HEADER HYDROLASE/HYDROLASE INHIBITOR 29-DEC-22 8FO7 TITLE CRYO-EM STRUCTURE OF LRRK2 BOUND TO TYPE I INHIBITOR LRRK2-IN-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEUCINE-RICH REPEAT SERINE/THREONINE-PROTEIN KINASE 2; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: DARDARIN; COMPND 5 EC: 2.7.11.1,3.6.5.-; COMPND 6 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: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606 KEYWDS CRYO-EM, PARKINSON'S DISEASE, KINASE, LRRK2, TYPE I INHIBITOR, LRRK2- KEYWDS 2 IN-1, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR H.ZHU,J.SUN REVDAT 2 31-JAN-24 8FO7 1 JRNL REVDAT 1 17-JAN-24 8FO7 0 JRNL AUTH H.ZHU,P.HIXSON,W.MA,J.SUN JRNL TITL PHARMACOLOGY OF LRRK2 WITH TYPE I AND II KINASE INHIBITORS JRNL TITL 2 REVEALED BY CRYO-EM. JRNL REF CELL DISCOV V. 10 10 2024 JRNL REFN ESSN 2056-5968 JRNL PMID 38263358 JRNL DOI 10.1038/S41421-023-00639-8 REMARK 2 REMARK 2 RESOLUTION. 3.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : EPU, GCTF, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL 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) : 3.520 REMARK 3 NUMBER OF PARTICLES : 187407 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8FO7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1000271080. 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 : LRRK2-LRRK2-IN-1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.50 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6250.00 REMARK 245 ILLUMINATION MODE : OTHER REMARK 245 NOMINAL MAGNIFICATION : NULL 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: C 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 LYS C 1327 REMARK 465 LYS C 1328 REMARK 465 THR C 1357 REMARK 465 LYS C 1358 REMARK 465 LYS C 1359 REMARK 465 SER C 1360 REMARK 465 ASP C 1361 REMARK 465 LEU C 1362 REMARK 465 GLY C 1363 REMARK 465 MET C 1364 REMARK 465 LYS C 1614 REMARK 465 VAL C 1615 REMARK 465 GLU C 1616 REMARK 465 GLY C 1617 REMARK 465 CYS C 1618 REMARK 465 PRO C 1619 REMARK 465 LYS C 1620 REMARK 465 HIS C 1621 REMARK 465 PRO C 1622 REMARK 465 LEU C 1653 REMARK 465 GLU C 1654 REMARK 465 LYS C 1655 REMARK 465 PHE C 1656 REMARK 465 GLN C 1657 REMARK 465 GLY C 1663 REMARK 465 GLU C 1664 REMARK 465 GLU C 1665 REMARK 465 ASP C 1799 REMARK 465 ILE C 1800 REMARK 465 CYS C 1801 REMARK 465 GLY C 1802 REMARK 465 GLU C 1803 REMARK 465 GLY C 1804 REMARK 465 GLU C 1805 REMARK 465 SER C 2254 REMARK 465 LYS C 2255 REMARK 465 GLN C 2256 REMARK 465 SER C 2257 REMARK 465 LYS C 2258 REMARK 465 VAL C 2398 REMARK 465 LYS C 2399 REMARK 465 GLU C 2400 REMARK 465 ASN C 2401 REMARK 465 LYS C 2402 REMARK 465 GLU C 2403 REMARK 465 SER C 2404 REMARK 465 LYS C 2405 REMARK 465 HIS C 2406 REMARK 465 LYS C 2407 REMARK 465 MET C 2408 REMARK 465 LYS C 2478 REMARK 465 ASN C 2479 REMARK 465 THR C 2480 REMARK 465 GLU C 2481 REMARK 465 GLY C 2482 REMARK 465 THR C 2483 REMARK 465 GLN C 2484 REMARK 465 LYS C 2485 REMARK 465 GLN C 2486 REMARK 465 LYS C 2487 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 VAL C1330 CG1 CG2 REMARK 470 ASN C1333 CG OD1 ND2 REMARK 470 SER C1345 OG REMARK 470 LYS C1347 CG CD CE NZ REMARK 470 GLN C1353 CG CD OE1 NE2 REMARK 470 GLN C1365 CG CD OE1 NE2 REMARK 470 ASP C1372 CG OD1 OD2 REMARK 470 GLN C1379 CG CD OE1 NE2 REMARK 470 ILE C1380 CG1 CG2 CD1 REMARK 470 ARG C1381 CG CD NE CZ NH1 NH2 REMARK 470 ASP C1382 CG OD1 OD2 REMARK 470 LYS C1383 CG CD CE NZ REMARK 470 ARG C1384 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1385 CG CD CE NZ REMARK 470 ARG C1386 CG CD NE CZ NH1 NH2 REMARK 470 ASP C1387 CG OD1 OD2 REMARK 470 GLN C1411 CG CD OE1 NE2 REMARK 470 SER C1422 OG REMARK 470 LYS C1423 CG CD CE NZ REMARK 470 GLN C1425 CG CD OE1 NE2 REMARK 470 GLU C1427 CG CD OE1 OE2 REMARK 470 ASP C1429 CG OD1 OD2 REMARK 470 LYS C1432 CG CD CE NZ REMARK 470 LYS C1439 CG CD CE NZ REMARK 470 ASP C1455 CG OD1 OD2 REMARK 470 SER C1457 OG REMARK 470 ASP C1458 CG OD1 OD2 REMARK 470 LYS C1460 CG CD CE NZ REMARK 470 GLN C1461 CG CD OE1 NE2 REMARK 470 ARG C1462 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1463 CG CD CE NZ REMARK 470 MET C1466 CG SD CE REMARK 470 LYS C1468 CG CD CE NZ REMARK 470 LYS C1471 CG CD CE NZ REMARK 470 GLU C1472 CG CD OE1 OE2 REMARK 470 LEU C1473 CG CD1 CD2 REMARK 470 LEU C1474 CG CD1 CD2 REMARK 470 ASN C1475 CG OD1 ND2 REMARK 470 LYS C1476 CG CD CE NZ REMARK 470 ARG C1477 CG CD NE CZ NH1 NH2 REMARK 470 ASP C1484 CG OD1 OD2 REMARK 470 TYR C1485 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE C1487 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN C1489 CG OD1 ND2 REMARK 470 GLU C1492 CG CD OE1 OE2 REMARK 470 SER C1494 OG REMARK 470 ASP C1495 CG OD1 OD2 REMARK 470 LYS C1499 CG CD CE NZ REMARK 470 LYS C1502 CG CD CE NZ REMARK 470 ASN C1510 CG OD1 ND2 REMARK 470 LYS C1512 CG CD CE NZ REMARK 470 ILE C1513 CG1 CG2 CD1 REMARK 470 ARG C1514 CG CD NE CZ NH1 NH2 REMARK 470 ASP C1515 CG OD1 OD2 REMARK 470 GLN C1516 CG CD OE1 NE2 REMARK 470 VAL C1519 CG1 CG2 REMARK 470 GLN C1521 CG CD OE1 NE2 REMARK 470 LEU C1522 CG CD1 CD2 REMARK 470 ASP C1525 CG OD1 OD2 REMARK 470 GLU C1529 CG CD OE1 OE2 REMARK 470 LYS C1532 CG CD CE NZ REMARK 470 LYS C1539 CG CD CE NZ REMARK 470 GLU C1544 CG CD OE1 OE2 REMARK 470 ARG C1550 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1551 CG CD CE NZ REMARK 470 LEU C1554 CG CD1 CD2 REMARK 470 GLN C1555 CG CD OE1 NE2 REMARK 470 ARG C1558 CG CD NE CZ NH1 NH2 REMARK 470 GLN C1561 CG CD OE1 NE2 REMARK 470 LEU C1562 CG CD1 CD2 REMARK 470 GLN C1563 CG CD OE1 NE2 REMARK 470 LEU C1564 CG CD1 CD2 REMARK 470 ASP C1565 CG OD1 OD2 REMARK 470 GLU C1566 CG CD OE1 OE2 REMARK 470 ASN C1567 CG OD1 ND2 REMARK 470 GLU C1578 CG CD OE1 OE2 REMARK 470 ASP C1594 CG OD1 OD2 REMARK 470 ARG C1629 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1633 CG CD CE NZ REMARK 470 LEU C1635 CG CD1 CD2 REMARK 470 SER C1636 OG REMARK 470 ARG C1639 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1640 CG CD CE NZ REMARK 470 PHE C1641 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS C1643 CG CD CE NZ REMARK 470 ASN C1644 CG OD1 ND2 REMARK 470 GLN C1648 CG CD OE1 NE2 REMARK 470 TYR C1666 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU C1681 CG CD OE1 OE2 REMARK 470 GLU C1686 CG CD OE1 OE2 REMARK 470 GLU C1689 CG CD OE1 OE2 REMARK 470 MET C1719 CG SD CE REMARK 470 LEU C1720 CG CD1 CD2 REMARK 470 ARG C1723 CG CD NE CZ NH1 NH2 REMARK 470 GLU C1724 CG CD OE1 OE2 REMARK 470 ARG C1725 CG CD NE CZ NH1 NH2 REMARK 470 ARG C1728 CG CD NE CZ NH1 NH2 REMARK 470 GLU C1745 CG CD OE1 OE2 REMARK 470 ASP C1756 CG OD1 OD2 REMARK 470 ASN C1757 CG OD1 ND2 REMARK 470 GLU C1797 CG CD OE1 OE2 REMARK 470 ILE C1798 CG1 CG2 CD1 REMARK 470 ASN C1817 CG OD1 ND2 REMARK 470 ASP C1818 CG OD1 OD2 REMARK 470 GLU C1820 CG CD OE1 OE2 REMARK 470 GLU C1821 CG CD OE1 OE2 REMARK 470 ASP C1844 CG OD1 OD2 REMARK 470 ARG C1847 CG CD NE CZ NH1 NH2 REMARK 470 ARG C1866 CG CD NE CZ NH1 NH2 REMARK 470 ASN C1867 CG OD1 ND2 REMARK 470 ASP C1873 CG OD1 OD2 REMARK 470 GLU C1874 CG CD OE1 OE2 REMARK 470 GLU C1876 CG CD OE1 OE2 REMARK 470 GLU C1878 CG CD OE1 OE2 REMARK 470 GLU C1882 CG CD OE1 OE2 REMARK 470 GLU C1901 CG CD OE1 OE2 REMARK 470 LYS C1910 CG CD CE NZ REMARK 470 HIS C1911 CG ND1 CD2 CE1 NE2 REMARK 470 SER C1965 OG REMARK 470 ARG C2026 CG CD NE CZ NH1 NH2 REMARK 470 LYS C2030 CG CD CE NZ REMARK 470 GLU C2075 CG CD OE1 OE2 REMARK 470 LEU C2077 CG CD1 CD2 REMARK 470 LYS C2078 CG CD CE NZ REMARK 470 PHE C2079 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASN C2081 CG OD1 ND2 REMARK 470 GLU C2082 CG CD OE1 OE2 REMARK 470 ASP C2084 CG OD1 OD2 REMARK 470 GLU C2085 CG CD OE1 OE2 REMARK 470 GLU C2087 CG CD OE1 OE2 REMARK 470 ILE C2088 CG1 CG2 CD1 REMARK 470 GLN C2089 CG CD OE1 NE2 REMARK 470 LYS C2091 CG CD CE NZ REMARK 470 LYS C2097 CG CD CE NZ REMARK 470 LYS C2148 CG CD CE NZ REMARK 470 GLU C2153 CG CD OE1 OE2 REMARK 470 HIS C2159 CG ND1 CD2 CE1 NE2 REMARK 470 HIS C2160 CG ND1 CD2 CE1 NE2 REMARK 470 ARG C2163 CG CD NE CZ NH1 NH2 REMARK 470 ASN C2164 CG OD1 ND2 REMARK 470 THR C2174 OG1 CG2 REMARK 470 ARG C2176 CG CD NE CZ NH1 NH2 REMARK 470 GLU C2193 CG CD OE1 OE2 REMARK 470 VAL C2209 CG1 CG2 REMARK 470 GLU C2210 CG CD OE1 OE2 REMARK 470 LYS C2211 CG CD CE NZ REMARK 470 GLU C2212 CG CD OE1 OE2 REMARK 470 SER C2213 OG REMARK 470 ASN C2228 CG OD1 ND2 REMARK 470 GLU C2230 CG CD OE1 OE2 REMARK 470 ASP C2231 CG OD1 OD2 REMARK 470 LYS C2233 CG CD CE NZ REMARK 470 LYS C2234 CG CD CE NZ REMARK 470 LYS C2240 CG CD CE NZ REMARK 470 ASN C2251 CG OD1 ND2 REMARK 470 GLN C2259 CG CD OE1 NE2 REMARK 470 GLU C2276 CG CD OE1 OE2 REMARK 470 ASP C2277 CG OD1 OD2 REMARK 470 LYS C2278 CG CD CE NZ REMARK 470 THR C2279 OG1 CG2 REMARK 470 LYS C2281 CG CD CE NZ REMARK 470 LEU C2282 CG CD1 CD2 REMARK 470 LYS C2283 CG CD CE NZ REMARK 470 ASN C2295 CG OD1 ND2 REMARK 470 GLU C2305 CG CD OE1 OE2 REMARK 470 THR C2307 OG1 CG2 REMARK 470 ASN C2308 CG OD1 ND2 REMARK 470 THR C2310 OG1 CG2 REMARK 470 ARG C2312 CG CD NE CZ NH1 NH2 REMARK 470 ASN C2313 CG OD1 ND2 REMARK 470 ASP C2329 CG OD1 OD2 REMARK 470 THR C2331 OG1 CG2 REMARK 470 LYS C2334 CG CD CE NZ REMARK 470 GLN C2342 CG CD OE1 NE2 REMARK 470 PHE C2344 CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR C2346 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP C2351 CG OD1 OD2 REMARK 470 ASP C2360 CG OD1 OD2 REMARK 470 ASP C2377 CG OD1 OD2 REMARK 470 LYS C2379 CG CD CE NZ REMARK 470 LYS C2382 CG CD CE NZ REMARK 470 ARG C2394 CG CD NE CZ NH1 NH2 REMARK 470 LYS C2421 CG CD CE NZ REMARK 470 ASN C2422 CG OD1 ND2 REMARK 470 THR C2441 OG1 CG2 REMARK 470 ARG C2442 CG CD NE CZ NH1 NH2 REMARK 470 ARG C2443 CG CD NE CZ NH1 NH2 REMARK 470 LYS C2467 CG CD CE NZ REMARK 470 ASN C2468 CG OD1 ND2 REMARK 470 ARG C2477 CG CD NE CZ NH1 NH2 REMARK 470 GLU C2488 CG CD OE1 OE2 REMARK 470 ARG C2523 CG CD NE CZ NH1 NH2 REMARK 470 SER C2525 OG REMARK 470 GLU C2527 CG CD OE1 OE2 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 LYS C1383 -155.10 59.57 REMARK 500 PHE C1395 128.30 -38.34 REMARK 500 ASN C1489 -164.92 -78.85 REMARK 500 PHE C1545 78.66 -159.99 REMARK 500 THR C1612 34.46 -99.15 REMARK 500 LEU C1713 54.98 -93.10 REMARK 500 SER C1716 61.60 -165.60 REMARK 500 LEU C1796 55.68 -92.38 REMARK 500 PHE C1883 54.21 -93.34 REMARK 500 ARG C1993 -1.82 67.14 REMARK 500 PRO C1997 44.19 -77.24 REMARK 500 HIS C1998 -31.08 -130.26 REMARK 500 LEU C2005 57.32 -96.63 REMARK 500 ASN C2161 -4.61 68.54 REMARK 500 SER C2162 -17.26 -140.18 REMARK 500 ALA C2268 0.43 -67.10 REMARK 500 MET C2301 39.15 -140.50 REMARK 500 PRO C2371 2.86 -66.38 REMARK 500 ASN C2422 18.48 -141.28 REMARK 500 SER C2440 -70.87 -61.48 REMARK 500 THR C2441 -64.88 -123.40 REMARK 500 ARG C2442 -20.50 -141.53 REMARK 500 LYS C2467 -165.75 -78.99 REMARK 500 ASN C2468 60.58 62.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET C 2106 VAL C 2107 148.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29340 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF LRRK2 BOUND WITH TYPE I INHIBITOR LRRK2-IN-1 DBREF 8FO7 C 1327 2527 UNP Q5S007 LRRK2_HUMAN 1327 2527 SEQADV 8FO7 THR C 1647 UNP Q5S007 SER 1647 CONFLICT SEQADV 8FO7 ARG C 1732 UNP Q5S007 MET 1732 CONFLICT SEQADV 8FO7 THR C 2397 UNP Q5S007 MET 2397 CONFLICT SEQRES 1 C 1201 LYS LYS ALA VAL PRO TYR ASN ARG MET LYS LEU MET ILE SEQRES 2 C 1201 VAL GLY ASN THR GLY SER GLY LYS THR THR LEU LEU GLN SEQRES 3 C 1201 GLN LEU MET LYS THR LYS LYS SER ASP LEU GLY MET GLN SEQRES 4 C 1201 SER ALA THR VAL GLY ILE ASP VAL LYS ASP TRP PRO ILE SEQRES 5 C 1201 GLN ILE ARG ASP LYS ARG LYS ARG ASP LEU VAL LEU ASN SEQRES 6 C 1201 VAL TRP ASP PHE ALA GLY ARG GLU GLU PHE TYR SER THR SEQRES 7 C 1201 HIS PRO HIS PHE MET THR GLN ARG ALA LEU TYR LEU ALA SEQRES 8 C 1201 VAL TYR ASP LEU SER LYS GLY GLN ALA GLU VAL ASP ALA SEQRES 9 C 1201 MET LYS PRO TRP LEU PHE ASN ILE LYS ALA ARG ALA SER SEQRES 10 C 1201 SER SER PRO VAL ILE LEU VAL GLY THR HIS LEU ASP VAL SEQRES 11 C 1201 SER ASP GLU LYS GLN ARG LYS ALA CYS MET SER LYS ILE SEQRES 12 C 1201 THR LYS GLU LEU LEU ASN LYS ARG GLY PHE PRO ALA ILE SEQRES 13 C 1201 ARG ASP TYR HIS PHE VAL ASN ALA THR GLU GLU SER ASP SEQRES 14 C 1201 ALA LEU ALA LYS LEU ARG LYS THR ILE ILE ASN GLU SER SEQRES 15 C 1201 LEU ASN PHE LYS ILE ARG ASP GLN LEU VAL VAL GLY GLN SEQRES 16 C 1201 LEU ILE PRO ASP CYS TYR VAL GLU LEU GLU LYS ILE ILE SEQRES 17 C 1201 LEU SER GLU ARG LYS ASN VAL PRO ILE GLU PHE PRO VAL SEQRES 18 C 1201 ILE ASP ARG LYS ARG LEU LEU GLN LEU VAL ARG GLU ASN SEQRES 19 C 1201 GLN LEU GLN LEU ASP GLU ASN GLU LEU PRO HIS ALA VAL SEQRES 20 C 1201 HIS PHE LEU ASN GLU SER GLY VAL LEU LEU HIS PHE GLN SEQRES 21 C 1201 ASP PRO ALA LEU GLN LEU SER ASP LEU TYR PHE VAL GLU SEQRES 22 C 1201 PRO LYS TRP LEU CYS LYS ILE MET ALA GLN ILE LEU THR SEQRES 23 C 1201 VAL LYS VAL GLU GLY CYS PRO LYS HIS PRO LYS GLY ILE SEQRES 24 C 1201 ILE SER ARG ARG ASP VAL GLU LYS PHE LEU SER LYS LYS SEQRES 25 C 1201 ARG LYS PHE PRO LYS ASN TYR MET THR GLN TYR PHE LYS SEQRES 26 C 1201 LEU LEU GLU LYS PHE GLN ILE ALA LEU PRO ILE GLY GLU SEQRES 27 C 1201 GLU TYR LEU LEU VAL PRO SER SER LEU SER ASP HIS ARG SEQRES 28 C 1201 PRO VAL ILE GLU LEU PRO HIS CYS GLU ASN SER GLU ILE SEQRES 29 C 1201 ILE ILE ARG LEU TYR GLU MET PRO TYR PHE PRO MET GLY SEQRES 30 C 1201 PHE TRP SER ARG LEU ILE ASN ARG LEU LEU GLU ILE SER SEQRES 31 C 1201 PRO TYR MET LEU SER GLY ARG GLU ARG ALA LEU ARG PRO SEQRES 32 C 1201 ASN ARG ARG TYR TRP ARG GLN GLY ILE TYR LEU ASN TRP SEQRES 33 C 1201 SER PRO GLU ALA TYR CYS LEU VAL GLY SER GLU VAL LEU SEQRES 34 C 1201 ASP ASN HIS PRO GLU SER PHE LEU LYS ILE THR VAL PRO SEQRES 35 C 1201 SER CYS ARG LYS GLY CYS ILE LEU LEU GLY GLN VAL VAL SEQRES 36 C 1201 ASP HIS ILE ASP SER LEU MET GLU GLU TRP PHE PRO GLY SEQRES 37 C 1201 LEU LEU GLU ILE ASP ILE CYS GLY GLU GLY GLU THR LEU SEQRES 38 C 1201 LEU LYS LYS TRP ALA LEU TYR SER PHE ASN ASP GLY GLU SEQRES 39 C 1201 GLU HIS GLN LYS ILE LEU LEU ASP ASP LEU MET LYS LYS SEQRES 40 C 1201 ALA GLU GLU GLY ASP LEU LEU VAL ASN PRO ASP GLN PRO SEQRES 41 C 1201 ARG LEU THR ILE PRO ILE SER GLN ILE ALA PRO ASP LEU SEQRES 42 C 1201 ILE LEU ALA ASP LEU PRO ARG ASN ILE MET LEU ASN ASN SEQRES 43 C 1201 ASP GLU LEU GLU PHE GLU GLN ALA PRO GLU PHE LEU LEU SEQRES 44 C 1201 GLY ASP GLY SER PHE GLY SER VAL TYR ARG ALA ALA TYR SEQRES 45 C 1201 GLU GLY GLU GLU VAL ALA VAL LYS ILE PHE ASN LYS HIS SEQRES 46 C 1201 THR SER LEU ARG LEU LEU ARG GLN GLU LEU VAL VAL LEU SEQRES 47 C 1201 CYS HIS LEU HIS HIS PRO SER LEU ILE SER LEU LEU ALA SEQRES 48 C 1201 ALA GLY ILE ARG PRO ARG MET LEU VAL MET GLU LEU ALA SEQRES 49 C 1201 SER LYS GLY SER LEU ASP ARG LEU LEU GLN GLN ASP LYS SEQRES 50 C 1201 ALA SER LEU THR ARG THR LEU GLN HIS ARG ILE ALA LEU SEQRES 51 C 1201 HIS VAL ALA ASP GLY LEU ARG TYR LEU HIS SER ALA MET SEQRES 52 C 1201 ILE ILE TYR ARG ASP LEU LYS PRO HIS ASN VAL LEU LEU SEQRES 53 C 1201 PHE THR LEU TYR PRO ASN ALA ALA ILE ILE ALA LYS ILE SEQRES 54 C 1201 ALA ASP TYR GLY ILE ALA GLN TYR CYS CYS ARG MET GLY SEQRES 55 C 1201 ILE LYS THR SER GLU GLY THR PRO GLY PHE ARG ALA PRO SEQRES 56 C 1201 GLU VAL ALA ARG GLY ASN VAL ILE TYR ASN GLN GLN ALA SEQRES 57 C 1201 ASP VAL TYR SER PHE GLY LEU LEU LEU TYR ASP ILE LEU SEQRES 58 C 1201 THR THR GLY GLY ARG ILE VAL GLU GLY LEU LYS PHE PRO SEQRES 59 C 1201 ASN GLU PHE ASP GLU LEU GLU ILE GLN GLY LYS LEU PRO SEQRES 60 C 1201 ASP PRO VAL LYS GLU TYR GLY CYS ALA PRO TRP PRO MET SEQRES 61 C 1201 VAL GLU LYS LEU ILE LYS GLN CYS LEU LYS GLU ASN PRO SEQRES 62 C 1201 GLN GLU ARG PRO THR SER ALA GLN VAL PHE ASP ILE LEU SEQRES 63 C 1201 ASN SER ALA GLU LEU VAL CYS LEU THR ARG ARG ILE LEU SEQRES 64 C 1201 LEU PRO LYS ASN VAL ILE VAL GLU CYS MET VAL ALA THR SEQRES 65 C 1201 HIS HIS ASN SER ARG ASN ALA SER ILE TRP LEU GLY CYS SEQRES 66 C 1201 GLY HIS THR ASP ARG GLY GLN LEU SER PHE LEU ASP LEU SEQRES 67 C 1201 ASN THR GLU GLY TYR THR SER GLU GLU VAL ALA ASP SER SEQRES 68 C 1201 ARG ILE LEU CYS LEU ALA LEU VAL HIS LEU PRO VAL GLU SEQRES 69 C 1201 LYS GLU SER TRP ILE VAL SER GLY THR GLN SER GLY THR SEQRES 70 C 1201 LEU LEU VAL ILE ASN THR GLU ASP GLY LYS LYS ARG HIS SEQRES 71 C 1201 THR LEU GLU LYS MET THR ASP SER VAL THR CYS LEU TYR SEQRES 72 C 1201 CYS ASN SER PHE SER LYS GLN SER LYS GLN LYS ASN PHE SEQRES 73 C 1201 LEU LEU VAL GLY THR ALA ASP GLY LYS LEU ALA ILE PHE SEQRES 74 C 1201 GLU ASP LYS THR VAL LYS LEU LYS GLY ALA ALA PRO LEU SEQRES 75 C 1201 LYS ILE LEU ASN ILE GLY ASN VAL SER THR PRO LEU MET SEQRES 76 C 1201 CYS LEU SER GLU SER THR ASN SER THR GLU ARG ASN VAL SEQRES 77 C 1201 MET TRP GLY GLY CYS GLY THR LYS ILE PHE SER PHE SER SEQRES 78 C 1201 ASN ASP PHE THR ILE GLN LYS LEU ILE GLU THR ARG THR SEQRES 79 C 1201 SER GLN LEU PHE SER TYR ALA ALA PHE SER ASP SER ASN SEQRES 80 C 1201 ILE ILE THR VAL VAL VAL ASP THR ALA LEU TYR ILE ALA SEQRES 81 C 1201 LYS GLN ASN SER PRO VAL VAL GLU VAL TRP ASP LYS LYS SEQRES 82 C 1201 THR GLU LYS LEU CYS GLY LEU ILE ASP CYS VAL HIS PHE SEQRES 83 C 1201 LEU ARG GLU VAL THR VAL LYS GLU ASN LYS GLU SER LYS SEQRES 84 C 1201 HIS LYS MET SER TYR SER GLY ARG VAL LYS THR LEU CYS SEQRES 85 C 1201 LEU GLN LYS ASN THR ALA LEU TRP ILE GLY THR GLY GLY SEQRES 86 C 1201 GLY HIS ILE LEU LEU LEU ASP LEU SER THR ARG ARG LEU SEQRES 87 C 1201 ILE ARG VAL ILE TYR ASN PHE CYS ASN SER VAL ARG VAL SEQRES 88 C 1201 MET MET THR ALA GLN LEU GLY SER LEU LYS ASN VAL MET SEQRES 89 C 1201 LEU VAL LEU GLY TYR ASN ARG LYS ASN THR GLU GLY THR SEQRES 90 C 1201 GLN LYS GLN LYS GLU ILE GLN SER CYS LEU THR VAL TRP SEQRES 91 C 1201 ASP ILE ASN LEU PRO HIS GLU VAL GLN ASN LEU GLU LYS SEQRES 92 C 1201 HIS ILE GLU VAL ARG LYS GLU LEU ALA GLU LYS MET ARG SEQRES 93 C 1201 ARG THR SER VAL GLU HET GDP C2601 28 HET 4K4 C2602 42 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM 4K4 2-[(2-METHOXY-4-{[4-(4-METHYLPIPERAZIN-1-YL)PIPERIDIN- HETNAM 2 4K4 1-YL]CARBONYL}PHENYL)AMINO]-5,11-DIMETHYL-5,11- HETNAM 3 4K4 DIHYDRO-6H-PYRIMIDO[4,5-B][1,4]BENZODIAZEPIN-6-ONE FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 4K4 C31 H38 N8 O3 HELIX 1 AA1 GLY C 1346 LYS C 1356 1 11 HELIX 2 AA2 ARG C 1398 THR C 1404 5 7 HELIX 3 AA3 HIS C 1405 MET C 1409 5 5 HELIX 4 AA4 GLN C 1425 MET C 1431 1 7 HELIX 5 AA5 MET C 1431 ALA C 1442 1 12 HELIX 6 AA6 GLU C 1459 GLU C 1472 1 14 HELIX 7 AA7 SER C 1494 PHE C 1511 1 18 HELIX 8 AA8 PRO C 1524 LYS C 1539 1 16 HELIX 9 AA9 ASP C 1549 GLN C 1561 1 13 HELIX 10 AB1 GLU C 1568 GLY C 1580 1 13 HELIX 11 AB2 GLU C 1599 CYS C 1604 1 6 HELIX 12 AB3 LYS C 1605 THR C 1612 1 8 HELIX 13 AB4 ARG C 1628 PHE C 1634 1 7 HELIX 14 AB5 ASN C 1644 PHE C 1650 1 7 HELIX 15 AB6 VAL C 1669 LEU C 1673 5 5 HELIX 16 AB7 GLY C 1703 LEU C 1712 1 10 HELIX 17 AB8 MET C 1719 ARG C 1723 5 5 HELIX 18 AB9 CYS C 1770 TRP C 1791 1 22 HELIX 19 AC1 LEU C 1827 GLY C 1837 1 11 HELIX 20 AC2 ILE C 1852 ALA C 1856 1 5 HELIX 21 AC3 SER C 1913 CYS C 1925 1 13 HELIX 22 AC4 SER C 1954 ASP C 1962 1 9 HELIX 23 AC5 THR C 1969 ALA C 1988 1 20 HELIX 24 AC6 ALA C 2040 ARG C 2045 1 6 HELIX 25 AC7 GLN C 2053 THR C 2068 1 16 HELIX 26 AC8 GLY C 2070 PHE C 2079 1 10 HELIX 27 AC9 PHE C 2079 GLY C 2090 1 12 HELIX 28 AD1 ASP C 2094 TYR C 2099 1 6 HELIX 29 AD2 VAL C 2107 CYS C 2114 1 8 HELIX 30 AD3 ASN C 2118 ARG C 2122 5 5 HELIX 31 AD4 THR C 2124 ASN C 2133 1 10 HELIX 32 AD5 SER C 2134 VAL C 2138 5 5 HELIX 33 AD6 PRO C 2208 LYS C 2211 5 4 HELIX 34 AD7 LYS C 2278 VAL C 2280 5 3 HELIX 35 AD8 CYS C 2389 ARG C 2394 1 6 HELIX 36 AD9 ASN C 2499 GLU C 2527 1 29 SHEET 1 AA1 3 ARG C1334 ILE C1339 0 SHEET 2 AA1 3 LEU C1388 ASP C1394 1 O ASN C1391 N LEU C1337 SHEET 3 AA1 3 VAL C1373 ILE C1378 -1 N ILE C1378 O LEU C1388 SHEET 1 AA2 3 VAL C1418 TYR C1419 0 SHEET 2 AA2 3 LEU C1449 GLY C1451 1 O VAL C1450 N TYR C1419 SHEET 3 AA2 3 TYR C1485 HIS C1486 1 O HIS C1486 N GLY C1451 SHEET 1 AA3 2 LYS C1512 ILE C1513 0 SHEET 2 AA3 2 GLN C1516 LEU C1517 -1 O GLN C1516 N ILE C1513 SHEET 1 AA4 2 ILE C1690 ILE C1692 0 SHEET 2 AA4 2 THR C1766 PRO C1768 -1 O VAL C1767 N ILE C1691 SHEET 1 AA5 3 TYR C1695 GLU C1696 0 SHEET 2 AA5 3 LYS C1809 TYR C1814 -1 O LYS C1809 N GLU C1696 SHEET 3 AA5 3 GLN C1823 LEU C1826 -1 O ILE C1825 N ALA C1812 SHEET 1 AA6 2 TYR C1733 TRP C1734 0 SHEET 2 AA6 2 GLY C1737 ILE C1738 -1 O GLY C1737 N TRP C1734 SHEET 1 AA7 2 ASN C1741 SER C1743 0 SHEET 2 AA7 2 ALA C1746 TYR C1747 -1 O ALA C1746 N SER C1743 SHEET 1 AA8 2 GLY C1751 GLU C1753 0 SHEET 2 AA8 2 PHE C1762 LYS C1764 -1 O PHE C1762 N GLU C1753 SHEET 1 AA9 2 LEU C1839 VAL C1841 0 SHEET 2 AA9 2 THR C1849 PRO C1851 -1 O ILE C1850 N LEU C1840 SHEET 1 AB1 5 LEU C1875 PHE C1877 0 SHEET 2 AB1 5 GLY C1891 TYR C1898 -1 O ALA C1897 N GLU C1876 SHEET 3 AB1 5 VAL C1903 PHE C1908 -1 O VAL C1905 N TYR C1894 SHEET 4 AB1 5 MET C1944 MET C1947 -1 O LEU C1945 N LYS C1906 SHEET 5 AB1 5 LEU C1935 ALA C1938 -1 N ALA C1937 O VAL C1946 SHEET 1 AB2 2 VAL C2000 LEU C2002 0 SHEET 2 AB2 2 ALA C2013 ILE C2015 -1 O LYS C2014 N LEU C2001 SHEET 1 AB3 4 LEU C2140 LEU C2145 0 SHEET 2 AB3 4 GLN C2490 TRP C2496 -1 O VAL C2495 N ARG C2142 SHEET 3 AB3 4 LEU C2466 ASN C2476 -1 N ASN C2476 O GLN C2490 SHEET 4 AB3 4 VAL C2455 LEU C2463 -1 N ALA C2461 O VAL C2469 SHEET 1 AB4 4 VAL C2152 ALA C2157 0 SHEET 2 AB4 4 SER C2166 CYS C2171 -1 O TRP C2168 N VAL C2156 SHEET 3 AB4 4 GLN C2178 ASP C2183 -1 O SER C2180 N LEU C2169 SHEET 4 AB4 4 TYR C2189 THR C2190 -1 O THR C2190 N PHE C2181 SHEET 1 AB5 3 ILE C2199 LEU C2207 0 SHEET 2 AB5 3 GLU C2212 THR C2219 -1 O GLY C2218 N LEU C2200 SHEET 3 AB5 3 VAL C2226 ASN C2228 -1 O ILE C2227 N ILE C2215 SHEET 1 AB6 5 VAL C2245 CYS C2247 0 SHEET 2 AB6 5 GLY C2266 THR C2267 -1 O GLY C2266 N CYS C2247 SHEET 3 AB6 5 LYS C2271 GLU C2276 -1 O LYS C2271 N THR C2267 SHEET 4 AB6 5 ASN C2261 LEU C2263 -1 N LEU C2263 O PHE C2275 SHEET 5 AB6 5 CYS C2250 SER C2252 -1 N ASN C2251 O PHE C2262 SHEET 1 AB7 4 VAL C2245 CYS C2247 0 SHEET 2 AB7 4 GLY C2266 THR C2267 -1 O GLY C2266 N CYS C2247 SHEET 3 AB7 4 LYS C2271 GLU C2276 -1 O LYS C2271 N THR C2267 SHEET 4 AB7 4 LYS C2289 ASN C2292 -1 O LEU C2291 N LEU C2272 SHEET 1 AB8 3 GLY C2317 CYS C2319 0 SHEET 2 AB8 3 LYS C2322 PHE C2324 -1 O PHE C2324 N GLY C2317 SHEET 3 AB8 3 LEU C2335 GLU C2337 -1 O ILE C2336 N ILE C2323 SHEET 1 AB9 4 ILE C2354 VAL C2359 0 SHEET 2 AB9 4 LEU C2363 LYS C2367 -1 O ALA C2366 N ILE C2355 SHEET 3 AB9 4 VAL C2372 TRP C2376 -1 O TRP C2376 N LEU C2363 SHEET 4 AB9 4 LEU C2383 ASP C2388 -1 O GLY C2385 N VAL C2375 SHEET 1 AC1 4 THR C2416 LEU C2419 0 SHEET 2 AC1 4 ALA C2424 GLY C2428 -1 O TRP C2426 N CYS C2418 SHEET 3 AC1 4 ILE C2434 ASP C2438 -1 O LEU C2435 N ILE C2427 SHEET 4 AC1 4 LEU C2444 ILE C2448 -1 O ILE C2445 N LEU C2436 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