER CYS TRP ASP ASP VAL LEU ILE PRO ASN ARG MET SER SEQRES 16 A 389 GLY GLU CYS GLN SER PRO HIS CYS PRO GLY THR SER ALA SEQRES 17 A 389 GLU PHE PHE PHE LYS CYS GLY ALA HIS PRO THR SER ASP SEQRES 18 A 389 LYS GLU THR SER VAL ALA LEU HIS LEU ILE ALA THR ASN SEQRES 19 A 389 SER ARG ASN ILE THR CYS ILE THR CYS THR ASP VAL ARG SEQRES 20 A 389 SER PRO VAL LEU VAL PHE GLN CYS ASN SER ARG HIS VAL SEQRES 21 A 389 ILE CYS LEU ASP CYS PHE HIS LEU TYR CYS VAL THR ARG SEQRES 22 A 389 LEU ASN ASP ARG GLN PHE VAL HIS ASP PRO GLN LEU GLY SEQRES 23 A 389 TYR SER LEU PRO CYS VAL ALA GLY CYS PRO ASN SER LEU SEQRES 24 A 389 ILE LYS GLU LEU HIS HIS PHE ARG ILE LEU GLY GLU GLU SEQRES 25 A 389 GLN TYR ASN ARG TYR GLN GLN TYR GLY ALA GLU GLU CYS SEQRES 26 A 389 VAL LEU GLN MET GLY GLY VAL LEU CYS PRO ARG PRO GLY SEQRES 27 A 389 CYS GLY ALA GLY LEU LEU PRO GLU PRO ASP CYS ARG LYS SEQRES 28 A 389 VAL THR CYS GLU GLY GLY ASN GLY LEU GLY CYS GLY PHE SEQRES 29 A 389 ALA PHE CYS ARG GLU CYS LYS GLU ALA TYR HIS GLU GLY SEQRES 30 A 389 GLU CYS SER ALA VAL PHE GLU ASN LEU TYR PHE GLN SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SEP SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY 3CN MODRES 6GLC SEP A 65 SER MODIFIED RESIDUE MODRES 6GLC SEP B 65 SER MODIFIED RESIDUE HET SEP A 65 10 HET SEP B 65 10 HET 3CN B 76 4 HET ZN A 501 1 HET ZN A 502 1 HET ZN A 503 1 HET ZN A 504 1 HET ZN A 505 1 HET ZN A 506 1 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HET MPD A 510 8 HET SO4 B 101 5 HETNAM SEP PHOSPHOSERINE HETNAM 3CN 3-AMINOPROPANE HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM SO4 SULFATE ION HETSYN SEP PHOSPHONOSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 SEP 2(C3 H8 N O6 P) FORMUL 2 3CN C3 H9 N FORMUL 3 ZN 6(ZN 2+) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 12 MPD C6 H14 O2 FORMUL 13 SO4 O4 S 2- FORMUL 14 HOH *165(H2 O) HELIX 1 AA1 SER A 22 GLY A 35 1 14 HELIX 2 AA2 PRO A 37 ASP A 39 5 3 HELIX 3 AA3 VAL A 56 ASP A 60 5 5 HELIX 4 AA4 SER A 101 VAL A 105 5 5 HELIX 5 AA5 CYS A 182 ILE A 188 1 7 HELIX 6 AA6 LEU A 261 ASP A 274 1 14 HELIX 7 AA7 GLU A 300 LEU A 307 5 8 HELIX 8 AA8 GLY A 308 MET A 327 1 20 HELIX 9 AA9 THR B 22 GLY B 35 1 14 HELIX 10 AB1 PRO B 37 ASP B 39 5 3 HELIX 11 AB2 LEU B 56 ASN B 60 5 5 SHEET 1 AA1 5 PHE A 13 VAL A 17 0 SHEET 2 AA1 5 MET A 1 PHE A 7 -1 N MET A 1 O VAL A 17 SHEET 3 AA1 5 ILE A 66 GLN A 71 1 O VAL A 67 N PHE A 4 SHEET 4 AA1 5 LEU A 41 PHE A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 AA1 5 LYS A 48 LEU A 50 -1 O LYS A 48 N PHE A 45 SHEET 1 AA2 4 ALA A 206 CYS A 212 0 SHEET 2 AA2 4 ARG A 156 CYS A 166 -1 N ARG A 163 O PHE A 209 SHEET 3 AA2 4 PHE A 146 CYS A 150 -1 N PHE A 146 O GLY A 160 SHEET 4 AA2 4 VAL A 224 ALA A 225 -1 O VAL A 224 N TYR A 149 SHEET 1 AA3 2 LEU A 174 LEU A 176 0 SHEET 2 AA3 2 GLY A 194 CYS A 196 -1 O GLU A 195 N THR A 175 SHEET 1 AA4 3 ILE A 229 ALA A 230 0 SHEET 2 AA4 3 VAL A 248 VAL A 250 -1 O VAL A 248 N ALA A 230 SHEET 3 AA4 3 VAL A 258 CYS A 260 -1 O ILE A 259 N LEU A 249 SHEET 1 AA5 2 VAL A 278 ASP A 280 0 SHEET 2 AA5 2 GLY A 284 SER A 286 -1 O SER A 286 N VAL A 278 SHEET 1 AA6 5 VAL A 330 LEU A 331 0 SHEET 2 AA6 5 GLY A 340 LEU A 342 -1 O LEU A 341 N VAL A 330 SHEET 3 AA6 5 THR B 66 ARG B 72 1 O LEU B 71 N LEU A 342 SHEET 4 AA6 5 GLN B 2 THR B 7 1 N PHE B 4 O LEU B 67 SHEET 5 AA6 5 THR B 12 GLU B 16 -1 O ILE B 13 N VAL B 5 SHEET 1 AA7 5 VAL A 330 LEU A 331 0 SHEET 2 AA7 5 GLY A 340 LEU A 342 -1 O LEU A 341 N VAL A 330 SHEET 3 AA7 5 THR B 66 ARG B 72 1 O LEU B 71 N LEU A 342 SHEET 4 AA7 5 GLN B 41 PHE B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA7 5 LYS B 48 GLN B 49 -1 O LYS B 48 N PHE B 45 SHEET 1 AA8 2 LYS A 349 THR A 351 0 SHEET 2 AA8 2 ALA A 363 CYS A 365 -1 O PHE A 364 N VAL A 350 LINK C GLN A 64 N SEP A 65 1555 1555 1.33 LINK C SEP A 65 N ILE A 66 1555 1555 1.33 LINK SG CYS A 347 CA 3CN B 76 1555 1555 1.66 LINK C GLU B 64 N SEP B 65 1555 1555 1.33 LINK C SEP B 65 N THR B 66 1555 1555 1.33 LINK C GLY B 75 ND 3CN B 76 1555 1555 1.35 LINK SG CYS A 150 ZN ZN A 506 1555 1555 2.36 LINK SG CYS A 154 ZN ZN A 506 1555 1555 2.35 LINK SG CYS A 166 ZN ZN A 503 1555 1555 2.41 LINK SG CYS A 169 ZN ZN A 503 1555 1555 2.34 LINK SG CYS A 196 ZN ZN A 503 1555 1555 2.13 LINK SG CYS A 201 ZN ZN A 503 1555 1555 2.45 LINK SG CYS A 212 ZN ZN A 506 1555 1555 2.27 LINK NE2 HIS A 215 ZN ZN A 506 1555 1555 2.00 LINK SG CYS A 238 ZN ZN A 504 1555 1555 2.43 LINK SG CYS A 241 ZN ZN A 504 1555 1555 2.32 LINK SG CYS A 253 ZN ZN A 501 1555 1555 2.29 LINK ND1 HIS A 257 ZN ZN A 501 1555 1555 2.19 LINK SG CYS A 260 ZN ZN A 504 1555 1555 2.36 LINK SG CYS A 263 ZN ZN A 504 1555 1555 2.36 LINK SG CYS A 289 ZN ZN A 501 1555 1555 2.31 LINK SG CYS A 293 ZN ZN A 501 1555 1555 2.27 LINK SG CYS A 332 ZN ZN A 505 1555 1555 2.33 LINK SG CYS A 337 ZN ZN A 505 1555 1555 2.29 LINK SG CYS A 352 ZN ZN A 505 1555 1555 2.37 LINK SG CYS A 360 ZN ZN A 505 1555 1555 2.28 LINK SG CYS A 365 ZN ZN A 502 1555 1555 2.35 LINK SG CYS A 368 ZN ZN A 502 1555 1555 2.25 LINK NE2 HIS A 373 ZN ZN A 502 1555 1555 2.01 LINK SG CYS A 377 ZN ZN A 502 1555 1555 2.39 CISPEP 1 GLY A 152 PRO A 153 0 7.41 CISPEP 2 SER A 246 PRO A 247 0 -6.42 SITE 1 AC1 4 CYS A 253 HIS A 257 CYS A 289 CYS A 293 SITE 1 AC2 4 CYS A 365 CYS A 368 HIS A 373 CYS A 377 SITE 1 AC3 4 CYS A 166 CYS A 169 CYS A 196 CYS A 201 SITE 1 AC4 4 CYS A 238 CYS A 241 CYS A 260 CYS A 263 SITE 1 AC5 4 CYS A 332 CYS A 337 CYS A 352 CYS A 360 SITE 1 AC6 4 CYS A 150 CYS A 154 CYS A 212 HIS A 215 SITE 1 AC7 3 PRO A 14 GLU A 16 CYS A 263 SITE 1 AC8 3 PRO A 14 ARG A 245 CYS A 263 SITE 1 AC9 6 PHE A 4 GLY A 12 ILE A 66 SER A 218 SITE 2 AC9 6 THR A 242 HOH A 649 SITE 1 AD1 7 LYS A 299 GLU A 300 LEU A 301 HIS A 302 SITE 2 AD1 7 PHE B 45 ASP B 58 TYR B 59 SITE 1 AD2 3 ARG B 42 ARG B 72 ARG B 74 CRYST1 83.931 83.931 105.119 90.00 90.00 120.00 P 32 2 1 6 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 0.011915 0.006879 0.000000 0.00000 SCALE2 0.000000 0.013758 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009513 0.00000