HEADER CYTOSOLIC PROTEIN 02-JUN-18 6DLP
TITLE CRYSTAL STRUCTURE OF LRRK2 WD40 DOMAIN DIMER
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LEUCINE-RICH REPEAT SERINE/THREONINE-PROTEIN KINASE 2;
COMPND 3 CHAIN: B, A;
COMPND 4 FRAGMENT: WD40 DOMAIN RESIDUES 2142-2527;
COMPND 5 SYNONYM: DARDARIN;
COMPND 6 EC: 2.7.11.1;
COMPND 7 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: LRRK2, PARK8;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108
KEYWDS PARKINSON'S DISEASE, LRRK2, WD40, CYTOSOLIC PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.ZHANG,H.RU,L.WANG,H.WU
REVDAT 4 13-MAR-24 6DLP 1 REMARK
REVDAT 3 13-FEB-19 6DLP 1 JRNL
REVDAT 2 23-JAN-19 6DLP 1 JRNL
REVDAT 1 09-JAN-19 6DLP 0
JRNL AUTH P.ZHANG,Y.FAN,H.RU,L.WANG,V.G.MAGUPALLI,S.S.TAYLOR,
JRNL AUTH 2 D.R.ALESSI,H.WU
JRNL TITL CRYSTAL STRUCTURE OF THE WD40 DOMAIN DIMER OF LRRK2.
JRNL REF PROC. NATL. ACAD. SCI. V. 116 1579 2019
JRNL REF 2 U.S.A.
JRNL REFN ESSN 1091-6490
JRNL PMID 30635421
JRNL DOI 10.1073/PNAS.1817889116
REMARK 2
REMARK 2 RESOLUTION. 4.00 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) : 4.00
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 76.26
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.580
REMARK 3 COMPLETENESS FOR RANGE (%) : 96.7
REMARK 3 NUMBER OF REFLECTIONS : 7975
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.230
REMARK 3 R VALUE (WORKING SET) : 0.228
REMARK 3 FREE R VALUE : 0.263
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870
REMARK 3 FREE R VALUE TEST SET COUNT : 388
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 76.2694 - 5.7687 0.99 2675 138 0.2454 0.3298
REMARK 3 2 5.7687 - 4.5789 0.97 2525 133 0.2057 0.2120
REMARK 3 3 4.5789 - 4.0002 0.94 2387 117 0.2304 0.2401
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) : 0.400
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.580
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 : 0.002 4891
REMARK 3 ANGLE : 0.537 6604
REMARK 3 CHIRALITY : 0.045 806
REMARK 3 PLANARITY : 0.003 803
REMARK 3 DIHEDRAL : 6.802 2923
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): 3.3759 -0.0916 11.0459
REMARK 3 T TENSOR
REMARK 3 T11: 0.2884 T22: 0.3195
REMARK 3 T33: 0.2429 T12: -0.1030
REMARK 3 T13: 0.0755 T23: -0.2020
REMARK 3 L TENSOR
REMARK 3 L11: 0.9536 L22: 0.8447
REMARK 3 L33: 0.4124 L12: 0.6854
REMARK 3 L13: 0.4740 L23: 0.3790
REMARK 3 S TENSOR
REMARK 3 S11: -0.1535 S12: 0.5476 S13: -0.0251
REMARK 3 S21: -0.2244 S22: 0.1939 S23: -0.2332
REMARK 3 S31: -0.0927 S32: 0.2158 S33: -0.1229
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 6DLP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-18.
REMARK 100 THE DEPOSITION ID IS D_1000234881.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 20-JUL-16
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 : APS
REMARK 200 BEAMLINE : 24-ID-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.89260
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12211
REMARK 200 RESOLUTION RANGE HIGH (A) : 3.450
REMARK 200 RESOLUTION RANGE LOW (A) : 112.660
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 95.8
REMARK 200 DATA REDUNDANCY : 6.100
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.6000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.45
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.78
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 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: AUTOSOL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.57
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL AT PH 8.5, 1 M LICL,
REMARK 280 16% POLYETHYLENE GLYCOL (PEG) 6000, AND 10% ADDITIVE OF 30%
REMARK 280 GALACTOSE. THE CRYSTAL WAS SOAKED IN 1 MM TRANS-PLATINUM (II)
REMARK 280 DIAMMINE DICHLORIDE FOR 1.5 HOURS, VAPOR DIFFUSION, SITTING DROP,
REMARK 280 TEMPERATURE 289K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 39.64650
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.33200
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.79500
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.33200
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.64650
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.79500
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 26900 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY B 2139
REMARK 465 GLY B 2140
REMARK 465 HIS B 2160
REMARK 465 ASN B 2161
REMARK 465 SER B 2162
REMARK 465 ARG B 2163
REMARK 465 ASN B 2164
REMARK 465 SER B 2252
REMARK 465 PHE B 2253
REMARK 465 SER B 2254
REMARK 465 LYS B 2255
REMARK 465 GLN B 2256
REMARK 465 SER B 2257
REMARK 465 LYS B 2258
REMARK 465 GLN B 2259
REMARK 465 GLU B 2305
REMARK 465 SER B 2306
REMARK 465 THR B 2307
REMARK 465 ASN B 2308
REMARK 465 SER B 2309
REMARK 465 THR B 2310
REMARK 465 GLU B 2311
REMARK 465 ARG B 2312
REMARK 465 ASN B 2313
REMARK 465 VAL B 2396
REMARK 465 MET B 2397
REMARK 465 VAL B 2398
REMARK 465 LYS B 2399
REMARK 465 GLU B 2400
REMARK 465 ASN B 2401
REMARK 465 LYS B 2402
REMARK 465 GLU B 2403
REMARK 465 SER B 2404
REMARK 465 LYS B 2405
REMARK 465 HIS B 2406
REMARK 465 LYS B 2407
REMARK 465 LYS B 2421
REMARK 465 ASN B 2422
REMARK 465 THR B 2423
REMARK 465 ARG B 2477
REMARK 465 LYS B 2478
REMARK 465 ASN B 2479
REMARK 465 THR B 2480
REMARK 465 GLU B 2481
REMARK 465 GLY B 2482
REMARK 465 THR B 2483
REMARK 465 GLN B 2484
REMARK 465 LYS B 2485
REMARK 465 GLN B 2486
REMARK 465 LYS B 2487
REMARK 465 ASN B 2499
REMARK 465 LEU B 2500
REMARK 465 PRO B 2501
REMARK 465 HIS B 2502
REMARK 465 GLU B 2503
REMARK 465 VAL B 2504
REMARK 465 GLN B 2505
REMARK 465 ASN B 2506
REMARK 465 LEU B 2507
REMARK 465 GLU B 2508
REMARK 465 LYS B 2509
REMARK 465 HIS B 2510
REMARK 465 ILE B 2511
REMARK 465 GLU B 2512
REMARK 465 VAL B 2513
REMARK 465 ARG B 2514
REMARK 465 LYS B 2515
REMARK 465 GLU B 2516
REMARK 465 LEU B 2517
REMARK 465 ALA B 2518
REMARK 465 GLU B 2519
REMARK 465 LYS B 2520
REMARK 465 MET B 2521
REMARK 465 ARG B 2522
REMARK 465 ARG B 2523
REMARK 465 THR B 2524
REMARK 465 SER B 2525
REMARK 465 VAL B 2526
REMARK 465 GLU B 2527
REMARK 465 GLY A 2139
REMARK 465 GLY A 2140
REMARK 465 HIS A 2159
REMARK 465 HIS A 2160
REMARK 465 ASN A 2161
REMARK 465 SER A 2162
REMARK 465 ARG A 2163
REMARK 465 SER A 2254
REMARK 465 LYS A 2255
REMARK 465 GLN A 2256
REMARK 465 SER A 2257
REMARK 465 LYS A 2258
REMARK 465 SER A 2306
REMARK 465 THR A 2307
REMARK 465 ASN A 2308
REMARK 465 SER A 2309
REMARK 465 THR A 2310
REMARK 465 GLU A 2311
REMARK 465 ARG A 2312
REMARK 465 ASN A 2313
REMARK 465 VAL A 2396
REMARK 465 MET A 2397
REMARK 465 VAL A 2398
REMARK 465 LYS A 2399
REMARK 465 GLU A 2400
REMARK 465 ASN A 2401
REMARK 465 LYS A 2402
REMARK 465 GLU A 2403
REMARK 465 SER A 2404
REMARK 465 LYS A 2405
REMARK 465 HIS A 2406
REMARK 465 LYS A 2407
REMARK 465 LEU A 2463
REMARK 465 GLY A 2464
REMARK 465 SER A 2465
REMARK 465 LEU A 2466
REMARK 465 LYS A 2467
REMARK 465 LYS A 2478
REMARK 465 ASN A 2479
REMARK 465 THR A 2480
REMARK 465 GLU A 2481
REMARK 465 GLY A 2482
REMARK 465 THR A 2483
REMARK 465 GLN A 2484
REMARK 465 LYS A 2485
REMARK 465 GLN A 2486
REMARK 465 LYS A 2487
REMARK 465 ASP A 2497
REMARK 465 ILE A 2498
REMARK 465 ASN A 2499
REMARK 465 LEU A 2500
REMARK 465 PRO A 2501
REMARK 465 HIS A 2502
REMARK 465 GLU A 2503
REMARK 465 VAL A 2504
REMARK 465 GLN A 2505
REMARK 465 ASN A 2506
REMARK 465 LEU A 2507
REMARK 465 GLU A 2508
REMARK 465 LYS A 2509
REMARK 465 HIS A 2510
REMARK 465 ILE A 2511
REMARK 465 GLU A 2512
REMARK 465 VAL A 2513
REMARK 465 ARG A 2514
REMARK 465 LYS A 2515
REMARK 465 GLU A 2516
REMARK 465 LEU A 2517
REMARK 465 ALA A 2518
REMARK 465 GLU A 2519
REMARK 465 LYS A 2520
REMARK 465 MET A 2521
REMARK 465 ARG A 2522
REMARK 465 ARG A 2523
REMARK 465 THR A 2524
REMARK 465 SER A 2525
REMARK 465 VAL A 2526
REMARK 465 GLU A 2527
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 GLU B2210 -9.56 72.98
REMARK 500 ASP B2329 -1.82 75.70
REMARK 500 SER B2345 -16.96 74.38
REMARK 500 TYR B2346 151.11 177.33
REMARK 500 ASP B2351 54.10 -92.18
REMARK 500 THR B2361 -36.85 -131.28
REMARK 500 SER B2454 119.33 -161.09
REMARK 500 GLU A2210 -9.02 73.06
REMARK 500 ASP A2351 53.79 -91.40
REMARK 500 ASN A2422 -36.56 -132.26
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 ARG A2142 0.26 SIDE CHAIN
REMARK 500 ARG A2143 0.15 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PT B 2601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PT B 2602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PT B 2603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 2601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 2602
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PT A 2603
DBREF 6DLP B 2142 2527 UNP Q5S007 LRRK2_HUMAN 2142 2527
DBREF 6DLP A 2142 2527 UNP Q5S007 LRRK2_HUMAN 2142 2527
SEQADV 6DLP GLY B 2139 UNP Q5S007 EXPRESSION TAG
SEQADV 6DLP GLY B 2140 UNP Q5S007 EXPRESSION TAG
SEQADV 6DLP SER B 2141 UNP Q5S007 EXPRESSION TAG
SEQADV 6DLP GLY A 2139 UNP Q5S007 EXPRESSION TAG
SEQADV 6DLP GLY A 2140 UNP Q5S007 EXPRESSION TAG
SEQADV 6DLP SER A 2141 UNP Q5S007 EXPRESSION TAG
SEQRES 1 B 389 GLY GLY SER ARG ARG ILE LEU LEU PRO LYS ASN VAL ILE
SEQRES 2 B 389 VAL GLU CYS MET VAL ALA THR HIS HIS ASN SER ARG ASN
SEQRES 3 B 389 ALA SER ILE TRP LEU GLY CYS GLY HIS THR ASP ARG GLY
SEQRES 4 B 389 GLN LEU SER PHE LEU ASP LEU ASN THR GLU GLY TYR THR
SEQRES 5 B 389 SER GLU GLU VAL ALA ASP SER ARG ILE LEU CYS LEU ALA
SEQRES 6 B 389 LEU VAL HIS LEU PRO VAL GLU LYS GLU SER TRP ILE VAL
SEQRES 7 B 389 SER GLY THR GLN SER GLY THR LEU LEU VAL ILE ASN THR
SEQRES 8 B 389 GLU ASP GLY LYS LYS ARG HIS THR LEU GLU LYS MET THR
SEQRES 9 B 389 ASP SER VAL THR CYS LEU TYR CYS ASN SER PHE SER LYS
SEQRES 10 B 389 GLN SER LYS GLN LYS ASN PHE LEU LEU VAL GLY THR ALA
SEQRES 11 B 389 ASP GLY LYS LEU ALA ILE PHE GLU ASP LYS THR VAL LYS
SEQRES 12 B 389 LEU LYS GLY ALA ALA PRO LEU LYS ILE LEU ASN ILE GLY
SEQRES 13 B 389 ASN VAL SER THR PRO LEU MET CYS LEU SER GLU SER THR
SEQRES 14 B 389 ASN SER THR GLU ARG ASN VAL MET TRP GLY GLY CYS GLY
SEQRES 15 B 389 THR LYS ILE PHE SER PHE SER ASN ASP PHE THR ILE GLN
SEQRES 16 B 389 LYS LEU ILE GLU THR ARG THR SER GLN LEU PHE SER TYR
SEQRES 17 B 389 ALA ALA PHE SER ASP SER ASN ILE ILE THR VAL VAL VAL
SEQRES 18 B 389 ASP THR ALA LEU TYR ILE ALA LYS GLN ASN SER PRO VAL
SEQRES 19 B 389 VAL GLU VAL TRP ASP LYS LYS THR GLU LYS LEU CYS GLY
SEQRES 20 B 389 LEU ILE ASP CYS VAL HIS PHE LEU ARG GLU VAL MET VAL
SEQRES 21 B 389 LYS GLU ASN LYS GLU SER LYS HIS LYS MET SER TYR SER
SEQRES 22 B 389 GLY ARG VAL LYS THR LEU CYS LEU GLN LYS ASN THR ALA
SEQRES 23 B 389 LEU TRP ILE GLY THR GLY GLY GLY HIS ILE LEU LEU LEU
SEQRES 24 B 389 ASP LEU SER THR ARG ARG LEU ILE ARG VAL ILE TYR ASN
SEQRES 25 B 389 PHE CYS ASN SER VAL ARG VAL MET MET THR ALA GLN LEU
SEQRES 26 B 389 GLY SER LEU LYS ASN VAL MET LEU VAL LEU GLY TYR ASN
SEQRES 27 B 389 ARG LYS ASN THR GLU GLY THR GLN LYS GLN LYS GLU ILE
SEQRES 28 B 389 GLN SER CYS LEU THR VAL TRP ASP ILE ASN LEU PRO HIS
SEQRES 29 B 389 GLU VAL GLN ASN LEU GLU LYS HIS ILE GLU VAL ARG LYS
SEQRES 30 B 389 GLU LEU ALA GLU LYS MET ARG ARG THR SER VAL GLU
SEQRES 1 A 389 GLY GLY SER ARG ARG ILE LEU LEU PRO LYS ASN VAL ILE
SEQRES 2 A 389 VAL GLU CYS MET VAL ALA THR HIS HIS ASN SER ARG ASN
SEQRES 3 A 389 ALA SER ILE TRP LEU GLY CYS GLY HIS THR ASP ARG GLY
SEQRES 4 A 389 GLN LEU SER PHE LEU ASP LEU ASN THR GLU GLY TYR THR
SEQRES 5 A 389 SER GLU GLU VAL ALA ASP SER ARG ILE LEU CYS LEU ALA
SEQRES 6 A 389 LEU VAL HIS LEU PRO VAL GLU LYS GLU SER TRP ILE VAL
SEQRES 7 A 389 SER GLY THR GLN SER GLY THR LEU LEU VAL ILE ASN THR
SEQRES 8 A 389 GLU ASP GLY LYS LYS ARG HIS THR LEU GLU LYS MET THR
SEQRES 9 A 389 ASP SER VAL THR CYS LEU TYR CYS ASN SER PHE SER LYS
SEQRES 10 A 389 GLN SER LYS GLN LYS ASN PHE LEU LEU VAL GLY THR ALA
SEQRES 11 A 389 ASP GLY LYS LEU ALA ILE PHE GLU ASP LYS THR VAL LYS
SEQRES 12 A 389 LEU LYS GLY ALA ALA PRO LEU LYS ILE LEU ASN ILE GLY
SEQRES 13 A 389 ASN VAL SER THR PRO LEU MET CYS LEU SER GLU SER THR
SEQRES 14 A 389 ASN SER THR GLU ARG ASN VAL MET TRP GLY GLY CYS GLY
SEQRES 15 A 389 THR LYS ILE PHE SER PHE SER ASN ASP PHE THR ILE GLN
SEQRES 16 A 389 LYS LEU ILE GLU THR ARG THR SER GLN LEU PHE SER TYR
SEQRES 17 A 389 ALA ALA PHE SER ASP SER ASN ILE ILE THR VAL VAL VAL
SEQRES 18 A 389 ASP THR ALA LEU TYR ILE ALA LYS GLN ASN SER PRO VAL
SEQRES 19 A 389 VAL GLU VAL TRP ASP LYS LYS THR GLU LYS LEU CYS GLY
SEQRES 20 A 389 LEU ILE ASP CYS VAL HIS PHE LEU ARG GLU VAL MET VAL
SEQRES 21 A 389 LYS GLU ASN LYS GLU SER LYS HIS LYS MET SER TYR SER
SEQRES 22 A 389 GLY ARG VAL LYS THR LEU CYS LEU GLN LYS ASN THR ALA
SEQRES 23 A 389 LEU TRP ILE GLY THR GLY GLY GLY HIS ILE LEU LEU LEU
SEQRES 24 A 389 ASP LEU SER THR ARG ARG LEU ILE ARG VAL ILE TYR ASN
SEQRES 25 A 389 PHE CYS ASN SER VAL ARG VAL MET MET THR ALA GLN LEU
SEQRES 26 A 389 GLY SER LEU LYS ASN VAL MET LEU VAL LEU GLY TYR ASN
SEQRES 27 A 389 ARG LYS ASN THR GLU GLY THR GLN LYS GLN LYS GLU ILE
SEQRES 28 A 389 GLN SER CYS LEU THR VAL TRP ASP ILE ASN LEU PRO HIS
SEQRES 29 A 389 GLU VAL GLN ASN LEU GLU LYS HIS ILE GLU VAL ARG LYS
SEQRES 30 A 389 GLU LEU ALA GLU LYS MET ARG ARG THR SER VAL GLU
HET PT B2601 1
HET PT B2602 1
HET PT B2603 1
HET PT A2601 1
HET PT A2602 1
HET PT A2603 1
HETNAM PT PLATINUM (II) ION
FORMUL 3 PT 6(PT 2+)
HELIX 1 AA1 LYS B 2278 LEU B 2282 5 5
HELIX 2 AA2 ARG B 2339 PHE B 2344 5 6
HELIX 3 AA3 CYS B 2389 ARG B 2394 1 6
HELIX 4 AA4 LYS A 2278 LEU A 2282 5 5
HELIX 5 AA5 TYR A 2346 ASP A 2351 1 6
HELIX 6 AA6 CYS A 2389 ARG A 2394 1 6
SHEET 1 AA1 4 ARG B2142 LEU B2145 0
SHEET 2 AA1 4 SER B2491 ASP B2497 -1 O LEU B2493 N ILE B2144
SHEET 3 AA1 4 ASN B2468 TYR B2475 -1 N MET B2470 O TRP B2496
SHEET 4 AA1 4 SER B2454 GLN B2462 -1 N MET B2459 O LEU B2471
SHEET 1 AA2 4 VAL B2152 THR B2158 0
SHEET 2 AA2 4 SER B2166 CYS B2171 -1 O TRP B2168 N VAL B2156
SHEET 3 AA2 4 GLY B2177 ASP B2183 -1 O SER B2180 N LEU B2169
SHEET 4 AA2 4 TYR B2189 ALA B2195 -1 O THR B2190 N PHE B2181
SHEET 1 AA3 4 ILE B2199 LEU B2207 0
SHEET 2 AA3 4 GLU B2212 THR B2219 -1 O VAL B2216 N ALA B2203
SHEET 3 AA3 4 LEU B2224 ASN B2228 -1 O ILE B2227 N ILE B2215
SHEET 4 AA3 4 ARG B2235 THR B2237 -1 O HIS B2236 N VAL B2226
SHEET 1 AA4 4 VAL B2245 ASN B2251 0
SHEET 2 AA4 4 PHE B2262 THR B2267 -1 O LEU B2264 N TYR B2249
SHEET 3 AA4 4 LYS B2271 GLU B2276 -1 O LYS B2271 N THR B2267
SHEET 4 AA4 4 LYS B2289 ASN B2292 -1 O LEU B2291 N LEU B2272
SHEET 1 AA5 4 LEU B2300 SER B2304 0
SHEET 2 AA5 4 MET B2315 CYS B2319 -1 O TRP B2316 N SER B2304
SHEET 3 AA5 4 LYS B2322 PHE B2326 -1 O LYS B2322 N CYS B2319
SHEET 4 AA5 4 LEU B2335 GLU B2337 -1 O ILE B2336 N ILE B2323
SHEET 1 AA6 4 ILE B2354 VAL B2359 0
SHEET 2 AA6 4 LEU B2363 LYS B2367 -1 O ALA B2366 N ILE B2355
SHEET 3 AA6 4 VAL B2372 TRP B2376 -1 O TRP B2376 N LEU B2363
SHEET 4 AA6 4 LEU B2383 ASP B2388 -1 O CYS B2384 N VAL B2375
SHEET 1 AA7 4 VAL B2414 CYS B2418 0
SHEET 2 AA7 4 LEU B2425 THR B2429 -1 O TRP B2426 N CYS B2418
SHEET 3 AA7 4 ILE B2434 LEU B2437 -1 O LEU B2435 N ILE B2427
SHEET 4 AA7 4 LEU B2444 ILE B2448 -1 O ILE B2448 N ILE B2434
SHEET 1 AA8 4 ARG A2142 LEU A2145 0
SHEET 2 AA8 4 GLN A2490 TRP A2496 -1 O LEU A2493 N ILE A2144
SHEET 3 AA8 4 VAL A2469 ASN A2476 -1 N VAL A2472 O THR A2494
SHEET 4 AA8 4 VAL A2455 ALA A2461 -1 N MET A2459 O LEU A2471
SHEET 1 AA9 4 VAL A2152 THR A2158 0
SHEET 2 AA9 4 SER A2166 CYS A2171 -1 O TRP A2168 N VAL A2156
SHEET 3 AA9 4 GLY A2177 ASP A2183 -1 O SER A2180 N LEU A2169
SHEET 4 AA9 4 GLY A2188 ALA A2195 -1 O THR A2190 N PHE A2181
SHEET 1 AB1 4 ILE A2199 LEU A2207 0
SHEET 2 AB1 4 GLU A2212 THR A2219 -1 O VAL A2216 N ALA A2203
SHEET 3 AB1 4 LEU A2224 ASN A2228 -1 O ILE A2227 N ILE A2215
SHEET 4 AB1 4 ARG A2235 THR A2237 -1 O HIS A2236 N VAL A2226
SHEET 1 AB2 4 VAL A2245 SER A2252 0
SHEET 2 AB2 4 ASN A2261 THR A2267 -1 O PHE A2262 N ASN A2251
SHEET 3 AB2 4 LYS A2271 GLU A2276 -1 O LYS A2271 N THR A2267
SHEET 4 AB2 4 LYS A2289 ASN A2292 -1 O LEU A2291 N LEU A2272
SHEET 1 AB3 4 LEU A2300 SER A2304 0
SHEET 2 AB3 4 MET A2315 CYS A2319 -1 O TRP A2316 N SER A2304
SHEET 3 AB3 4 LYS A2322 PHE A2326 -1 O PHE A2326 N MET A2315
SHEET 4 AB3 4 ILE A2332 GLU A2337 -1 O ILE A2336 N ILE A2323
SHEET 1 AB4 4 ILE A2354 VAL A2359 0
SHEET 2 AB4 4 LEU A2363 LYS A2367 -1 O ALA A2366 N ILE A2355
SHEET 3 AB4 4 VAL A2372 TRP A2376 -1 O TRP A2376 N LEU A2363
SHEET 4 AB4 4 LEU A2383 ASP A2388 -1 O CYS A2384 N VAL A2375
SHEET 1 AB5 4 VAL A2414 LEU A2419 0
SHEET 2 AB5 4 ALA A2424 THR A2429 -1 O TRP A2426 N CYS A2418
SHEET 3 AB5 4 ILE A2434 ASP A2438 -1 O LEU A2435 N ILE A2427
SHEET 4 AB5 4 LEU A2444 ILE A2448 -1 O ILE A2448 N ILE A2434
LINK SG CYS B2201 PT PT B2601 1555 1555 2.56
LINK SG CYS B2302 PT PT B2602 1555 1555 2.12
LINK SG CYS B2418 PT PT B2603 1555 1555 2.53
LINK SG CYS A2201 PT PT A2603 1555 1555 2.59
LINK SG CYS A2302 PT PT A2602 1555 1555 2.13
LINK SG CYS A2418 PT PT A2601 1555 1555 2.77
SITE 1 AC1 2 CYS B2154 CYS B2201
SITE 1 AC2 2 CYS B2302 LEU B2303
SITE 1 AC3 1 CYS B2418
SITE 1 AC4 1 CYS A2418
SITE 1 AC5 1 CYS A2302
SITE 1 AC6 2 CYS A2154 CYS A2201
CRYST1 79.293 103.590 112.664 90.00 90.00 90.00 P 21 21 21 8
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 0.012611 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009653 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008876 0.00000
(ATOM LINES ARE NOT SHOWN.)
END