HEADER PROTEIN BINDING 26-AUG-23 8TZG TITLE STRUCTURE OF C-TERMINAL LRRK2 BOUND TO MLI-2 (I2020T MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-RICH REPEAT SERINE/THREONINE-PROTEIN KINASE 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DARDARIN; COMPND 5 EC: 2.7.11.1,3.6.5.-; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: SEVERAL LOOPS ARE MISSING AT THE STRUCTURE DUE TO THE COMPND 8 LACK OF DENSITY 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; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS GTPASE, KINASE, INHIBITORS, PROTEIN BINDING EXPDTA ELECTRON MICROSCOPY AUTHOR M.SANZ-MURILLO,A.VILLAGRAN-SUAREZ,J.ALEGRIO LOURO,A.LESCHZINER REVDAT 2 13-DEC-23 8TZG 1 JRNL REVDAT 1 06-DEC-23 8TZG 0 JRNL AUTH M.SANZ MURILLO,A.VILLAGRAN SUAREZ,V.DEDERER,D.CHATTERJEE, JRNL AUTH 2 J.ALEGRIO LOURO,S.KNAPP,S.MATHEA,A.E.LESCHZINER JRNL TITL INHIBITION OF PARKINSON'S DISEASE-RELATED LRRK2 BY TYPE I JRNL TITL 2 AND TYPE II KINASE INHIBITORS: ACTIVITY AND STRUCTURES. JRNL REF SCI ADV V. 9 K6191 2023 JRNL REFN ESSN 2375-2548 JRNL PMID 38039358 JRNL DOI 10.1126/SCIADV.ADK6191 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : TOPAZ, CRYOSPARC, CTFFIND, UCSF REMARK 3 CHIMERAX, PHENIX, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 6VP7 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 2.700 REMARK 3 NUMBER OF PARTICLES : 380487 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8TZG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1000276910. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : C-TERMINAL LRRK2 (I2020T REMARK 245 MUTATION) BOUND TO MLI-2 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 0.82 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : BLOT FORCE = 3 BLOT TIME = 4 REMARK 245 SECONDS WAIT TIME = 20 SECONDS REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 10050 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : FEI FALCON IV (4K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 4000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5500.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 130000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 LEU A 1354 REMARK 465 MET A 1355 REMARK 465 LYS A 1356 REMARK 465 THR A 1357 REMARK 465 LYS A 1358 REMARK 465 LYS A 1359 REMARK 465 SER A 1360 REMARK 465 ASP A 1361 REMARK 465 LEU A 1362 REMARK 465 GLY A 1363 REMARK 465 MET A 1364 REMARK 465 GLN A 1365 REMARK 465 SER A 1366 REMARK 465 ALA A 1367 REMARK 465 ILE A 1378 REMARK 465 GLN A 1379 REMARK 465 ILE A 1380 REMARK 465 ARG A 1381 REMARK 465 ASP A 1382 REMARK 465 LYS A 1383 REMARK 465 ARG A 1384 REMARK 465 LYS A 1385 REMARK 465 ARG A 1386 REMARK 465 ASP A 1387 REMARK 465 GLY A 1397 REMARK 465 TYR A 1419 REMARK 465 ASP A 1420 REMARK 465 LEU A 1421 REMARK 465 SER A 1422 REMARK 465 LYS A 1423 REMARK 465 GLY A 1424 REMARK 465 GLN A 1425 REMARK 465 ALA A 1426 REMARK 465 GLU A 1427 REMARK 465 VAL A 1428 REMARK 465 ASP A 1429 REMARK 465 HIS A 1453 REMARK 465 LEU A 1454 REMARK 465 ASP A 1455 REMARK 465 VAL A 1456 REMARK 465 SER A 1457 REMARK 465 ASP A 1458 REMARK 465 GLU A 1459 REMARK 465 LYS A 1460 REMARK 465 GLN A 1461 REMARK 465 ARG A 1462 REMARK 465 LYS A 1463 REMARK 465 ALA A 1464 REMARK 465 CYS A 1465 REMARK 465 MET A 1466 REMARK 465 SER A 1467 REMARK 465 LYS A 1468 REMARK 465 ILE A 1469 REMARK 465 THR A 1470 REMARK 465 LYS A 1471 REMARK 465 GLU A 1472 REMARK 465 LEU A 1473 REMARK 465 LEU A 1474 REMARK 465 ASN A 1475 REMARK 465 LYS A 1476 REMARK 465 ARG A 1477 REMARK 465 GLY A 1478 REMARK 465 PHE A 1479 REMARK 465 PRO A 1480 REMARK 465 ASN A 1489 REMARK 465 ALA A 1490 REMARK 465 THR A 1491 REMARK 465 GLU A 1492 REMARK 465 GLU A 1493 REMARK 465 SER A 1494 REMARK 465 ASP A 1495 REMARK 465 ALA A 1496 REMARK 465 GLN A 1516 REMARK 465 LEU A 1517 REMARK 465 VAL A 1518 REMARK 465 VAL A 1519 REMARK 465 GLY A 1520 REMARK 465 GLN A 1521 REMARK 465 LEU A 1522 REMARK 465 ILE A 1523 REMARK 465 PRO A 1524 REMARK 465 ASP A 1525 REMARK 465 CYS A 1526 REMARK 465 TYR A 1527 REMARK 465 GLU A 1559 REMARK 465 ASN A 1560 REMARK 465 GLN A 1561 REMARK 465 LEU A 1562 REMARK 465 GLN A 1563 REMARK 465 LEU A 1564 REMARK 465 ASP A 1565 REMARK 465 GLU A 1566 REMARK 465 THR A 1612 REMARK 465 VAL A 1613 REMARK 465 LYS A 1614 REMARK 465 VAL A 1615 REMARK 465 GLU A 1616 REMARK 465 GLY A 1617 REMARK 465 CYS A 1618 REMARK 465 PRO A 1619 REMARK 465 LYS A 1620 REMARK 465 HIS A 1621 REMARK 465 PRO A 1622 REMARK 465 LEU A 1635 REMARK 465 SER A 1636 REMARK 465 LYS A 1637 REMARK 465 LYS A 1638 REMARK 465 ARG A 1639 REMARK 465 LYS A 1640 REMARK 465 PHE A 1641 REMARK 465 PRO A 1642 REMARK 465 LYS A 1643 REMARK 465 ASN A 1644 REMARK 465 TYR A 1645 REMARK 465 ARG A 1723 REMARK 465 GLU A 1724 REMARK 465 ARG A 1725 REMARK 465 LEU A 1755 REMARK 465 ASP A 1756 REMARK 465 ASN A 1757 REMARK 465 HIS A 1758 REMARK 465 PRO A 1759 REMARK 465 GLU A 1797 REMARK 465 ILE A 1798 REMARK 465 ASP A 1799 REMARK 465 ILE A 1800 REMARK 465 CYS A 1801 REMARK 465 GLY A 1802 REMARK 465 GLU A 1803 REMARK 465 GLY A 1804 REMARK 465 GLU A 1805 REMARK 465 PRO A 1843 REMARK 465 ASP A 1844 REMARK 465 GLN A 1845 REMARK 465 PRO A 1846 REMARK 465 ARG A 1847 REMARK 465 LEU A 1848 REMARK 465 THR A 1849 REMARK 465 ILE A 2088 REMARK 465 GLN A 2089 REMARK 465 ARG A 2142 REMARK 465 THR A 2158 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 ASN A 2164 REMARK 465 ALA A 2165 REMARK 465 GLY A 2172 REMARK 465 HIS A 2173 REMARK 465 THR A 2174 REMARK 465 ASP A 2175 REMARK 465 ARG A 2176 REMARK 465 GLY A 2177 REMARK 465 ASP A 2183 REMARK 465 LEU A 2184 REMARK 465 ASN A 2185 REMARK 465 THR A 2186 REMARK 465 GLU A 2187 REMARK 465 GLY A 2188 REMARK 465 TYR A 2189 REMARK 465 THR A 2190 REMARK 465 SER A 2191 REMARK 465 GLU A 2192 REMARK 465 GLU A 2193 REMARK 465 VAL A 2194 REMARK 465 ALA A 2195 REMARK 465 ASP A 2196 REMARK 465 SER A 2197 REMARK 465 ARG A 2198 REMARK 465 LEU A 2207 REMARK 465 PRO A 2208 REMARK 465 VAL A 2209 REMARK 465 GLU A 2210 REMARK 465 LYS A 2211 REMARK 465 GLU A 2212 REMARK 465 SER A 2213 REMARK 465 TRP A 2214 REMARK 465 THR A 2219 REMARK 465 GLN A 2220 REMARK 465 SER A 2221 REMARK 465 GLY A 2222 REMARK 465 THR A 2223 REMARK 465 LEU A 2224 REMARK 465 LEU A 2225 REMARK 465 VAL A 2226 REMARK 465 ILE A 2227 REMARK 465 ASN A 2228 REMARK 465 THR A 2229 REMARK 465 GLU A 2230 REMARK 465 ASP A 2231 REMARK 465 GLY A 2232 REMARK 465 LYS A 2233 REMARK 465 LYS A 2234 REMARK 465 ARG A 2235 REMARK 465 HIS A 2236 REMARK 465 THR A 2237 REMARK 465 LEU A 2238 REMARK 465 GLU A 2239 REMARK 465 LYS A 2240 REMARK 465 MET A 2241 REMARK 465 THR A 2242 REMARK 465 ASP A 2243 REMARK 465 SER A 2244 REMARK 465 VAL A 2245 REMARK 465 ASN A 2251 REMARK 465 SER A 2252 REMARK 465 PHE A 2253 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 GLN A 2259 REMARK 465 LYS A 2260 REMARK 465 ASN A 2261 REMARK 465 PHE A 2262 REMARK 465 ALA A 2268 REMARK 465 ASP A 2269 REMARK 465 PHE A 2275 REMARK 465 GLU A 2276 REMARK 465 ASP A 2277 REMARK 465 LYS A 2278 REMARK 465 THR A 2279 REMARK 465 VAL A 2280 REMARK 465 LYS A 2281 REMARK 465 LEU A 2282 REMARK 465 LYS A 2283 REMARK 465 GLY A 2284 REMARK 465 ALA A 2285 REMARK 465 ALA A 2286 REMARK 465 PRO A 2287 REMARK 465 LEU A 2288 REMARK 465 LYS A 2289 REMARK 465 ILE A 2290 REMARK 465 LEU A 2291 REMARK 465 ASN A 2292 REMARK 465 ILE A 2293 REMARK 465 GLY A 2294 REMARK 465 ASN A 2295 REMARK 465 VAL A 2296 REMARK 465 SER A 2297 REMARK 465 THR A 2298 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 ASN A 2328 REMARK 465 ASP A 2329 REMARK 465 PHE A 2330 REMARK 465 THR A 2331 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 MET A 2408 REMARK 465 SER A 2409 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 GLU A 2488 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 ASN A1333 CG OD1 ND2 REMARK 470 ASN A1342 CG OD1 ND2 REMARK 470 ARG A1398 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1399 CG CD OE1 OE2 REMARK 470 LYS A1432 CG CD CE NZ REMARK 470 TYR A1485 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS A1486 CG ND1 CD2 CE1 NE2 REMARK 470 PHE A1487 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A1497 CG CD1 CD2 REMARK 470 LYS A1499 CG CD CE NZ REMARK 470 LEU A1500 CG CD1 CD2 REMARK 470 ARG A1501 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1502 CG CD CE NZ REMARK 470 ASN A1506 CG OD1 ND2 REMARK 470 GLU A1507 CG CD OE1 OE2 REMARK 470 LEU A1509 CG CD1 CD2 REMARK 470 ASN A1510 CG OD1 ND2 REMARK 470 PHE A1511 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A1512 CG CD CE NZ REMARK 470 ILE A1513 CG1 CG2 CD1 REMARK 470 ARG A1514 CG CD NE CZ NH1 NH2 REMARK 470 ASP A1515 CG OD1 OD2 REMARK 470 GLU A1529 CG CD OE1 OE2 REMARK 470 LEU A1530 CG CD1 CD2 REMARK 470 LYS A1532 CG CD CE NZ REMARK 470 GLU A1537 CG CD OE1 OE2 REMARK 470 ARG A1538 CG CD NE CZ NH1 NH2 REMARK 470 ASN A1540 CG OD1 ND2 REMARK 470 ASP A1549 CG OD1 OD2 REMARK 470 GLN A1555 CG CD OE1 NE2 REMARK 470 VAL A1557 CG1 CG2 REMARK 470 ARG A1558 CG CD NE CZ NH1 NH2 REMARK 470 ASN A1567 CG OD1 ND2 REMARK 470 GLU A1568 CG CD OE1 OE2 REMARK 470 HIS A1571 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A1601 CG CD CE NZ REMARK 470 ARG A1629 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1632 CG CD OE1 OE2 REMARK 470 LYS A1633 CG CD CE NZ REMARK 470 GLN A1648 CG CD OE1 NE2 REMARK 470 LYS A1651 CG CD CE NZ REMARK 470 GLU A1686 CG CD OE1 OE2 REMARK 470 GLU A1760 CG CD OE1 OE2 REMARK 470 ARG A1866 CG CD NE CZ NH1 NH2 REMARK 470 LYS A1910 CG CD CE NZ REMARK 470 HIS A1911 CG ND1 CD2 CE1 NE2 REMARK 470 ARG A1957 CG CD NE CZ NH1 NH2 REMARK 470 ARG A2143 O REMARK 470 LYS A2271 CG CD CE NZ REMARK 470 GLU A2305 CG CD OE1 OE2 REMARK 470 ILE A2332 CG1 CG2 CD1 REMARK 470 LYS A2334 CG CD CE NZ REMARK 470 LYS A2378 CG CD CE NZ REMARK 470 LYS A2379 CG CD CE NZ REMARK 470 ARG A2394 CG CD NE CZ NH1 NH2 REMARK 470 GLU A2395 CG CD OE1 OE2 REMARK 470 TYR A2410 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 TYR A2449 CG CD1 CD2 CE1 CE2 CZ OH 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 LYS A1910 CB - CA - C ANGL. DEV. = -12.7 DEGREES REMARK 500 LYS A1910 N - CA - C ANGL. DEV. = 17.5 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 SER A1345 -7.65 -35.65 REMARK 500 PRO A1406 44.24 -91.37 REMARK 500 HIS A1407 -35.77 -131.48 REMARK 500 THR A1410 -150.64 46.62 REMARK 500 PHE A1545 70.33 57.36 REMARK 500 ALA A1589 46.49 -92.93 REMARK 500 GLU A1599 77.11 49.02 REMARK 500 PRO A1600 4.38 -61.64 REMARK 500 VAL A1669 73.49 52.41 REMARK 500 ARG A1735 -13.80 71.39 REMARK 500 LYS A1910 -45.78 18.91 REMARK 500 HIS A1911 51.06 -110.12 REMARK 500 GLU A1948 169.93 176.49 REMARK 500 ARG A1993 -7.06 70.02 REMARK 500 THR A2069 -118.78 60.16 REMARK 500 ASN A2081 -3.11 62.63 REMARK 500 MET A2106 -8.85 74.32 REMARK 500 SER A2345 171.84 65.09 REMARK 500 ILE A2355 -61.41 -94.64 REMARK 500 PRO A2371 2.48 -67.44 REMARK 500 ARG A2446 149.88 -173.29 REMARK 500 CYS A2452 -167.53 -166.59 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 MG A2603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A1348 OG1 REMARK 620 2 GDP A2602 O1B 99.1 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8TXZ RELATED DB: PDB REMARK 900 RELATED ID: EMD-41758 RELATED DB: EMDB REMARK 900 STRUCTURE OF C-TERMINAL LRRK2 BOUND TO MLI-2 (I2020T MUTANT) DBREF 8TZG A 1333 2522 UNP Q5S007 LRRK2_HUMAN 1333 2522 SEQADV 8TZG THR A 2020 UNP Q5S007 ILE 2020 ENGINEERED MUTATION SEQRES 1 A 1190 ASN ARG MET LYS LEU MET ILE VAL GLY ASN THR GLY SER SEQRES 2 A 1190 GLY LYS THR THR LEU LEU GLN GLN LEU MET LYS THR LYS SEQRES 3 A 1190 LYS SER ASP LEU GLY MET GLN SER ALA THR VAL GLY ILE SEQRES 4 A 1190 ASP VAL LYS ASP TRP PRO ILE GLN ILE ARG ASP LYS ARG SEQRES 5 A 1190 LYS ARG ASP LEU VAL LEU ASN VAL TRP ASP PHE ALA GLY SEQRES 6 A 1190 ARG GLU GLU PHE TYR SER THR HIS PRO HIS PHE MET THR SEQRES 7 A 1190 GLN ARG ALA LEU TYR LEU ALA VAL TYR ASP LEU SER LYS SEQRES 8 A 1190 GLY GLN ALA GLU VAL ASP ALA MET LYS PRO TRP LEU PHE SEQRES 9 A 1190 ASN ILE LYS ALA ARG ALA SER SER SER PRO VAL ILE LEU SEQRES 10 A 1190 VAL GLY THR HIS LEU ASP VAL SER ASP GLU LYS GLN ARG SEQRES 11 A 1190 LYS ALA CYS MET SER LYS ILE THR LYS GLU LEU LEU ASN SEQRES 12 A 1190 LYS ARG GLY PHE PRO ALA ILE ARG ASP TYR HIS PHE VAL SEQRES 13 A 1190 ASN ALA THR GLU GLU SER ASP ALA LEU ALA LYS LEU ARG SEQRES 14 A 1190 LYS THR ILE ILE ASN GLU SER LEU ASN PHE LYS ILE ARG SEQRES 15 A 1190 ASP GLN LEU VAL VAL GLY GLN LEU ILE PRO ASP CYS TYR SEQRES 16 A 1190 VAL GLU LEU GLU LYS ILE ILE LEU SER GLU ARG LYS ASN SEQRES 17 A 1190 VAL PRO ILE GLU PHE PRO VAL ILE ASP ARG LYS ARG LEU SEQRES 18 A 1190 LEU GLN LEU VAL ARG GLU ASN GLN LEU GLN LEU ASP GLU SEQRES 19 A 1190 ASN GLU LEU PRO HIS ALA VAL HIS PHE LEU ASN GLU SER SEQRES 20 A 1190 GLY VAL LEU LEU HIS PHE GLN ASP PRO ALA LEU GLN LEU SEQRES 21 A 1190 SER ASP LEU TYR PHE VAL GLU PRO LYS TRP LEU CYS LYS SEQRES 22 A 1190 ILE MET ALA GLN ILE LEU THR VAL LYS VAL GLU GLY CYS SEQRES 23 A 1190 PRO LYS HIS PRO LYS GLY ILE ILE SER ARG ARG ASP VAL SEQRES 24 A 1190 GLU LYS PHE LEU SER LYS LYS ARG LYS PHE PRO LYS ASN SEQRES 25 A 1190 TYR MET SER GLN TYR PHE LYS LEU LEU GLU LYS PHE GLN SEQRES 26 A 1190 ILE ALA LEU PRO ILE GLY GLU GLU TYR LEU LEU VAL PRO SEQRES 27 A 1190 SER SER LEU SER ASP HIS ARG PRO VAL ILE GLU LEU PRO SEQRES 28 A 1190 HIS CYS GLU ASN SER GLU ILE ILE ILE ARG LEU TYR GLU SEQRES 29 A 1190 MET PRO TYR PHE PRO MET GLY PHE TRP SER ARG LEU ILE SEQRES 30 A 1190 ASN ARG LEU LEU GLU ILE SER PRO TYR MET LEU SER GLY SEQRES 31 A 1190 ARG GLU ARG ALA LEU ARG PRO ASN ARG MET TYR TRP ARG SEQRES 32 A 1190 GLN GLY ILE TYR LEU ASN TRP SER PRO GLU ALA TYR CYS SEQRES 33 A 1190 LEU VAL GLY SER GLU VAL LEU ASP ASN HIS PRO GLU SER SEQRES 34 A 1190 PHE LEU LYS ILE THR VAL PRO SER CYS ARG LYS GLY CYS SEQRES 35 A 1190 ILE LEU LEU GLY GLN VAL VAL ASP HIS ILE ASP SER LEU SEQRES 36 A 1190 MET GLU GLU TRP PHE PRO GLY LEU LEU GLU ILE ASP ILE SEQRES 37 A 1190 CYS GLY GLU GLY GLU THR LEU LEU LYS LYS TRP ALA LEU SEQRES 38 A 1190 TYR SER PHE ASN ASP GLY GLU GLU HIS GLN LYS ILE LEU SEQRES 39 A 1190 LEU ASP ASP LEU MET LYS LYS ALA GLU GLU GLY ASP LEU SEQRES 40 A 1190 LEU VAL ASN PRO ASP GLN PRO ARG LEU THR ILE PRO ILE SEQRES 41 A 1190 SER GLN ILE ALA PRO ASP LEU ILE LEU ALA ASP LEU PRO SEQRES 42 A 1190 ARG ASN ILE MET LEU ASN ASN ASP GLU LEU GLU PHE GLU SEQRES 43 A 1190 GLN ALA PRO GLU PHE LEU LEU GLY ASP GLY SER PHE GLY SEQRES 44 A 1190 SER VAL TYR ARG ALA ALA TYR GLU GLY GLU GLU VAL ALA SEQRES 45 A 1190 VAL LYS ILE PHE ASN LYS HIS THR SER LEU ARG LEU LEU SEQRES 46 A 1190 ARG GLN GLU LEU VAL VAL LEU CYS HIS LEU HIS HIS PRO SEQRES 47 A 1190 SER LEU ILE SER LEU LEU ALA ALA GLY ILE ARG PRO ARG SEQRES 48 A 1190 MET LEU VAL MET GLU LEU ALA SER LYS GLY SER LEU ASP SEQRES 49 A 1190 ARG LEU LEU GLN GLN ASP LYS ALA SER LEU THR ARG THR SEQRES 50 A 1190 LEU GLN HIS ARG ILE ALA LEU HIS VAL ALA ASP GLY LEU SEQRES 51 A 1190 ARG TYR LEU HIS SER ALA MET ILE ILE TYR ARG ASP LEU SEQRES 52 A 1190 LYS PRO HIS ASN VAL LEU LEU PHE THR LEU TYR PRO ASN SEQRES 53 A 1190 ALA ALA ILE ILE ALA LYS ILE ALA ASP TYR GLY THR ALA SEQRES 54 A 1190 GLN TYR CYS CYS ARG MET GLY ILE LYS THR SER GLU GLY SEQRES 55 A 1190 THR PRO GLY PHE ARG ALA PRO GLU VAL ALA ARG GLY ASN SEQRES 56 A 1190 VAL ILE TYR ASN GLN GLN ALA ASP VAL TYR SER PHE GLY SEQRES 57 A 1190 LEU LEU LEU TYR ASP ILE LEU THR THR GLY GLY ARG ILE SEQRES 58 A 1190 VAL GLU GLY LEU LYS PHE PRO ASN GLU PHE ASP GLU LEU SEQRES 59 A 1190 GLU ILE GLN GLY LYS LEU PRO ASP PRO VAL LYS GLU TYR SEQRES 60 A 1190 GLY CYS ALA PRO TRP PRO MET VAL GLU LYS LEU ILE LYS SEQRES 61 A 1190 GLN CYS LEU LYS GLU ASN PRO GLN GLU ARG PRO THR SER SEQRES 62 A 1190 ALA GLN VAL PHE ASP ILE LEU ASN SER ALA GLU LEU VAL SEQRES 63 A 1190 CYS LEU THR ARG ARG ILE LEU LEU PRO LYS ASN VAL ILE SEQRES 64 A 1190 VAL GLU CYS MET VAL ALA THR HIS HIS ASN SER ARG ASN SEQRES 65 A 1190 ALA SER ILE TRP LEU GLY CYS GLY HIS THR ASP ARG GLY SEQRES 66 A 1190 GLN LEU SER PHE LEU ASP LEU ASN THR GLU GLY TYR THR SEQRES 67 A 1190 SER GLU GLU VAL ALA ASP SER ARG ILE LEU CYS LEU ALA SEQRES 68 A 1190 LEU VAL HIS LEU PRO VAL GLU LYS GLU SER TRP ILE VAL SEQRES 69 A 1190 SER GLY THR GLN SER GLY THR LEU LEU VAL ILE ASN THR SEQRES 70 A 1190 GLU ASP GLY LYS LYS ARG HIS THR LEU GLU LYS MET THR SEQRES 71 A 1190 ASP SER VAL THR CYS LEU TYR CYS ASN SER PHE SER LYS SEQRES 72 A 1190 GLN SER LYS GLN LYS ASN PHE LEU LEU VAL GLY THR ALA SEQRES 73 A 1190 ASP GLY LYS LEU ALA ILE PHE GLU ASP LYS THR VAL LYS SEQRES 74 A 1190 LEU LYS GLY ALA ALA PRO LEU LYS ILE LEU ASN ILE GLY SEQRES 75 A 1190 ASN VAL SER THR PRO LEU MET CYS LEU SER GLU SER THR SEQRES 76 A 1190 ASN SER THR GLU ARG ASN VAL MET TRP GLY GLY CYS GLY SEQRES 77 A 1190 THR LYS ILE PHE SER PHE SER ASN ASP PHE THR ILE GLN SEQRES 78 A 1190 LYS LEU ILE GLU THR ARG THR SER GLN LEU PHE SER TYR SEQRES 79 A 1190 ALA ALA PHE SER ASP SER ASN ILE ILE THR VAL VAL VAL SEQRES 80 A 1190 ASP THR ALA LEU TYR ILE ALA LYS GLN ASN SER PRO VAL SEQRES 81 A 1190 VAL GLU VAL TRP ASP LYS LYS THR GLU LYS LEU CYS GLY SEQRES 82 A 1190 LEU ILE ASP CYS VAL HIS PHE LEU ARG GLU VAL MET VAL SEQRES 83 A 1190 LYS GLU ASN LYS GLU SER LYS HIS LYS MET SER TYR SER SEQRES 84 A 1190 GLY ARG VAL LYS THR LEU CYS LEU GLN LYS ASN THR ALA SEQRES 85 A 1190 LEU TRP ILE GLY THR GLY GLY GLY HIS ILE LEU LEU LEU SEQRES 86 A 1190 ASP LEU SER THR ARG ARG LEU ILE ARG VAL ILE TYR ASN SEQRES 87 A 1190 PHE CYS ASN SER VAL ARG VAL MET MET THR ALA GLN LEU SEQRES 88 A 1190 GLY SER LEU LYS ASN VAL MET LEU VAL LEU GLY TYR ASN SEQRES 89 A 1190 ARG LYS ASN THR GLU GLY THR GLN LYS GLN LYS GLU ILE SEQRES 90 A 1190 GLN SER CYS LEU THR VAL TRP ASP ILE ASN LEU PRO HIS SEQRES 91 A 1190 GLU VAL GLN ASN LEU GLU LYS HIS ILE GLU VAL ARG LYS SEQRES 92 A 1190 GLU LEU ALA GLU LYS MET ARG HET A1N A2601 28 HET GDP A2602 28 HET MG A2603 1 HETNAM A1N (2~{R},6~{S})-2,6-DIMETHYL-4-[6-[5-(1- HETNAM 2 A1N METHYLCYCLOPROPYL)OXY-1~{H}-INDAZOL-3-YL]PYRIMIDIN-4- HETNAM 3 A1N YL]MORPHOLINE HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 2 A1N C21 H25 N5 O2 FORMUL 3 GDP C10 H15 N5 O11 P2 FORMUL 4 MG MG 2+ FORMUL 5 HOH *(H2 O) HELIX 1 AA1 GLY A 1346 GLN A 1352 1 7 HELIX 2 AA2 LYS A 1432 ALA A 1442 1 11 HELIX 3 AA3 ALA A 1498 ASP A 1515 1 18 HELIX 4 AA4 LEU A 1530 ASN A 1540 1 11 HELIX 5 AA5 ARG A 1552 ARG A 1558 1 7 HELIX 6 AA6 GLU A 1568 GLU A 1578 1 11 HELIX 7 AA7 ASP A 1587 GLN A 1591 5 5 HELIX 8 AA8 LYS A 1601 LYS A 1605 5 5 HELIX 9 AA9 SER A 1627 LYS A 1633 1 7 HELIX 10 AB1 SER A 1647 PHE A 1656 1 10 HELIX 11 AB2 VAL A 1669 LEU A 1673 5 5 HELIX 12 AB3 GLU A 1686 SER A 1688 5 3 HELIX 13 AB4 GLY A 1703 SER A 1716 1 14 HELIX 14 AB5 PRO A 1717 MET A 1719 5 3 HELIX 15 AB6 CYS A 1770 PHE A 1792 1 23 HELIX 16 AB7 LEU A 1827 GLU A 1835 1 9 HELIX 17 AB8 PRO A 1851 ALA A 1856 1 6 HELIX 18 AB9 PRO A 1865 MET A 1869 5 5 HELIX 19 AC1 ASN A 1871 ASP A 1873 5 3 HELIX 20 AC2 ALA A 1880 GLU A 1882 5 3 HELIX 21 AC3 SER A 1913 LEU A 1927 1 15 HELIX 22 AC4 SER A 1954 GLN A 1961 1 8 HELIX 23 AC5 THR A 1967 ALA A 1988 1 22 HELIX 24 AC6 ALA A 2040 ARG A 2045 1 6 HELIX 25 AC7 GLN A 2052 THR A 2069 1 18 HELIX 26 AC8 GLY A 2071 LEU A 2077 1 7 HELIX 27 AC9 GLU A 2082 GLU A 2087 1 6 HELIX 28 AD1 ASP A 2094 GLY A 2100 1 7 HELIX 29 AD2 VAL A 2107 LEU A 2115 1 9 HELIX 30 AD3 THR A 2124 ASN A 2133 1 10 HELIX 31 AD4 SER A 2134 LEU A 2140 1 7 HELIX 32 AD5 ARG A 2339 LEU A 2343 5 5 HELIX 33 AD6 TYR A 2346 ASP A 2351 1 6 HELIX 34 AD7 CYS A 2389 VAL A 2396 1 8 HELIX 35 AD8 ASN A 2499 ARG A 2522 1 24 SHEET 1 AA1 4 ASP A1372 TRP A1376 0 SHEET 2 AA1 4 LEU A1390 ASP A1394 -1 O LEU A1390 N TRP A1376 SHEET 3 AA1 4 MET A1335 ILE A1339 1 N MET A1335 O ASN A1391 SHEET 4 AA1 4 LEU A1414 TYR A1415 1 O LEU A1414 N MET A1338 SHEET 1 AA2 2 VAL A1447 VAL A1450 0 SHEET 2 AA2 2 ILE A1482 HIS A1486 1 O HIS A1486 N LEU A1449 SHEET 1 AA3 2 LEU A1582 LEU A1583 0 SHEET 2 AA3 2 PHE A1597 VAL A1598 -1 O PHE A1597 N LEU A1583 SHEET 1 AA4 2 PRO A1661 GLY A1663 0 SHEET 2 AA4 2 TYR A1666 LEU A1667 -1 O TYR A1666 N GLY A1663 SHEET 1 AA5 7 ASN A1730 TYR A1733 0 SHEET 2 AA5 7 ILE A1738 ASN A1741 -1 O ASN A1741 N ASN A1730 SHEET 3 AA5 7 TYR A1747 GLY A1751 -1 O CYS A1748 N LEU A1740 SHEET 4 AA5 7 PHE A1762 PRO A1768 -1 O THR A1766 N LEU A1749 SHEET 5 AA5 7 ILE A1690 GLU A1696 -1 N ILE A1691 O VAL A1767 SHEET 6 AA5 7 LYS A1809 TYR A1814 -1 O LYS A1809 N GLU A1696 SHEET 7 AA5 7 GLN A1823 LEU A1826 -1 O ILE A1825 N ALA A1812 SHEET 1 AA6 3 LEU A1875 GLU A1876 0 SHEET 2 AA6 3 GLY A1891 TYR A1898 -1 O ALA A1897 N GLU A1876 SHEET 3 AA6 3 LEU A1884 GLY A1886 -1 N LEU A1885 O VAL A1893 SHEET 1 AA7 5 LEU A1875 GLU A1876 0 SHEET 2 AA7 5 GLY A1891 TYR A1898 -1 O ALA A1897 N GLU A1876 SHEET 3 AA7 5 GLU A1901 PHE A1908 -1 O VAL A1905 N TYR A1894 SHEET 4 AA7 5 MET A1944 VAL A1946 -1 O LEU A1945 N LYS A1906 SHEET 5 AA7 5 ALA A1937 ALA A1938 -1 N ALA A1937 O VAL A1946 SHEET 1 AA8 2 ILE A1990 ILE A1991 0 SHEET 2 AA8 2 GLN A2022 TYR A2023 -1 O GLN A2022 N ILE A1991 SHEET 1 AA9 2 VAL A2000 LEU A2002 0 SHEET 2 AA9 2 ALA A2013 ILE A2015 -1 O LYS A2014 N LEU A2001 SHEET 1 AB1 3 MET A2155 VAL A2156 0 SHEET 2 AB1 3 ILE A2167 LEU A2169 -1 O TRP A2168 N VAL A2156 SHEET 3 AB1 3 SER A2180 LEU A2182 -1 O SER A2180 N LEU A2169 SHEET 1 AB2 2 LEU A2202 ALA A2203 0 SHEET 2 AB2 2 VAL A2216 SER A2217 -1 O VAL A2216 N ALA A2203 SHEET 1 AB3 3 CYS A2247 TYR A2249 0 SHEET 2 AB3 3 LEU A2264 GLY A2266 -1 O GLY A2266 N CYS A2247 SHEET 3 AB3 3 LEU A2272 ALA A2273 -1 O ALA A2273 N VAL A2265 SHEET 1 AB4 4 LEU A2300 SER A2304 0 SHEET 2 AB4 4 TRP A2316 CYS A2319 -1 O TRP A2316 N SER A2304 SHEET 3 AB4 4 LYS A2322 SER A2325 -1 O LYS A2322 N CYS A2319 SHEET 4 AB4 4 ILE A2336 GLU A2337 -1 O ILE A2336 N ILE A2323 SHEET 1 AB5 4 ILE A2354 VAL A2359 0 SHEET 2 AB5 4 ALA A2362 LYS A2367 -1 O ALA A2366 N ILE A2355 SHEET 3 AB5 4 VAL A2372 ASP A2377 -1 O GLU A2374 N ILE A2365 SHEET 4 AB5 4 LYS A2382 ASP A2388 -1 O CYS A2384 N VAL A2375 SHEET 1 AB6 4 VAL A2414 GLN A2420 0 SHEET 2 AB6 4 ALA A2424 THR A2429 -1 O GLY A2428 N LYS A2415 SHEET 3 AB6 4 ILE A2434 ASP A2438 -1 O LEU A2437 N LEU A2425 SHEET 4 AB6 4 LEU A2444 ILE A2448 -1 O ILE A2445 N LEU A2436 SHEET 1 AB7 3 SER A2454 ALA A2461 0 SHEET 2 AB7 3 VAL A2469 TYR A2475 -1 O LEU A2471 N MET A2459 SHEET 3 AB7 3 SER A2491 ASP A2497 -1 O CYS A2492 N GLY A2474 LINK OG1 THR A1348 MG MG A2603 1555 1555 2.29 LINK O1B GDP A2602 MG MG A2603 1555 1555 2.11 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000