HEADER IMMUNE SYSTEM 19-APR-13 4K9E TITLE CRYSTAL STRUCTURE OF KIT D4D5 FRAGMENT IN COMPLEX WITH ANTI-KIT TITLE 2 ANTIBODIES FAB79D COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: HEAVY CHAIN; COMPND 7 CHAIN: H; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: MAST/STEM CELL GROWTH FACTOR RECEPTOR KIT; COMPND 11 CHAIN: C; COMPND 12 SYNONYM: SCFR, PIEBALD TRAIT PROTEIN, PBT, PROTO-ONCOGENE C-KIT, COMPND 13 TYROSINE-PROTEIN KINASE KIT, P145 C-KIT, V-KIT HARDY-ZUCKERMAN 4 COMPND 14 FELINE SARCOMA VIRAL ONCOGENE HOMOLOG; COMPND 15 EC: 2.7.10.1; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_TAXID: 10090; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: KIT, SCFR; SOURCE 16 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 10469 KEYWDS RECEPTOR TYROSINE KINASE (RTK), IGG, FAB, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR A.V.RESHEYNYAK,T.J.BOGGON,I.LAX,J.SCHLESSINGER REVDAT 3 29-JUL-20 4K9E 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 12-MAR-14 4K9E 1 JRNL REVDAT 1 16-OCT-13 4K9E 0 JRNL AUTH A.V.RESHETNYAK,B.NELSON,X.SHI,T.J.BOGGON,A.PAVLENCO, JRNL AUTH 2 E.M.MANDEL-BAUSCH,F.TOME,Y.SUZUKI,S.S.SIDHU,I.LAX, JRNL AUTH 3 J.SCHLESSINGER JRNL TITL STRUCTURAL BASIS FOR KIT RECEPTOR TYROSINE KINASE INHIBITION JRNL TITL 2 BY ANTIBODIES TARGETING THE D4 MEMBRANE-PROXIMAL REGION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 17832 2013 JRNL REFN ISSN 0027-8424 JRNL PMID 24127596 JRNL DOI 10.1073/PNAS.1317118110 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 22010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.248 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.282 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1138 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 44.7854 - 5.4070 1.00 3136 159 0.2368 0.2923 REMARK 3 2 5.4070 - 4.2928 1.00 2927 143 0.1967 0.1972 REMARK 3 3 4.2928 - 3.7505 1.00 2868 173 0.2167 0.2752 REMARK 3 4 3.7505 - 3.4077 1.00 2828 158 0.2411 0.2630 REMARK 3 5 3.4077 - 3.1635 1.00 2825 140 0.2723 0.2894 REMARK 3 6 3.1635 - 2.9770 1.00 2796 164 0.3125 0.3602 REMARK 3 7 2.9770 - 2.8280 0.97 2709 159 0.3392 0.3547 REMARK 3 8 2.8280 - 2.7000 0.28 783 42 0.3279 0.4389 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.42 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 : 0.004 4991 REMARK 3 ANGLE : 0.756 6786 REMARK 3 CHIRALITY : 0.051 767 REMARK 3 PLANARITY : 0.003 865 REMARK 3 DIHEDRAL : 13.046 1757 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN L AND (RESID 2:109) REMARK 3 ORIGIN FOR THE GROUP (A): 18.1070 -11.8473 -30.7038 REMARK 3 T TENSOR REMARK 3 T11: 0.8197 T22: 0.6409 REMARK 3 T33: 0.3089 T12: -0.2589 REMARK 3 T13: -0.0058 T23: -0.0352 REMARK 3 L TENSOR REMARK 3 L11: 6.4596 L22: 1.3338 REMARK 3 L33: 5.3410 L12: 0.3192 REMARK 3 L13: -0.0007 L23: 0.7649 REMARK 3 S TENSOR REMARK 3 S11: -0.5881 S12: 0.7494 S13: -0.0422 REMARK 3 S21: -0.6665 S22: 0.4357 S23: -0.1669 REMARK 3 S31: -0.6258 S32: 1.1329 S33: 0.1645 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN L AND (RESID 110:227) REMARK 3 ORIGIN FOR THE GROUP (A): 53.4201 1.3519 -28.1874 REMARK 3 T TENSOR REMARK 3 T11: 0.4194 T22: 0.3454 REMARK 3 T33: 0.4363 T12: 0.0185 REMARK 3 T13: 0.1639 T23: 0.0320 REMARK 3 L TENSOR REMARK 3 L11: 4.3334 L22: 1.9578 REMARK 3 L33: 5.3318 L12: 1.2034 REMARK 3 L13: -0.9600 L23: -0.5471 REMARK 3 S TENSOR REMARK 3 S11: -0.4150 S12: -0.0860 S13: -0.2824 REMARK 3 S21: -0.3278 S22: 0.1743 S23: -0.1113 REMARK 3 S31: 0.7636 S32: -0.3397 S33: 0.1747 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN H AND (RESID 0:100) REMARK 3 ORIGIN FOR THE GROUP (A): 18.4475 -12.0358 -7.9880 REMARK 3 T TENSOR REMARK 3 T11: 0.2494 T22: 0.3529 REMARK 3 T33: 0.2439 T12: -0.0190 REMARK 3 T13: -0.0336 T23: -0.0230 REMARK 3 L TENSOR REMARK 3 L11: 6.5317 L22: 2.8331 REMARK 3 L33: 3.8070 L12: 3.1130 REMARK 3 L13: 1.8632 L23: 0.3372 REMARK 3 S TENSOR REMARK 3 S11: -0.3420 S12: -0.2402 S13: -0.2646 REMARK 3 S21: -0.1434 S22: 0.0734 S23: -0.1553 REMARK 3 S31: -0.4356 S32: 0.6223 S33: 0.1706 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN H AND (RESID 101:138) REMARK 3 ORIGIN FOR THE GROUP (A): 35.6408 -0.0001 -16.2500 REMARK 3 T TENSOR REMARK 3 T11: 0.3265 T22: 0.5683 REMARK 3 T33: 0.3900 T12: -0.0328 REMARK 3 T13: 0.0877 T23: -0.0389 REMARK 3 L TENSOR REMARK 3 L11: 3.2044 L22: 2.1110 REMARK 3 L33: 0.0151 L12: 1.9061 REMARK 3 L13: -0.5010 L23: 0.1107 REMARK 3 S TENSOR REMARK 3 S11: -0.2548 S12: -0.2466 S13: 0.6571 REMARK 3 S21: -0.6907 S22: 0.2387 S23: -0.1161 REMARK 3 S31: 0.4649 S32: 0.4978 S33: -0.0270 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN H AND (RESID 139:219) REMARK 3 ORIGIN FOR THE GROUP (A): 44.0380 9.6489 -16.8604 REMARK 3 T TENSOR REMARK 3 T11: 0.1843 T22: 0.6246 REMARK 3 T33: 0.4233 T12: 0.0495 REMARK 3 T13: 0.0226 T23: -0.0145 REMARK 3 L TENSOR REMARK 3 L11: 2.3893 L22: 2.7828 REMARK 3 L33: 5.3985 L12: 0.9290 REMARK 3 L13: -0.1675 L23: -1.5811 REMARK 3 S TENSOR REMARK 3 S11: -0.0975 S12: -0.5147 S13: 0.3314 REMARK 3 S21: -0.2015 S22: -0.0999 S23: -0.3654 REMARK 3 S31: -0.1677 S32: -0.6308 S33: 0.0545 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN C AND (RESID 311:387) REMARK 3 ORIGIN FOR THE GROUP (A): -3.4668 -20.7219 -16.0686 REMARK 3 T TENSOR REMARK 3 T11: 0.3206 T22: 0.1848 REMARK 3 T33: 0.3409 T12: 0.0641 REMARK 3 T13: -0.0954 T23: -0.1517 REMARK 3 L TENSOR REMARK 3 L11: 6.1960 L22: 3.4060 REMARK 3 L33: 4.8965 L12: 2.7657 REMARK 3 L13: 1.5929 L23: 0.4242 REMARK 3 S TENSOR REMARK 3 S11: -0.5541 S12: -0.1615 S13: 0.3858 REMARK 3 S21: -0.3410 S22: 0.1846 S23: 0.1490 REMARK 3 S31: -0.0148 S32: -0.3666 S33: 0.1590 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN C AND (RESID 388:457) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0596 5.3649 -7.9446 REMARK 3 T TENSOR REMARK 3 T11: 0.2251 T22: 0.6514 REMARK 3 T33: 0.4270 T12: 0.1011 REMARK 3 T13: -0.1173 T23: -0.1970 REMARK 3 L TENSOR REMARK 3 L11: 0.4110 L22: 3.9321 REMARK 3 L33: 1.2045 L12: -0.8375 REMARK 3 L13: -0.6907 L23: 0.1947 REMARK 3 S TENSOR REMARK 3 S11: 0.2304 S12: 0.0274 S13: -0.0397 REMARK 3 S21: -0.1630 S22: -0.0428 S23: 0.2782 REMARK 3 S31: -0.3259 S32: -0.0361 S33: -0.2025 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN C AND (RESID 458:509) REMARK 3 ORIGIN FOR THE GROUP (A): -12.6549 17.4675 -6.7019 REMARK 3 T TENSOR REMARK 3 T11: 0.4378 T22: 0.7609 REMARK 3 T33: 0.2980 T12: 0.1475 REMARK 3 T13: 0.0185 T23: -0.1045 REMARK 3 L TENSOR REMARK 3 L11: 5.0205 L22: 6.0354 REMARK 3 L33: 5.4229 L12: 0.6346 REMARK 3 L13: 0.5034 L23: -2.0791 REMARK 3 S TENSOR REMARK 3 S11: 0.1471 S12: 0.4133 S13: 0.0672 REMARK 3 S21: 0.3172 S22: 0.1592 S23: 0.4816 REMARK 3 S31: -0.1738 S32: 0.3564 S33: -0.3942 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 4K9E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079056. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X29A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0750 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24161 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 FOR THE DATA SET : 10.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.51800 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20-24% PEG 400, 0.1 M TRIS-HCL, PH REMARK 280 8.2, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 213.91733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.95867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 160.43800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 53.47933 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 267.39667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 213.91733 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 106.95867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 53.47933 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 160.43800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 267.39667 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, 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 ASP L 1 REMARK 465 CYS L 217 REMARK 465 GLY L 218 REMARK 465 GLY L 219 REMARK 465 SER L 220 REMARK 465 ASP L 221 REMARK 465 LYS L 228 REMARK 465 CYS H 220 REMARK 465 GLY C 305 REMARK 465 ALA C 306 REMARK 465 MET C 307 REMARK 465 VAL C 308 REMARK 465 ASP C 309 REMARK 465 LYS C 310 REMARK 465 GLY C 445 REMARK 465 THR C 446 REMARK 465 GLU C 447 REMARK 465 GLY C 466 REMARK 465 PRO C 467 REMARK 465 PRO C 468 REMARK 465 GLY C 510 REMARK 465 ASN C 511 REMARK 465 ASN C 512 REMARK 465 LYS C 513 REMARK 465 GLU C 514 REMARK 465 GLN C 515 REMARK 465 ILE C 516 REMARK 465 HIS C 517 REMARK 465 PRO C 518 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 GLU L 216 CG CD OE1 OE2 REMARK 470 TYR L 222 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS L 223 CG CD CE NZ REMARK 470 ASP L 226 CG OD1 OD2 REMARK 470 ASP L 227 CG OD1 OD2 REMARK 470 PHE C 469 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS C 484 CG CD CE NZ REMARK 470 HIS C 485 CG ND1 CD2 CE1 NE2 REMARK 470 ASN C 486 CG OD1 ND2 REMARK 470 LYS C 509 CG CD CE NZ 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 L 316 O HOH L 320 1.80 REMARK 500 O HOH L 301 O HOH H 318 1.88 REMARK 500 OH TYR C 408 O HOH C 717 1.90 REMARK 500 OG SER L 211 O HOH L 308 1.96 REMARK 500 O THR C 389 O HOH C 711 1.97 REMARK 500 O HOH L 311 O HOH L 314 1.98 REMARK 500 NE2 GLN L 127 O HOH L 301 1.99 REMARK 500 ND2 ASN C 352 O HOH C 728 2.08 REMARK 500 OD1 ASP C 439 O HOH C 718 2.08 REMARK 500 OG SER H 134 O ALA H 141 2.13 REMARK 500 OD2 ASP C 458 O HOH C 715 2.14 REMARK 500 OE2 GLU L 108 OH TYR L 176 2.16 REMARK 500 O GLY L 102 O HOH L 323 2.17 REMARK 500 CB CYS H 144 SG CYS H 200 2.17 REMARK 500 OG SER L 78 O HOH L 311 2.18 REMARK 500 OD1 ASP C 327 O HOH C 705 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 GLN L 3 -123.33 -127.88 REMARK 500 GLN L 27 -90.53 -146.01 REMARK 500 ALA L 53 -56.69 66.68 REMARK 500 SER L 69 -167.08 -128.34 REMARK 500 THR L 71 -35.14 -133.75 REMARK 500 SER L 79 88.50 56.57 REMARK 500 ALA L 86 -153.68 -168.03 REMARK 500 SER L 97 -24.55 80.20 REMARK 500 LEU L 98 -111.30 61.38 REMARK 500 GLU L 108 -160.17 -127.05 REMARK 500 LYS L 172 -70.59 -134.10 REMARK 500 LYS L 193 -68.47 -127.08 REMARK 500 VAL H 48 -61.99 -97.39 REMARK 500 PRO H 151 -156.92 -101.27 REMARK 500 ASN C 367 -157.68 -85.53 REMARK 500 ASN C 396 -160.51 -116.14 REMARK 500 TYR C 418 87.67 -152.99 REMARK 500 LYS C 471 -153.30 -154.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4K94 RELATED DB: PDB DBREF 4K9E C 308 518 UNP P10721 KIT_HUMAN 308 518 DBREF 4K9E L 1 228 PDB 4K9E 4K9E 1 228 DBREF 4K9E H 0 220 PDB 4K9E 4K9E 0 220 SEQADV 4K9E GLY C 305 UNP P10721 EXPRESSION TAG SEQADV 4K9E ALA C 306 UNP P10721 EXPRESSION TAG SEQADV 4K9E MET C 307 UNP P10721 EXPRESSION TAG SEQRES 1 L 228 ASP ILE GLN MET THR GLN SER PRO SER SER LEU SER ALA SEQRES 2 L 228 SER VAL GLY ASP ARG VAL THR ILE THR CYS ARG ALA SER SEQRES 3 L 228 GLN ARG GLY LEU ARG ASN VAL ALA VAL ALA TRP TYR GLN SEQRES 4 L 228 GLN LYS PRO GLY LYS ALA PRO LYS LEU LEU ILE TYR SER SEQRES 5 L 228 ALA SER SER LEU TYR SER GLY VAL PRO SER ARG PHE SER SEQRES 6 L 228 GLY SER ARG SER GLY THR ASP PHE THR LEU THR ILE SER SEQRES 7 L 228 SER LEU GLN PRO GLU ASP PHE ALA THR TYR TYR CYS GLN SEQRES 8 L 228 GLN TRP ALA VAL HIS SER LEU ILE THR PHE GLY GLN GLY SEQRES 9 L 228 THR LYS VAL GLU ILE LYS ARG THR VAL ALA ALA PRO SER SEQRES 10 L 228 VAL PHE ILE PHE PRO PRO SER ASP SER GLN LEU LYS SER SEQRES 11 L 228 GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN PHE TYR SEQRES 12 L 228 PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP ASN ALA SEQRES 13 L 228 LEU GLN SER GLY ASN SER GLN GLU SER VAL THR GLU GLN SEQRES 14 L 228 ASP SER LYS ASP SER THR TYR SER LEU SER SER THR LEU SEQRES 15 L 228 THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS VAL TYR SEQRES 16 L 228 ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER PRO VAL SEQRES 17 L 228 THR LYS SER PHE ASN ARG GLY GLU CYS GLY GLY SER ASP SEQRES 18 L 228 TYR LYS ASP ASP ASP ASP LYS SEQRES 1 H 221 SER GLU VAL GLN LEU VAL GLU SER GLY GLY GLY LEU VAL SEQRES 2 H 221 GLN PRO GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER SEQRES 3 H 221 GLY PHE ASN ILE SER VAL TYR MET MET HIS TRP VAL ARG SEQRES 4 H 221 GLN ALA PRO GLY LYS GLY LEU GLU TRP VAL ALA SER ILE SEQRES 5 H 221 TYR PRO TYR SER GLY TYR THR TYR TYR ALA ASP SER VAL SEQRES 6 H 221 LYS GLY ARG PHE THR ILE SER ALA ASP THR SER LYS ASN SEQRES 7 H 221 THR ALA TYR LEU GLN MET ASN SER LEU ARG ALA GLU ASP SEQRES 8 H 221 THR ALA VAL TYR TYR CYS ALA ARG TYR VAL TYR HIS ALA SEQRES 9 H 221 LEU ASP TYR TRP GLY GLN GLY THR LEU VAL THR VAL SER SEQRES 10 H 221 SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA SEQRES 11 H 221 PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU SEQRES 12 H 221 GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR SEQRES 13 H 221 VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS SEQRES 14 H 221 THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER SEQRES 15 H 221 LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY SEQRES 16 H 221 THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER SEQRES 17 H 221 ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 C 214 GLY ALA MET VAL ASP LYS GLY PHE ILE ASN ILE PHE PRO SEQRES 2 C 214 MET ILE ASN THR THR VAL PHE VAL ASN ASP GLY GLU ASN SEQRES 3 C 214 VAL ASP LEU ILE VAL GLU TYR GLU ALA PHE PRO LYS PRO SEQRES 4 C 214 GLU HIS GLN GLN TRP ILE TYR MET ASN ARG THR PHE THR SEQRES 5 C 214 ASP LYS TRP GLU ASP TYR PRO LYS SER GLU ASN GLU SER SEQRES 6 C 214 ASN ILE ARG TYR VAL SER GLU LEU HIS LEU THR ARG LEU SEQRES 7 C 214 LYS GLY THR GLU GLY GLY THR TYR THR PHE LEU VAL SER SEQRES 8 C 214 ASN SER ASP VAL ASN ALA ALA ILE ALA PHE ASN VAL TYR SEQRES 9 C 214 VAL ASN THR LYS PRO GLU ILE LEU THR TYR ASP ARG LEU SEQRES 10 C 214 VAL ASN GLY MET LEU GLN CYS VAL ALA ALA GLY PHE PRO SEQRES 11 C 214 GLU PRO THR ILE ASP TRP TYR PHE CYS PRO GLY THR GLU SEQRES 12 C 214 GLN ARG CYS SER ALA SER VAL LEU PRO VAL ASP VAL GLN SEQRES 13 C 214 THR LEU ASN SER SER GLY PRO PRO PHE GLY LYS LEU VAL SEQRES 14 C 214 VAL GLN SER SER ILE ASP SER SER ALA PHE LYS HIS ASN SEQRES 15 C 214 GLY THR VAL GLU CYS LYS ALA TYR ASN ASP VAL GLY LYS SEQRES 16 C 214 THR SER ALA TYR PHE ASN PHE ALA PHE LYS GLY ASN ASN SEQRES 17 C 214 LYS GLU GLN ILE HIS PRO MODRES 4K9E ASN C 320 ASN GLYCOSYLATION SITE HET NAG C 601 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE FORMUL 4 NAG C8 H15 N O6 FORMUL 5 HOH *79(H2 O) HELIX 1 1 GLN L 81 PHE L 85 5 5 HELIX 2 2 SER L 124 GLY L 131 1 8 HELIX 3 3 LYS L 186 HIS L 192 1 7 HELIX 4 4 ARG H 87 THR H 91 5 5 HELIX 5 5 SER H 191 LEU H 193 5 3 HELIX 6 6 LYS H 205 ASN H 208 5 4 HELIX 7 7 ALA C 507 LYS C 509 5 3 SHEET 1 A 4 MET L 4 SER L 7 0 SHEET 2 A 4 ARG L 18 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 A 4 PHE L 73 SER L 78 -1 O PHE L 73 N CYS L 23 SHEET 4 A 4 PHE L 64 ARG L 68 -1 N SER L 67 O THR L 74 SHEET 1 B 6 SER L 10 ALA L 13 0 SHEET 2 B 6 THR L 105 ILE L 109 1 O LYS L 106 N LEU L 11 SHEET 3 B 6 THR L 87 ALA L 94 -1 N TYR L 88 O THR L 105 SHEET 4 B 6 ALA L 34 GLN L 40 -1 N ALA L 34 O TRP L 93 SHEET 5 B 6 LYS L 47 TYR L 51 -1 O LYS L 47 N GLN L 39 SHEET 6 B 6 SER L 55 LEU L 56 -1 O SER L 55 N TYR L 51 SHEET 1 C 4 SER L 10 ALA L 13 0 SHEET 2 C 4 THR L 105 ILE L 109 1 O LYS L 106 N LEU L 11 SHEET 3 C 4 THR L 87 ALA L 94 -1 N TYR L 88 O THR L 105 SHEET 4 C 4 LEU L 98 PHE L 101 -1 O THR L 100 N GLN L 92 SHEET 1 D 4 SER L 117 PHE L 121 0 SHEET 2 D 4 THR L 132 PHE L 142 -1 O VAL L 136 N PHE L 121 SHEET 3 D 4 TYR L 176 SER L 185 -1 O LEU L 184 N ALA L 133 SHEET 4 D 4 SER L 162 VAL L 166 -1 N GLN L 163 O THR L 181 SHEET 1 E 4 ALA L 156 LEU L 157 0 SHEET 2 E 4 LYS L 148 VAL L 153 -1 N VAL L 153 O ALA L 156 SHEET 3 E 4 VAL L 194 THR L 200 -1 O ALA L 196 N LYS L 152 SHEET 4 E 4 VAL L 208 ASN L 213 -1 O VAL L 208 N VAL L 199 SHEET 1 F 4 GLN H 3 SER H 7 0 SHEET 2 F 4 LEU H 18 SER H 25 -1 O ALA H 23 N VAL H 5 SHEET 3 F 4 THR H 78 MET H 83 -1 O LEU H 81 N LEU H 20 SHEET 4 F 4 PHE H 68 ASP H 73 -1 N ASP H 73 O THR H 78 SHEET 1 G 6 LEU H 11 VAL H 12 0 SHEET 2 G 6 THR H 111 VAL H 115 1 O THR H 114 N VAL H 12 SHEET 3 G 6 ALA H 92 VAL H 100 -1 N TYR H 94 O THR H 111 SHEET 4 G 6 MET H 33 GLN H 39 -1 N HIS H 35 O ALA H 97 SHEET 5 G 6 LEU H 45 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 G 6 THR H 58 TYR H 60 -1 O TYR H 59 N SER H 50 SHEET 1 H 4 LEU H 11 VAL H 12 0 SHEET 2 H 4 THR H 111 VAL H 115 1 O THR H 114 N VAL H 12 SHEET 3 H 4 ALA H 92 VAL H 100 -1 N TYR H 94 O THR H 111 SHEET 4 H 4 ALA H 103 TRP H 107 -1 O ALA H 103 N VAL H 100 SHEET 1 I 4 SER H 124 LEU H 128 0 SHEET 2 I 4 THR H 139 TYR H 149 -1 O LYS H 147 N SER H 124 SHEET 3 I 4 TYR H 180 PRO H 189 -1 O LEU H 182 N VAL H 146 SHEET 4 I 4 VAL H 167 THR H 169 -1 N HIS H 168 O VAL H 185 SHEET 1 J 4 SER H 124 LEU H 128 0 SHEET 2 J 4 THR H 139 TYR H 149 -1 O LYS H 147 N SER H 124 SHEET 3 J 4 TYR H 180 PRO H 189 -1 O LEU H 182 N VAL H 146 SHEET 4 J 4 VAL H 173 LEU H 174 -1 N VAL H 173 O SER H 181 SHEET 1 K 3 THR H 155 TRP H 158 0 SHEET 2 K 3 ILE H 199 HIS H 204 -1 O ASN H 201 N SER H 157 SHEET 3 K 3 THR H 209 LYS H 214 -1 O VAL H 211 N VAL H 202 SHEET 1 L 4 PHE C 312 PRO C 317 0 SHEET 2 L 4 VAL C 331 PHE C 340 -1 O GLU C 338 N ASN C 314 SHEET 3 L 4 ARG C 372 LEU C 379 -1 O LEU C 379 N VAL C 331 SHEET 4 L 4 TRP C 359 PRO C 363 -1 N TYR C 362 O VAL C 374 SHEET 1 M 5 THR C 322 ASN C 326 0 SHEET 2 M 5 ASN C 400 ARG C 420 1 O TYR C 408 N VAL C 323 SHEET 3 M 5 GLY C 388 SER C 395 -1 N GLY C 388 O VAL C 407 SHEET 4 M 5 HIS C 345 TYR C 350 -1 N GLN C 347 O LEU C 393 SHEET 5 M 5 ARG C 353 THR C 354 -1 O ARG C 353 N TYR C 350 SHEET 1 N 5 THR C 322 ASN C 326 0 SHEET 2 N 5 ASN C 400 ARG C 420 1 O TYR C 408 N VAL C 323 SHEET 3 N 5 LEU C 426 PHE C 433 -1 O ALA C 431 N GLU C 414 SHEET 4 N 5 LEU C 472 ILE C 478 -1 O VAL C 474 N ALA C 430 SHEET 5 N 5 ASP C 458 LEU C 462 -1 N GLN C 460 O GLN C 475 SHEET 1 O 3 THR C 437 CYS C 443 0 SHEET 2 O 3 THR C 488 TYR C 494 -1 O LYS C 492 N ASP C 439 SHEET 3 O 3 LYS C 499 ASN C 505 -1 O ALA C 502 N CYS C 491 SSBOND 1 CYS L 23 CYS L 90 1555 1555 2.03 SSBOND 2 CYS L 137 CYS L 197 1555 1555 2.03 SSBOND 3 CYS H 22 CYS H 96 1555 1555 2.03 SSBOND 4 CYS H 144 CYS H 200 1555 1555 2.03 SSBOND 5 CYS C 428 CYS C 491 1555 1555 2.03 SSBOND 6 CYS C 443 CYS C 450 1555 1555 2.03 LINK ND2 ASN C 320 C1 NAG C 601 1555 1555 1.44 CISPEP 1 ILE L 2 GLN L 3 0 -0.98 CISPEP 2 SER L 7 PRO L 8 0 0.05 CISPEP 3 SER L 26 GLN L 27 0 -2.47 CISPEP 4 TYR L 143 PRO L 144 0 -0.97 CISPEP 5 PHE H 150 PRO H 151 0 -2.76 CISPEP 6 GLU H 152 PRO H 153 0 -2.76 CISPEP 7 PHE C 340 PRO C 341 0 1.85 CISPEP 8 PHE C 433 PRO C 434 0 -0.79 CISPEP 9 HIS C 485 ASN C 486 0 1.58 CRYST1 94.577 94.577 320.876 90.00 90.00 120.00 P 65 2 2 12 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 0.010573 0.006105 0.000000 0.00000 SCALE2 0.000000 0.012209 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003116 0.00000