HEADER PROTEIN BINDING 17-MAR-17 5V6R TITLE STRUCTURE OF PLEXIN D1 INTRACELLULAR DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLEXIN-D1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 1339-1925; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: PLXND1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RAP GAP, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR G.SHANG,X.ZHANG REVDAT 5 04-OCT-23 5V6R 1 REMARK REVDAT 4 01-JAN-20 5V6R 1 REMARK REVDAT 3 27-SEP-17 5V6R 1 REMARK REVDAT 2 07-JUN-17 5V6R 1 JRNL REVDAT 1 31-MAY-17 5V6R 0 JRNL AUTH G.SHANG,C.A.BRAUTIGAM,R.CHEN,D.LU,J.TORRES-VAZQUEZ,X.ZHANG JRNL TITL STRUCTURE ANALYSES REVEAL A REGULATED OLIGOMERIZATION JRNL TITL 2 MECHANISM OF THE PLEXIND1/GIPC/MYOSIN VI COMPLEX. JRNL REF ELIFE V. 6 2017 JRNL REFN ESSN 2050-084X JRNL PMID 28537552 JRNL DOI 10.7554/ELIFE.27322 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.490 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 47172 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.730 REMARK 3 FREE R VALUE TEST SET COUNT : 1759 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 37.0986 - 6.3389 0.87 3363 130 0.1730 0.2241 REMARK 3 2 6.3389 - 5.0353 0.91 3478 135 0.2079 0.2567 REMARK 3 3 5.0353 - 4.4000 0.90 3450 134 0.1845 0.2383 REMARK 3 4 4.4000 - 3.9982 0.91 3488 135 0.1949 0.2151 REMARK 3 5 3.9982 - 3.7119 0.92 3504 136 0.2200 0.2452 REMARK 3 6 3.7119 - 3.4933 0.93 3547 137 0.2272 0.2680 REMARK 3 7 3.4933 - 3.3184 0.93 3556 138 0.2367 0.3010 REMARK 3 8 3.3184 - 3.1741 0.94 3561 138 0.2534 0.2891 REMARK 3 9 3.1741 - 3.0519 0.94 3597 140 0.2659 0.3109 REMARK 3 10 3.0519 - 2.9467 0.95 3604 139 0.2709 0.2867 REMARK 3 11 2.9467 - 2.8546 0.94 3593 137 0.2752 0.3073 REMARK 3 12 2.8546 - 2.7730 0.92 3463 136 0.2875 0.3149 REMARK 3 13 2.7730 - 2.7000 0.85 3209 124 0.3182 0.3691 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) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.640 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 : 0.003 8266 REMARK 3 ANGLE : 0.616 11191 REMARK 3 CHIRALITY : 0.022 1271 REMARK 3 PLANARITY : 0.003 1415 REMARK 3 DIHEDRAL : 11.847 3043 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND RESI 1552:1690 REMARK 3 ORIGIN FOR THE GROUP (A): -49.5378 -31.5711 -54.9669 REMARK 3 T TENSOR REMARK 3 T11: 0.7725 T22: 0.7097 REMARK 3 T33: 0.3432 T12: -0.1128 REMARK 3 T13: 0.0202 T23: 0.0119 REMARK 3 L TENSOR REMARK 3 L11: 6.2448 L22: 4.6042 REMARK 3 L33: 4.3637 L12: 0.5933 REMARK 3 L13: 2.7103 L23: 2.9217 REMARK 3 S TENSOR REMARK 3 S11: 0.1807 S12: 0.3938 S13: -0.2079 REMARK 3 S21: -0.6749 S22: 0.1327 S23: -0.1698 REMARK 3 S31: -0.4030 S32: 0.5071 S33: -0.3301 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND NOT RESI 1552:1690 REMARK 3 ORIGIN FOR THE GROUP (A): -26.6428 -39.5551 -22.4054 REMARK 3 T TENSOR REMARK 3 T11: 0.3653 T22: 0.4193 REMARK 3 T33: 0.3707 T12: -0.0255 REMARK 3 T13: -0.0182 T23: 0.0139 REMARK 3 L TENSOR REMARK 3 L11: 5.8529 L22: 1.2303 REMARK 3 L33: 1.1441 L12: -0.6485 REMARK 3 L13: 1.2190 L23: -0.3446 REMARK 3 S TENSOR REMARK 3 S11: 0.1392 S12: 0.0294 S13: -0.5914 REMARK 3 S21: 0.0185 S22: -0.0258 S23: 0.0378 REMARK 3 S31: -0.0233 S32: -0.0516 S33: -0.0801 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN B AND RESI 1552:1690 REMARK 3 ORIGIN FOR THE GROUP (A): 23.4544 -93.5788 25.6926 REMARK 3 T TENSOR REMARK 3 T11: 0.8311 T22: 0.8138 REMARK 3 T33: 1.3268 T12: 0.0358 REMARK 3 T13: 0.1660 T23: 0.2973 REMARK 3 L TENSOR REMARK 3 L11: 8.5024 L22: 3.5627 REMARK 3 L33: 1.9575 L12: -2.8565 REMARK 3 L13: 0.5322 L23: 0.3491 REMARK 3 S TENSOR REMARK 3 S11: 0.2516 S12: 0.1366 S13: -1.5281 REMARK 3 S21: 0.2725 S22: -0.4220 S23: -0.2054 REMARK 3 S31: 0.3360 S32: 0.4151 S33: 0.2051 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN B AND NOT RESI 1552:1690 REMARK 3 ORIGIN FOR THE GROUP (A): 1.3506 -63.9068 9.5277 REMARK 3 T TENSOR REMARK 3 T11: 0.4053 T22: 0.5523 REMARK 3 T33: 0.6388 T12: -0.0211 REMARK 3 T13: -0.0517 T23: 0.1104 REMARK 3 L TENSOR REMARK 3 L11: 4.0803 L22: 1.6161 REMARK 3 L33: 2.0631 L12: -1.1044 REMARK 3 L13: 0.5139 L23: -0.9822 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: 0.0522 S13: -0.7214 REMARK 3 S21: 0.0723 S22: 0.0537 S23: 0.0446 REMARK 3 S31: 0.0208 S32: -0.1603 S33: -0.0501 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 5V6R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000226971. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51129 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: 3IG3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 65.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE (PH 7.8) AND 15% (W/V) REMARK 280 PEG8000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 82.27200 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 GLU A 1339 REMARK 465 LEU A 1340 REMARK 465 ASN A 1341 REMARK 465 ARG A 1342 REMARK 465 SER A 1343 REMARK 465 GLN A 1344 REMARK 465 LYS A 1362 REMARK 465 CYS A 1363 REMARK 465 SER A 1364 REMARK 465 SER A 1365 REMARK 465 LEU A 1366 REMARK 465 TYR A 1367 REMARK 465 GLU A 1368 REMARK 465 GLU A 1369 REMARK 465 ARG A 1370 REMARK 465 TYR A 1371 REMARK 465 VAL A 1372 REMARK 465 LEU A 1373 REMARK 465 PRO A 1374 REMARK 465 SER A 1375 REMARK 465 LYS A 1376 REMARK 465 THR A 1377 REMARK 465 LEU A 1378 REMARK 465 ASN A 1379 REMARK 465 SER A 1380 REMARK 465 GLN A 1381 REMARK 465 GLY A 1382 REMARK 465 GLY A 1383 REMARK 465 SER A 1384 REMARK 465 PRO A 1385 REMARK 465 PRO A 1386 REMARK 465 GLN A 1387 REMARK 465 GLU A 1388 REMARK 465 GLY A 1564 REMARK 465 CYS A 1565 REMARK 465 GLY A 1566 REMARK 465 MET A 1567 REMARK 465 ASP A 1656 REMARK 465 LYS A 1657 REMARK 465 LYS A 1658 REMARK 465 ASP A 1659 REMARK 465 SER A 1660 REMARK 465 THR A 1661 REMARK 465 LEU A 1662 REMARK 465 GLY A 1663 REMARK 465 ARG A 1664 REMARK 465 VAL A 1665 REMARK 465 LYS A 1666 REMARK 465 ASP A 1667 REMARK 465 LEU A 1668 REMARK 465 ASP A 1669 REMARK 465 LEU A 1678 REMARK 465 PRO A 1679 REMARK 465 THR A 1680 REMARK 465 ASP A 1681 REMARK 465 GLU A 1682 REMARK 465 LEU A 1683 REMARK 465 VAL A 1684 REMARK 465 GLU A 1685 REMARK 465 PRO A 1686 REMARK 465 LYS A 1687 REMARK 465 LYS A 1688 REMARK 465 SER A 1689 REMARK 465 HIS A 1690 REMARK 465 ARG A 1691 REMARK 465 GLN A 1692 REMARK 465 SER A 1693 REMARK 465 HIS A 1694 REMARK 465 ARG A 1695 REMARK 465 LYS A 1696 REMARK 465 ASP A 1810 REMARK 465 LEU A 1811 REMARK 465 GLN A 1812 REMARK 465 LEU A 1813 REMARK 465 GLY A 1814 REMARK 465 LYS A 1815 REMARK 465 ASP A 1816 REMARK 465 SER A 1817 REMARK 465 PRO A 1818 REMARK 465 THR A 1819 REMARK 465 GLU A 1924 REMARK 465 ALA A 1925 REMARK 465 GLU B 1339 REMARK 465 LEU B 1340 REMARK 465 ASN B 1341 REMARK 465 ARG B 1342 REMARK 465 SER B 1343 REMARK 465 GLN B 1344 REMARK 465 LYS B 1362 REMARK 465 CYS B 1363 REMARK 465 SER B 1364 REMARK 465 SER B 1365 REMARK 465 LEU B 1366 REMARK 465 TYR B 1367 REMARK 465 GLU B 1368 REMARK 465 GLU B 1369 REMARK 465 ARG B 1370 REMARK 465 TYR B 1371 REMARK 465 VAL B 1372 REMARK 465 LEU B 1373 REMARK 465 PRO B 1374 REMARK 465 SER B 1375 REMARK 465 LYS B 1376 REMARK 465 THR B 1377 REMARK 465 LEU B 1378 REMARK 465 ASN B 1379 REMARK 465 SER B 1380 REMARK 465 GLN B 1381 REMARK 465 GLY B 1382 REMARK 465 GLY B 1383 REMARK 465 SER B 1384 REMARK 465 PRO B 1385 REMARK 465 PRO B 1386 REMARK 465 GLN B 1387 REMARK 465 GLU B 1388 REMARK 465 GLY B 1564 REMARK 465 CYS B 1565 REMARK 465 GLY B 1566 REMARK 465 MET B 1567 REMARK 465 LYS B 1657 REMARK 465 LYS B 1658 REMARK 465 ASP B 1659 REMARK 465 SER B 1660 REMARK 465 THR B 1661 REMARK 465 LEU B 1662 REMARK 465 GLY B 1663 REMARK 465 ARG B 1664 REMARK 465 VAL B 1665 REMARK 465 LYS B 1666 REMARK 465 ASP B 1667 REMARK 465 LEU B 1668 REMARK 465 ASP B 1669 REMARK 465 LEU B 1678 REMARK 465 PRO B 1679 REMARK 465 THR B 1680 REMARK 465 ASP B 1681 REMARK 465 GLU B 1682 REMARK 465 LEU B 1683 REMARK 465 VAL B 1684 REMARK 465 GLU B 1685 REMARK 465 PRO B 1686 REMARK 465 LYS B 1687 REMARK 465 LYS B 1688 REMARK 465 SER B 1689 REMARK 465 HIS B 1690 REMARK 465 ARG B 1691 REMARK 465 GLN B 1692 REMARK 465 SER B 1693 REMARK 465 HIS B 1694 REMARK 465 ARG B 1695 REMARK 465 LYS B 1696 REMARK 465 LYS B 1697 REMARK 465 ASP B 1810 REMARK 465 LEU B 1811 REMARK 465 GLN B 1812 REMARK 465 LEU B 1813 REMARK 465 GLY B 1814 REMARK 465 LYS B 1815 REMARK 465 ASP B 1816 REMARK 465 SER B 1817 REMARK 465 PRO B 1818 REMARK 465 THR B 1819 REMARK 465 ASN B 1820 REMARK 465 SER B 1923 REMARK 465 GLU B 1924 REMARK 465 ALA B 1925 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 THR A1389 OG1 CG2 REMARK 470 ASN A1397 CG OD1 ND2 REMARK 470 GLU A1400 CG CD OE1 OE2 REMARK 470 LYS A1554 CG CD CE NZ REMARK 470 GLN A1563 CG CD OE1 NE2 REMARK 470 ASP A1568 CG OD1 OD2 REMARK 470 LYS A1593 CG CD CE NZ REMARK 470 GLU A1630 CG CD OE1 OE2 REMARK 470 ASP A1631 CG OD1 OD2 REMARK 470 ARG A1633 CG CD NE CZ NH1 NH2 REMARK 470 THR A1670 OG1 CG2 REMARK 470 GLU A1671 CG CD OE1 OE2 REMARK 470 LYS A1672 CG CD CE NZ REMARK 470 LYS A1697 CG CD CE NZ REMARK 470 SER A1809 OG REMARK 470 ASN A1820 CG OD1 ND2 REMARK 470 LYS A1821 CG CD CE NZ REMARK 470 PRO B1361 CG CD REMARK 470 THR B1389 OG1 CG2 REMARK 470 ASN B1397 CG OD1 ND2 REMARK 470 GLU B1400 CG CD OE1 OE2 REMARK 470 GLU B1408 CG CD OE1 OE2 REMARK 470 GLU B1549 CG CD OE1 OE2 REMARK 470 ILE B1551 CG1 CG2 CD1 REMARK 470 GLU B1552 CG CD OE1 OE2 REMARK 470 LYS B1554 CG CD CE NZ REMARK 470 GLN B1563 CG CD OE1 NE2 REMARK 470 ASP B1568 CG OD1 OD2 REMARK 470 LYS B1593 CG CD CE NZ REMARK 470 SER B1614 OG REMARK 470 GLU B1630 CG CD OE1 OE2 REMARK 470 ASP B1631 CG OD1 OD2 REMARK 470 ARG B1633 CG CD NE CZ NH1 NH2 REMARK 470 LYS B1634 CG CD CE NZ REMARK 470 ASP B1656 CG OD1 OD2 REMARK 470 THR B1670 OG1 CG2 REMARK 470 GLU B1671 CG CD OE1 OE2 REMARK 470 LYS B1672 CG CD CE NZ REMARK 470 SER B1809 OG REMARK 470 LYS B1821 CG CD CE NZ REMARK 470 LYS B1863 CG CD CE NZ REMARK 470 TYR B1922 CG CD1 CD2 CE1 CE2 CZ OH 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 B 2025 O HOH B 2031 1.80 REMARK 500 O HOH B 2018 O HOH B 2039 1.91 REMARK 500 O THR B 1846 O HOH B 2001 1.92 REMARK 500 O SER A 1474 O HOH A 2001 2.00 REMARK 500 OE1 GLU B 1431 O HOH B 2002 2.17 REMARK 500 OG1 THR B 1581 OD2 ASP B 1622 2.19 REMARK 500 OG1 THR A 1581 OD2 ASP A 1622 2.19 REMARK 500 N ARG A 1729 O HOH A 2002 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A1397 36.56 -79.24 REMARK 500 THR A1509 -49.10 -131.49 REMARK 500 LEU A1547 88.97 -67.60 REMARK 500 ARG A1548 21.58 -73.37 REMARK 500 ALA A1574 -159.62 -139.53 REMARK 500 ASN A1594 44.89 -86.70 REMARK 500 SER A1613 -152.53 -133.76 REMARK 500 ASP A1624 -152.34 -157.89 REMARK 500 HIS A1675 -73.78 -118.78 REMARK 500 LYS A1732 85.86 -151.13 REMARK 500 LEU A1767 -56.83 -124.48 REMARK 500 SER A1807 -167.71 -71.37 REMARK 500 ILE A1808 -32.01 -130.91 REMARK 500 TYR A1864 66.30 -104.58 REMARK 500 ASN B1397 36.25 -81.52 REMARK 500 ASN B1550 78.77 -100.18 REMARK 500 ASN B1594 42.20 -102.89 REMARK 500 SER B1613 -153.95 -127.39 REMARK 500 ASP B1624 -149.96 -156.61 REMARK 500 HIS B1675 -59.76 -127.74 REMARK 500 LEU B1726 43.55 -101.79 REMARK 500 LEU B1767 -58.83 -131.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5V6B RELATED DB: PDB REMARK 900 RELATED ID: 5V6E RELATED DB: PDB REMARK 900 RELATED ID: 5V6H RELATED DB: PDB REMARK 900 RELATED ID: 5V6T RELATED DB: PDB DBREF 5V6R A 1339 1925 UNP Q3UH93 PLXD1_MOUSE 1339 1925 DBREF 5V6R B 1339 1925 UNP Q3UH93 PLXD1_MOUSE 1339 1925 SEQRES 1 A 587 GLU LEU ASN ARG SER GLN GLY ILE PRO PHE LEU GLU TYR SEQRES 2 A 587 LYS HIS PHE VAL THR ARG THR PHE PHE PRO LYS CYS SER SEQRES 3 A 587 SER LEU TYR GLU GLU ARG TYR VAL LEU PRO SER LYS THR SEQRES 4 A 587 LEU ASN SER GLN GLY GLY SER PRO PRO GLN GLU THR HIS SEQRES 5 A 587 PRO LEU LEU GLY GLU TRP ASN ILE PRO GLU HIS CYS ARG SEQRES 6 A 587 PRO SER MET GLU GLU GLY ILE SER LEU PHE SER SER LEU SEQRES 7 A 587 LEU ASN ASN LYS HIS PHE LEU ILE VAL PHE VAL HIS ALA SEQRES 8 A 587 LEU GLU GLN GLN LYS ASP PHE ALA VAL ARG ASP ARG CYS SEQRES 9 A 587 SER LEU ALA SER LEU LEU THR ILE ALA LEU HIS GLY LYS SEQRES 10 A 587 LEU GLU TYR TYR THR SER ILE MET LYS GLU LEU LEU VAL SEQRES 11 A 587 ASP LEU ILE ASP ALA SER ALA ALA LYS ASN PRO LYS LEU SEQRES 12 A 587 MET LEU ARG ARG THR GLU SER VAL VAL GLU LYS MET LEU SEQRES 13 A 587 THR ASN TRP MET SER ILE CYS MET TYR GLY CYS LEU ARG SEQRES 14 A 587 GLU THR VAL GLY GLU PRO PHE PHE LEU LEU LEU CYS ALA SEQRES 15 A 587 ILE LYS GLN GLN ILE ASN LYS GLY SER ILE ASP ALA ILE SEQRES 16 A 587 THR GLY LYS ALA ARG TYR THR LEU ASN GLU GLU TRP LEU SEQRES 17 A 587 LEU ARG GLU ASN ILE GLU ALA LYS PRO ARG ASN LEU ASN SEQRES 18 A 587 VAL SER PHE GLN GLY CYS GLY MET ASP SER LEU SER VAL SEQRES 19 A 587 ARG ALA MET ASP THR ASP THR LEU THR GLN VAL LYS GLU SEQRES 20 A 587 LYS ILE LEU GLU ALA PHE CYS LYS ASN VAL PRO TYR SER SEQRES 21 A 587 GLN TRP PRO ARG ALA GLU ASP VAL ASP LEU GLU TRP PHE SEQRES 22 A 587 ALA SER SER THR GLN SER TYR VAL LEU ARG ASP LEU ASP SEQRES 23 A 587 ASP THR SER VAL VAL GLU ASP GLY ARG LYS LYS LEU ASN SEQRES 24 A 587 THR LEU ALA HIS TYR LYS ILE PRO GLU GLY ALA SER LEU SEQRES 25 A 587 ALA MET SER LEU THR ASP LYS LYS ASP SER THR LEU GLY SEQRES 26 A 587 ARG VAL LYS ASP LEU ASP THR GLU LYS TYR PHE HIS LEU SEQRES 27 A 587 VAL LEU PRO THR ASP GLU LEU VAL GLU PRO LYS LYS SER SEQRES 28 A 587 HIS ARG GLN SER HIS ARG LYS LYS VAL LEU PRO GLU ILE SEQRES 29 A 587 TYR LEU THR ARG LEU LEU SER THR LYS GLY THR LEU GLN SEQRES 30 A 587 LYS PHE LEU ASP ASP LEU PHE LYS ALA ILE LEU SER ILE SEQRES 31 A 587 ARG GLU ASP LYS PRO PRO LEU ALA VAL LYS TYR PHE PHE SEQRES 32 A 587 ASP PHE LEU GLU GLU GLN ALA GLU LYS ARG GLY ILE SER SEQRES 33 A 587 ASP PRO ASP THR LEU HIS ILE TRP LYS THR ASN SER LEU SEQRES 34 A 587 PRO LEU ARG PHE TRP VAL ASN ILE LEU LYS ASN PRO GLN SEQRES 35 A 587 PHE VAL PHE ASP ILE GLU LYS THR ASP HIS ILE ASP ALA SEQRES 36 A 587 CYS LEU SER VAL ILE ALA GLN ALA PHE ILE ASP ALA CYS SEQRES 37 A 587 SER ILE SER ASP LEU GLN LEU GLY LYS ASP SER PRO THR SEQRES 38 A 587 ASN LYS LEU LEU TYR ALA LYS GLU ILE PRO GLU TYR ARG SEQRES 39 A 587 LYS THR VAL GLN ARG TYR TYR LYS GLN ILE GLN ASP MET SEQRES 40 A 587 THR PRO LEU SER GLU GLN GLU MET ASN ALA HIS LEU ALA SEQRES 41 A 587 GLU GLU SER ARG LYS TYR GLN ASN GLU PHE ASN THR ASN SEQRES 42 A 587 VAL ALA MET ALA GLU ILE TYR LYS TYR ALA LYS ARG TYR SEQRES 43 A 587 ARG PRO GLN ILE MET ALA ALA LEU GLU ALA ASN PRO THR SEQRES 44 A 587 ALA ARG ARG THR GLN LEU GLN HIS LYS PHE GLU GLN VAL SEQRES 45 A 587 VAL ALA LEU MET GLU ASN ASN ILE TYR GLU CYS TYR SER SEQRES 46 A 587 GLU ALA SEQRES 1 B 587 GLU LEU ASN ARG SER GLN GLY ILE PRO PHE LEU GLU TYR SEQRES 2 B 587 LYS HIS PHE VAL THR ARG THR PHE PHE PRO LYS CYS SER SEQRES 3 B 587 SER LEU TYR GLU GLU ARG TYR VAL LEU PRO SER LYS THR SEQRES 4 B 587 LEU ASN SER GLN GLY GLY SER PRO PRO GLN GLU THR HIS SEQRES 5 B 587 PRO LEU LEU GLY GLU TRP ASN ILE PRO GLU HIS CYS ARG SEQRES 6 B 587 PRO SER MET GLU GLU GLY ILE SER LEU PHE SER SER LEU SEQRES 7 B 587 LEU ASN ASN LYS HIS PHE LEU ILE VAL PHE VAL HIS ALA SEQRES 8 B 587 LEU GLU GLN GLN LYS ASP PHE ALA VAL ARG ASP ARG CYS SEQRES 9 B 587 SER LEU ALA SER LEU LEU THR ILE ALA LEU HIS GLY LYS SEQRES 10 B 587 LEU GLU TYR TYR THR SER ILE MET LYS GLU LEU LEU VAL SEQRES 11 B 587 ASP LEU ILE ASP ALA SER ALA ALA LYS ASN PRO LYS LEU SEQRES 12 B 587 MET LEU ARG ARG THR GLU SER VAL VAL GLU LYS MET LEU SEQRES 13 B 587 THR ASN TRP MET SER ILE CYS MET TYR GLY CYS LEU ARG SEQRES 14 B 587 GLU THR VAL GLY GLU PRO PHE PHE LEU LEU LEU CYS ALA SEQRES 15 B 587 ILE LYS GLN GLN ILE ASN LYS GLY SER ILE ASP ALA ILE SEQRES 16 B 587 THR GLY LYS ALA ARG TYR THR LEU ASN GLU GLU TRP LEU SEQRES 17 B 587 LEU ARG GLU ASN ILE GLU ALA LYS PRO ARG ASN LEU ASN SEQRES 18 B 587 VAL SER PHE GLN GLY CYS GLY MET ASP SER LEU SER VAL SEQRES 19 B 587 ARG ALA MET ASP THR ASP THR LEU THR GLN VAL LYS GLU SEQRES 20 B 587 LYS ILE LEU GLU ALA PHE CYS LYS ASN VAL PRO TYR SER SEQRES 21 B 587 GLN TRP PRO ARG ALA GLU ASP VAL ASP LEU GLU TRP PHE SEQRES 22 B 587 ALA SER SER THR GLN SER TYR VAL LEU ARG ASP LEU ASP SEQRES 23 B 587 ASP THR SER VAL VAL GLU ASP GLY ARG LYS LYS LEU ASN SEQRES 24 B 587 THR LEU ALA HIS TYR LYS ILE PRO GLU GLY ALA SER LEU SEQRES 25 B 587 ALA MET SER LEU THR ASP LYS LYS ASP SER THR LEU GLY SEQRES 26 B 587 ARG VAL LYS ASP LEU ASP THR GLU LYS TYR PHE HIS LEU SEQRES 27 B 587 VAL LEU PRO THR ASP GLU LEU VAL GLU PRO LYS LYS SER SEQRES 28 B 587 HIS ARG GLN SER HIS ARG LYS LYS VAL LEU PRO GLU ILE SEQRES 29 B 587 TYR LEU THR ARG LEU LEU SER THR LYS GLY THR LEU GLN SEQRES 30 B 587 LYS PHE LEU ASP ASP LEU PHE LYS ALA ILE LEU SER ILE SEQRES 31 B 587 ARG GLU ASP LYS PRO PRO LEU ALA VAL LYS TYR PHE PHE SEQRES 32 B 587 ASP PHE LEU GLU GLU GLN ALA GLU LYS ARG GLY ILE SER SEQRES 33 B 587 ASP PRO ASP THR LEU HIS ILE TRP LYS THR ASN SER LEU SEQRES 34 B 587 PRO LEU ARG PHE TRP VAL ASN ILE LEU LYS ASN PRO GLN SEQRES 35 B 587 PHE VAL PHE ASP ILE GLU LYS THR ASP HIS ILE ASP ALA SEQRES 36 B 587 CYS LEU SER VAL ILE ALA GLN ALA PHE ILE ASP ALA CYS SEQRES 37 B 587 SER ILE SER ASP LEU GLN LEU GLY LYS ASP SER PRO THR SEQRES 38 B 587 ASN LYS LEU LEU TYR ALA LYS GLU ILE PRO GLU TYR ARG SEQRES 39 B 587 LYS THR VAL GLN ARG TYR TYR LYS GLN ILE GLN ASP MET SEQRES 40 B 587 THR PRO LEU SER GLU GLN GLU MET ASN ALA HIS LEU ALA SEQRES 41 B 587 GLU GLU SER ARG LYS TYR GLN ASN GLU PHE ASN THR ASN SEQRES 42 B 587 VAL ALA MET ALA GLU ILE TYR LYS TYR ALA LYS ARG TYR SEQRES 43 B 587 ARG PRO GLN ILE MET ALA ALA LEU GLU ALA ASN PRO THR SEQRES 44 B 587 ALA ARG ARG THR GLN LEU GLN HIS LYS PHE GLU GLN VAL SEQRES 45 B 587 VAL ALA LEU MET GLU ASN ASN ILE TYR GLU CYS TYR SER SEQRES 46 B 587 GLU ALA FORMUL 3 HOH *98(H2 O) HELIX 1 AA1 GLU A 1350 PHE A 1360 1 11 HELIX 2 AA2 THR A 1389 LEU A 1393 5 5 HELIX 3 AA3 CYS A 1402 ASN A 1418 1 17 HELIX 4 AA4 ASN A 1419 GLN A 1432 1 14 HELIX 5 AA5 ALA A 1437 LEU A 1452 1 16 HELIX 6 AA6 LYS A 1455 SER A 1474 1 20 HELIX 7 AA7 ASN A 1478 MET A 1482 5 5 HELIX 8 AA8 SER A 1488 THR A 1509 1 22 HELIX 9 AA9 VAL A 1510 ASN A 1526 1 17 HELIX 10 AB1 ASN A 1542 LEU A 1546 5 5 HELIX 11 AB2 THR A 1579 CYS A 1592 1 14 HELIX 12 AB3 PRO A 1596 TRP A 1600 5 5 HELIX 13 AB4 ARG A 1602 GLU A 1604 5 3 HELIX 14 AB5 PRO A 1700 LEU A 1726 1 27 HELIX 15 AB6 PRO A 1734 LYS A 1750 1 17 HELIX 16 AB7 ASP A 1755 ASN A 1765 1 11 HELIX 17 AB8 PHE A 1771 ASN A 1778 1 8 HELIX 18 AB9 PRO A 1779 VAL A 1782 5 4 HELIX 19 AC1 THR A 1788 SER A 1807 1 20 HELIX 20 AC2 GLU A 1827 MET A 1845 1 19 HELIX 21 AC3 SER A 1849 TYR A 1864 1 16 HELIX 22 AC4 ASN A 1869 TYR A 1884 1 16 HELIX 23 AC5 TYR A 1884 ALA A 1894 1 11 HELIX 24 AC6 ASN A 1895 THR A 1901 1 7 HELIX 25 AC7 GLN A 1902 TYR A 1922 1 21 HELIX 26 AC8 GLU B 1350 PHE B 1360 1 11 HELIX 27 AC9 THR B 1389 LEU B 1393 5 5 HELIX 28 AD1 CYS B 1402 ASN B 1418 1 17 HELIX 29 AD2 ASN B 1419 GLU B 1431 1 13 HELIX 30 AD3 ALA B 1437 LEU B 1452 1 16 HELIX 31 AD4 LYS B 1455 SER B 1474 1 20 HELIX 32 AD5 ASN B 1478 MET B 1482 5 5 HELIX 33 AD6 SER B 1488 ARG B 1507 1 20 HELIX 34 AD7 VAL B 1510 LYS B 1527 1 18 HELIX 35 AD8 ASN B 1542 LEU B 1546 5 5 HELIX 36 AD9 THR B 1579 CYS B 1592 1 14 HELIX 37 AE1 PRO B 1596 TRP B 1600 5 5 HELIX 38 AE2 ARG B 1602 GLU B 1604 5 3 HELIX 39 AE3 PRO B 1700 LEU B 1726 1 27 HELIX 40 AE4 PRO B 1734 ARG B 1751 1 18 HELIX 41 AE5 ASP B 1755 LEU B 1767 1 13 HELIX 42 AE6 PHE B 1771 ASN B 1778 1 8 HELIX 43 AE7 PRO B 1779 VAL B 1782 5 4 HELIX 44 AE8 THR B 1788 SER B 1807 1 20 HELIX 45 AE9 GLU B 1827 ASP B 1844 1 18 HELIX 46 AF1 SER B 1849 TYR B 1864 1 16 HELIX 47 AF2 ASN B 1869 TYR B 1884 1 16 HELIX 48 AF3 TYR B 1884 ASN B 1895 1 12 HELIX 49 AF4 ASN B 1895 THR B 1901 1 7 HELIX 50 AF5 GLN B 1902 TYR B 1922 1 21 SHEET 1 AA1 5 LEU A1570 MET A1575 0 SHEET 2 AA1 5 PRO A1555 PHE A1562 -1 N VAL A1560 O LEU A1570 SHEET 3 AA1 5 ALA A1648 LEU A1654 1 O MET A1652 N SER A1561 SHEET 4 AA1 5 VAL A1606 TRP A1610 -1 N ASP A1607 O SER A1653 SHEET 5 AA1 5 TYR A1618 VAL A1619 -1 O TYR A1618 N TRP A1610 SHEET 1 AA2 3 VAL A1629 GLU A1630 0 SHEET 2 AA2 3 ARG A1633 LYS A1635 -1 O ARG A1633 N GLU A1630 SHEET 3 AA2 3 TYR A1673 PHE A1674 1 O PHE A1674 N LYS A1634 SHEET 1 AA3 5 SER B1569 MET B1575 0 SHEET 2 AA3 5 PRO B1555 PHE B1562 -1 N LEU B1558 O VAL B1572 SHEET 3 AA3 5 ALA B1648 LEU B1654 1 O LEU B1650 N ASN B1559 SHEET 4 AA3 5 VAL B1606 PHE B1611 -1 N GLU B1609 O ALA B1651 SHEET 5 AA3 5 TYR B1618 LEU B1620 -1 O TYR B1618 N TRP B1610 SHEET 1 AA4 2 LYS B1634 LYS B1635 0 SHEET 2 AA4 2 TYR B1673 PHE B1674 1 O PHE B1674 N LYS B1634 SSBOND 1 CYS A 1402 CYS A 1921 1555 1555 2.03 SSBOND 2 CYS B 1402 CYS B 1921 1555 1555 2.04 CRYST1 69.852 164.544 84.268 90.00 99.47 90.00 P 1 21 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 0.014316 0.000000 0.002389 0.00000 SCALE2 0.000000 0.006077 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012031 0.00000