HEADER LIGASE 02-NOV-23 8WZO TITLE PARKIN IN COMPLEX WITH PHOSPHO NEDD8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE PARKIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NEDD8; COMPND 7 CHAIN: B; COMPND 8 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; 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: NEDD8; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR D.R.LENKA,A.KUMAR REVDAT 1 18-SEP-24 8WZO 0 JRNL AUTH D.R.LENKA,A.KUMAR JRNL TITL PARKIN IN COMPLEX WITH PHOSPHO NEDD8 JRNL REF STRUCTURE JRNL REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21769 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.039 REMARK 3 FREE R VALUE TEST SET COUNT : 1097 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) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1513 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2740 REMARK 3 BIN FREE R VALUE SET COUNT : 71 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2929 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 20 REMARK 3 SOLVENT ATOMS : 174 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.35000 REMARK 3 B22 (A**2) : -0.21600 REMARK 3 B33 (A**2) : 1.13300 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.34200 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.294 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.221 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.173 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.117 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.946 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3035 ; 0.004 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4098 ; 1.026 ; 1.667 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 374 ; 5.645 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 157 ;34.260 ;22.038 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 495 ;16.868 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.773 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 383 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2321 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1205 ; 0.184 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2017 ; 0.299 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 179 ; 0.131 ; 0.200 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): 1508 ; 1.616 ; 4.516 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1878 ; 2.858 ; 6.757 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1527 ; 1.774 ; 4.577 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2220 ; 2.890 ; 6.801 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8WZO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042258. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-SEP-23 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 : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8731 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 : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21772 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 44.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 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 : NULL 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 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M SODIUM/POTASSIUM PHOSPHATE, 0.1 REMARK 280 M BIS-TRIS PROPANE, 7.5, 20% W/V PEG 3350, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 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+1/2 REMARK 290 4555 -X+1/2,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 22.03265 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.87350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 61.64006 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 22.03265 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.87350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 61.64006 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: 3240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -45.0 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 A 647 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 141 REMARK 465 VAL A 380 REMARK 465 PHE A 381 REMARK 465 GLU A 382 REMARK 465 ALA A 383 REMARK 465 SER A 384 REMARK 465 GLY A 385 REMARK 465 THR A 386 REMARK 465 THR A 387 REMARK 465 THR A 388 REMARK 465 GLN A 389 REMARK 465 ALA A 390 REMARK 465 TYR A 391 REMARK 465 SER A 407 REMARK 465 LYS A 408 REMARK 465 GLU A 409 REMARK 465 THR A 410 REMARK 465 ILE A 411 REMARK 465 LYS A 412 REMARK 465 LYS A 413 REMARK 465 LEU B 73 REMARK 465 ARG B 74 REMARK 465 GLY B 75 REMARK 465 GLY B 76 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 347 CG CD OE1 NE2 REMARK 470 GLU A 367 CG CD OE1 OE2 REMARK 470 LYS A 369 CG CD CE NZ REMARK 470 GLU A 376 CG CD OE1 OE2 REMARK 470 ARG A 392 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 428 CG OD1 ND2 REMARK 470 LYS A 435 CG CD CE NZ REMARK 470 ARG A 455 NE CZ NH1 NH2 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 608 O HOH A 672 2.18 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 168 -60.75 -91.10 REMARK 500 THR A 242 -1.04 71.40 REMARK 500 CYS A 337 -83.64 -108.58 REMARK 500 ALA A 405 42.55 -94.33 REMARK 500 HIS A 422 11.04 56.32 REMARK 500 HIS A 461 52.34 -157.11 REMARK 500 LYS B 33 -8.24 -145.32 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 508 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 150 SG REMARK 620 2 CYS A 154 SG 108.6 REMARK 620 3 CYS A 212 SG 111.6 111.9 REMARK 620 4 HIS A 215 ND1 102.3 120.1 101.9 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 166 SG REMARK 620 2 CYS A 169 SG 104.6 REMARK 620 3 CYS A 196 SG 106.6 108.7 REMARK 620 4 CYS A 201 SG 110.8 116.8 108.8 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 238 SG REMARK 620 2 CYS A 241 SG 103.7 REMARK 620 3 CYS A 260 SG 113.7 118.9 REMARK 620 4 CYS A 263 SG 108.3 114.3 97.9 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 111.4 REMARK 620 3 CYS A 289 SG 114.5 100.9 REMARK 620 4 CYS A 293 SG 112.4 104.1 112.3 REMARK 620 N 1 2 3 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 332 SG REMARK 620 2 CYS A 337 SG 110.0 REMARK 620 3 CYS A 352 SG 111.1 109.1 REMARK 620 4 CYS A 360 SG 112.5 108.4 105.5 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 122.6 REMARK 620 3 HIS A 373 ND1 82.3 137.2 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 507 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 418 SG REMARK 620 2 CYS A 421 SG 97.7 REMARK 620 3 CYS A 436 SG 98.7 91.5 REMARK 620 4 CYS A 441 SG 112.8 120.5 129.4 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 446 SG REMARK 620 2 CYS A 449 SG 114.8 REMARK 620 3 CYS A 457 SG 114.8 112.5 REMARK 620 4 HIS A 461 NE2 105.0 104.4 103.8 REMARK 620 N 1 2 3 DBREF 8WZO A 141 465 UNP O60260 PRKN_HUMAN 141 465 DBREF 8WZO B 1 76 UNP Q15843 NEDD8_HUMAN 1 76 SEQADV 8WZO SER B 0 UNP Q15843 EXPRESSION TAG SEQRES 1 A 325 SER ILE TYR ASN SER PHE TYR VAL TYR CYS LYS GLY PRO SEQRES 2 A 325 CYS GLN ARG VAL GLN PRO GLY LYS LEU ARG VAL GLN CYS SEQRES 3 A 325 SER THR CYS ARG GLN ALA THR LEU THR LEU THR GLN GLY SEQRES 4 A 325 PRO SER CYS TRP ASP ASP VAL LEU ILE PRO ASN ARG MET SEQRES 5 A 325 SER GLY GLU CYS GLN SER PRO HIS CYS PRO GLY THR SER SEQRES 6 A 325 ALA GLU PHE PHE PHE LYS CYS GLY ALA HIS PRO THR SER SEQRES 7 A 325 ASP LYS GLU THR SER VAL ALA LEU HIS LEU ILE ALA THR SEQRES 8 A 325 ASN SER ARG ASN ILE THR CYS ILE THR CYS THR ASP VAL SEQRES 9 A 325 ARG SER PRO VAL LEU VAL PHE GLN CYS ASN SER ARG HIS SEQRES 10 A 325 VAL ILE CYS LEU ASP CYS PHE HIS LEU TYR CYS VAL THR SEQRES 11 A 325 ARG LEU ASN ASP ARG GLN PHE VAL HIS ASP PRO GLN LEU SEQRES 12 A 325 GLY TYR SER LEU PRO CYS VAL ALA GLY CYS PRO ASN SER SEQRES 13 A 325 LEU ILE LYS GLU LEU HIS HIS PHE ARG ILE LEU GLY GLU SEQRES 14 A 325 GLU GLN TYR ASN ARG TYR GLN GLN TYR GLY ALA GLU GLU SEQRES 15 A 325 CYS VAL LEU GLN MET GLY GLY VAL LEU CYS PRO ARG PRO SEQRES 16 A 325 GLY CYS GLY ALA GLY LEU LEU PRO GLU PRO ASP GLN ARG SEQRES 17 A 325 LYS VAL THR CYS GLU GLY GLY ASN GLY LEU GLY CYS GLY SEQRES 18 A 325 PHE ALA PHE CYS ARG GLU CYS LYS GLU ALA TYR HIS GLU SEQRES 19 A 325 GLY GLU CYS SER ALA VAL PHE GLU ALA SER GLY THR THR SEQRES 20 A 325 THR GLN ALA TYR ARG VAL ASP GLU ARG ALA ALA GLU GLN SEQRES 21 A 325 ALA ARG TRP GLU ALA ALA SER LYS GLU THR ILE LYS LYS SEQRES 22 A 325 THR THR LYS PRO CYS PRO ARG CYS HIS VAL PRO VAL GLU SEQRES 23 A 325 LYS ASN GLY GLY CYS MET HIS MET LYS CYS PRO GLN PRO SEQRES 24 A 325 GLN CYS ARG LEU GLU TRP CYS TRP ASN CYS GLY CYS GLU SEQRES 25 A 325 TRP ASN ARG VAL CYS MET GLY ASP HIS TRP PHE ASP VAL SEQRES 1 B 77 SER MET LEU ILE LYS VAL LYS THR LEU THR GLY LYS GLU SEQRES 2 B 77 ILE GLU ILE ASP ILE GLU PRO THR ASP LYS VAL GLU ARG SEQRES 3 B 77 ILE LYS GLU ARG VAL GLU GLU LYS GLU GLY ILE PRO PRO SEQRES 4 B 77 GLN GLN GLN ARG LEU ILE TYR SER GLY LYS GLN MET ASN SEQRES 5 B 77 ASP GLU LYS THR ALA ALA ASP TYR LYS ILE LEU GLY GLY SEQRES 6 B 77 SEP VAL LEU HIS LEU VAL LEU ALA LEU ARG GLY GLY MODRES 8WZO SEP B 65 SER MODIFIED RESIDUE HET SEP B 65 10 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 ZN A 507 1 HET ZN A 508 1 HET EDO A 509 4 HET EDO A 510 4 HET EDO A 511 4 HETNAM SEP PHOSPHOSERINE HETNAM ZN ZINC ION HETNAM EDO 1,2-ETHANEDIOL HETSYN SEP PHOSPHONOSERINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 SEP C3 H8 N O6 P FORMUL 3 ZN 8(ZN 2+) FORMUL 11 EDO 3(C2 H6 O2) FORMUL 14 HOH *174(H2 O) HELIX 1 AA1 CYS A 182 ILE A 188 1 7 HELIX 2 AA2 LEU A 261 ASP A 274 1 14 HELIX 3 AA3 GLU A 300 LEU A 307 5 8 HELIX 4 AA4 GLY A 308 MET A 327 1 20 HELIX 5 AA5 ASP A 394 ALA A 401 1 8 HELIX 6 AA6 ASN A 454 TRP A 462 1 9 HELIX 7 AA7 LYS B 22 GLY B 35 1 14 HELIX 8 AA8 PRO B 37 GLN B 39 5 3 HELIX 9 AA9 THR B 55 TYR B 59 5 5 SHEET 1 AA1 4 ALA A 206 CYS A 212 0 SHEET 2 AA1 4 ARG A 156 CYS A 166 -1 N GLN A 165 O GLU A 207 SHEET 3 AA1 4 TYR A 147 CYS A 150 -1 N VAL A 148 O GLN A 158 SHEET 4 AA1 4 VAL A 224 ALA A 225 -1 O VAL A 224 N TYR A 149 SHEET 1 AA2 2 LEU A 174 LEU A 176 0 SHEET 2 AA2 2 GLY A 194 CYS A 196 -1 O GLU A 195 N THR A 175 SHEET 1 AA3 3 ILE A 229 ALA A 230 0 SHEET 2 AA3 3 VAL A 248 VAL A 250 -1 O VAL A 248 N ALA A 230 SHEET 3 AA3 3 VAL A 258 CYS A 260 -1 O ILE A 259 N LEU A 249 SHEET 1 AA4 2 VAL A 278 ASP A 280 0 SHEET 2 AA4 2 GLY A 284 SER A 286 -1 O SER A 286 N VAL A 278 SHEET 1 AA5 2 VAL A 330 LEU A 331 0 SHEET 2 AA5 2 GLY A 340 LEU A 341 -1 O LEU A 341 N VAL A 330 SHEET 1 AA6 2 LYS A 349 THR A 351 0 SHEET 2 AA6 2 ALA A 363 CYS A 365 -1 O PHE A 364 N VAL A 350 SHEET 1 AA7 2 THR A 415 PRO A 417 0 SHEET 2 AA7 2 PRO A 424 GLU A 426 -1 O VAL A 425 N LYS A 416 SHEET 1 AA8 2 HIS A 433 LYS A 435 0 SHEET 2 AA8 2 GLU A 444 CYS A 446 -1 O TRP A 445 N MET A 434 SHEET 1 AA9 5 GLU B 12 ILE B 17 0 SHEET 2 AA9 5 MET B 1 THR B 7 -1 N MET B 1 O ILE B 17 SHEET 3 AA9 5 VAL B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 AA9 5 GLN B 41 TYR B 45 -1 N ILE B 44 O HIS B 68 SHEET 5 AA9 5 LYS B 48 GLN B 49 -1 O LYS B 48 N TYR B 45 LINK C GLY B 64 N SEP B 65 1555 1555 1.34 LINK C SEP B 65 N VAL B 66 1555 1555 1.34 LINK SG CYS A 150 ZN ZN A 508 1555 1555 2.33 LINK SG CYS A 154 ZN ZN A 508 1555 1555 2.33 LINK SG CYS A 166 ZN ZN A 504 1555 1555 2.34 LINK SG CYS A 169 ZN ZN A 504 1555 1555 2.32 LINK SG CYS A 196 ZN ZN A 504 1555 1555 2.33 LINK SG CYS A 201 ZN ZN A 504 1555 1555 2.34 LINK SG CYS A 212 ZN ZN A 508 1555 1555 2.32 LINK ND1 HIS A 215 ZN ZN A 508 1555 1555 2.18 LINK SG CYS A 238 ZN ZN A 505 1555 1555 2.34 LINK SG CYS A 241 ZN ZN A 505 1555 1555 2.33 LINK SG CYS A 253 ZN ZN A 501 1555 1555 2.33 LINK ND1 HIS A 257 ZN ZN A 501 1555 1555 2.11 LINK SG CYS A 260 ZN ZN A 505 1555 1555 2.35 LINK SG CYS A 263 ZN ZN A 505 1555 1555 2.32 LINK SG CYS A 289 ZN ZN A 501 1555 1555 2.35 LINK SG CYS A 293 ZN ZN A 501 1555 1555 2.35 LINK SG CYS A 332 ZN ZN A 506 1555 1555 2.32 LINK SG CYS A 337 ZN ZN A 506 1555 1555 2.34 LINK SG CYS A 352 ZN ZN A 506 1555 1555 2.33 LINK SG CYS A 360 ZN ZN A 506 1555 1555 2.35 LINK SG CYS A 365 ZN ZN A 502 1555 1555 2.34 LINK SG CYS A 368 ZN ZN A 502 1555 1555 2.33 LINK ND1 HIS A 373 ZN ZN A 502 1555 1555 2.04 LINK SG CYS A 418 ZN ZN A 507 1555 1555 2.36 LINK SG CYS A 421 ZN ZN A 507 1555 1555 2.35 LINK SG CYS A 436 ZN ZN A 507 1555 1555 2.34 LINK SG CYS A 441 ZN ZN A 507 1555 1555 2.33 LINK SG CYS A 446 ZN ZN A 503 1555 1555 2.33 LINK SG CYS A 449 ZN ZN A 503 1555 1555 2.35 LINK SG CYS A 457 ZN ZN A 503 1555 1555 2.33 LINK NE2 HIS A 461 ZN ZN A 503 1555 1555 2.05 CISPEP 1 SER A 246 PRO A 247 0 -3.55 CRYST1 77.976 47.747 127.859 90.00 105.38 90.00 I 1 2 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 0.012824 0.000000 0.003528 0.00000 SCALE2 0.000000 0.020944 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008112 0.00000