10 20 30 40 50 60 70 80 3DKO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSFERASE 25-JUN-08 3DKO
TITLE COMPLEX BETWEEN THE KINASE DOMAIN OF HUMAN EPHRIN TYPE-A TITLE 2 RECEPTOR 7 (EPHA7) AND INHIBITOR ALW-II-49-7
COMPND MOL_ID: 1; COMPND 2 MOLECULE: EPHRIN TYPE-A RECEPTOR 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KINASE DOMAIN, UNP RESIDUES 590-899; COMPND 5 SYNONYM: TYROSINE-PROTEIN KINASE RECEPTOR EHK-3, EPH COMPND 6 HOMOLOGY KINASE 3, RECEPTOR PROTEIN-TYROSINE KINASE HEK11; COMPND 7 EC: 2.7.10.1; COMPND 8 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BRAIN; SOURCE 6 GENE: EPHA7, EHK3, HEK11; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNIC-CH
KEYWDS ATP-BINDING, KINASE, NUCLEOTIDE-BINDING, RECEPTOR, SIGNAL, KEYWDS 2 TRANSFERASE, PHOSPHORYLATION, TRANSMEMBRANE, TYROSINE- KEYWDS 3 PROTEIN KINASE, ALTERNATIVE SPLICING, GLYCOPROTEIN, KEYWDS 4 INHIBITOR, STRUCTURAL GENOMICS CONSORTIUM, SGC, MEMBRANE, KEYWDS 5 PHOSPHOPROTEIN, POLYMORPHISM, NPPSFA, NATIONAL PROJECT ON KEYWDS 6 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES
EXPDTA X-RAY DIFFRACTION
AUTHOR J.R.WALKER,F.SYEDA,N.GRAY,C.BUTLER-COLE,C.BOUNTRA, AUTHOR 2 M.WOLKSTROM,C.H.ARROWSMITH,A.M.EDWARDS,A.BOCHKAREV,S.DHE- AUTHOR 3 PAGANON,STRUCTURAL GENOMICS CONSORTIUM (SGC)
REVDAT 2 24-FEB-09 3DKO 1 VERSN REVDAT 1 19-AUG-08 3DKO 0
JRNL AUTH J.R.WALKER,F.SYEDA,N.GRAY,C.BUTLER-COLE,C.BOUNTRA, JRNL AUTH 2 M.WOLKSTROM,C.H.ARROWSMITH,A.M.EDWARDS,A.BOCHKAREV, JRNL AUTH 3 S.DHE-PAGANON JRNL TITL KINASE DOMAIN OF HUMAN EPHRIN TYPE-A RECEPTOR 7 JRNL TITL 2 (EPHA7) IN COMPLEX WITH ALW-II-49-7 JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 20747 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1062 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1549 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2172 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.06000 REMARK 3 B22 (A**2) : 1.06000 REMARK 3 B33 (A**2) : -1.59000 REMARK 3 B12 (A**2) : 0.53000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.179 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.161 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.119 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.289 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2254 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3057 ; 1.156 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 278 ; 5.130 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;32.222 ;23.529 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 372 ;12.401 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;20.531 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 328 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1733 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1067 ; 0.195 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1562 ; 0.300 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 144 ; 0.121 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 41 ; 0.155 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.107 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1433 ; 0.599 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2223 ; 0.939 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 961 ; 1.451 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 834 ; 2.329 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 607 A 618 REMARK 3 ORIGIN FOR THE GROUP (A): -23.5049 15.8950 6.7817 REMARK 3 T TENSOR REMARK 3 T11: 0.5822 T22: 0.3980 REMARK 3 T33: 0.3728 T12: 0.2976 REMARK 3 T13: 0.2799 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 52.3212 L22: 16.7594 REMARK 3 L33: 1.2027 L12: -10.2619 REMARK 3 L13: 3.0468 L23: -4.1977 REMARK 3 S TENSOR REMARK 3 S11: -1.3328 S12: -3.8486 S13: -0.8284 REMARK 3 S21: 1.6378 S22: 1.4336 S23: 2.3378 REMARK 3 S31: -0.8689 S32: -0.2590 S33: -0.1008 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 619 A 628 REMARK 3 ORIGIN FOR THE GROUP (A): -24.5506 23.3388 -2.2199 REMARK 3 T TENSOR REMARK 3 T11: 0.2177 T22: -0.0546 REMARK 3 T33: 0.1554 T12: 0.0751 REMARK 3 T13: 0.0634 T23: -0.0442 REMARK 3 L TENSOR REMARK 3 L11: 5.6051 L22: 15.8154 REMARK 3 L33: 29.9614 L12: -4.3126 REMARK 3 L13: 6.4159 L23: -12.0783 REMARK 3 S TENSOR REMARK 3 S11: -0.0209 S12: -0.1316 S13: 0.1512 REMARK 3 S21: 1.0372 S22: 0.2688 S23: -0.1928 REMARK 3 S31: -0.1092 S32: 0.3311 S33: -0.2479 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 629 A 654 REMARK 3 ORIGIN FOR THE GROUP (A): -26.3481 16.8901 -19.0731 REMARK 3 T TENSOR REMARK 3 T11: 0.2131 T22: 0.0183 REMARK 3 T33: 0.1242 T12: 0.0652 REMARK 3 T13: -0.0064 T23: 0.0334 REMARK 3 L TENSOR REMARK 3 L11: 3.5596 L22: 15.3352 REMARK 3 L33: 11.4513 L12: -1.4400 REMARK 3 L13: -1.7272 L23: 3.3101 REMARK 3 S TENSOR REMARK 3 S11: -0.0798 S12: 0.2148 S13: -0.2242 REMARK 3 S21: 0.3223 S22: -0.0615 S23: 0.4156 REMARK 3 S31: 0.8852 S32: -0.1297 S33: 0.1413 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 655 A 696 REMARK 3 ORIGIN FOR THE GROUP (A): -24.1384 15.7756 -8.0540 REMARK 3 T TENSOR REMARK 3 T11: 0.3580 T22: 0.0023 REMARK 3 T33: 0.1223 T12: 0.0244 REMARK 3 T13: 0.0712 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 6.3916 L22: 1.0820 REMARK 3 L33: 4.5529 L12: -2.6059 REMARK 3 L13: 0.8989 L23: -0.0721 REMARK 3 S TENSOR REMARK 3 S11: -0.1467 S12: -0.2665 S13: -0.1607 REMARK 3 S21: 0.1439 S22: -0.0111 S23: -0.0156 REMARK 3 S31: 0.3753 S32: -0.3753 S33: 0.1579 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 697 A 770 REMARK 3 ORIGIN FOR THE GROUP (A): -12.5487 7.8593 -11.7383 REMARK 3 T TENSOR REMARK 3 T11: 0.2173 T22: 0.1042 REMARK 3 T33: 0.1338 T12: 0.0149 REMARK 3 T13: 0.0310 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 0.9278 L22: 1.7382 REMARK 3 L33: 0.0551 L12: -1.0216 REMARK 3 L13: 0.0987 L23: 0.0568 REMARK 3 S TENSOR REMARK 3 S11: 0.1714 S12: 0.1004 S13: 0.0465 REMARK 3 S21: -0.1808 S22: -0.0892 S23: -0.0147 REMARK 3 S31: -0.1583 S32: -0.0306 S33: -0.0822 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 771 A 841 REMARK 3 ORIGIN FOR THE GROUP (A): -11.9762 -5.2213 -4.5360 REMARK 3 T TENSOR REMARK 3 T11: 0.1343 T22: 0.1158 REMARK 3 T33: 0.1558 T12: 0.0006 REMARK 3 T13: 0.0059 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.9816 L22: 2.3233 REMARK 3 L33: 2.4454 L12: 0.3196 REMARK 3 L13: -0.6064 L23: 0.2680 REMARK 3 S TENSOR REMARK 3 S11: 0.0660 S12: 0.0866 S13: -0.0768 REMARK 3 S21: 0.0556 S22: -0.0729 S23: 0.0815 REMARK 3 S31: 0.1043 S32: -0.2141 S33: 0.0069 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 842 A 893 REMARK 3 ORIGIN FOR THE GROUP (A): -2.4782 -7.6459 -2.1622 REMARK 3 T TENSOR REMARK 3 T11: 0.1136 T22: 0.0881 REMARK 3 T33: 0.1843 T12: 0.0216 REMARK 3 T13: -0.0191 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 1.3403 L22: 3.8604 REMARK 3 L33: 3.6522 L12: 0.0946 REMARK 3 L13: -0.1955 L23: 0.6872 REMARK 3 S TENSOR REMARK 3 S11: -0.0602 S12: -0.0963 S13: -0.1140 REMARK 3 S21: 0.2218 S22: 0.0203 S23: -0.2590 REMARK 3 S31: 0.2027 S32: 0.2173 S33: 0.0400 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 894 A 902 REMARK 3 ORIGIN FOR THE GROUP (A): 11.4070 -0.3139 -12.0321 REMARK 3 T TENSOR REMARK 3 T11: 0.5296 T22: 0.6858 REMARK 3 T33: 0.4681 T12: 0.0908 REMARK 3 T13: 0.1500 T23: -0.1846 REMARK 3 L TENSOR REMARK 3 L11: 15.6746 L22: 96.0936 REMARK 3 L33: 25.3694 L12: -2.6792 REMARK 3 L13: 16.0375 L23: -32.0150 REMARK 3 S TENSOR REMARK 3 S11: -2.0645 S12: -2.9190 S13: -1.9897 REMARK 3 S21: 2.7216 S22: 4.9309 S23: -4.0892 REMARK 3 S31: -1.1194 S32: -0.8358 S33: -2.8664 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL REMARK 3 B FACTORS, ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U REMARK 3 FACTORS.
REMARK 4 REMARK 4 3DKO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JUN-08. REMARK 100 THE RCSB ID CODE IS RCSB048157.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-08 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21903 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 9.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 38.9200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.41700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.190 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: PDB ENTRY 2REI REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: WELL SOLUTION: 25% PEG 3350, 0.1 M REMARK 280 NH4 SULPHATE, 0.1 M HEPES PH 7.5. PROTEIN SOLUTION: 15 MG/ML. REMARK 280 DROPS: 1:1 RATIO OF WELL:PROTEIN SOLUTION. CRYSTALS REMARK 280 CRYOPROTECTED BY TRANSFER TO DROP CONTAINING MOTHER LIQUOR TO REMARK 280 WHICH MPD WAS ADDED TO 25%, , PH 7.50, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 298.0K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 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 144.70600 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 72.35300 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 108.52950 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 36.17650 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 180.88250 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: 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 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 MET A 589 REMARK 465 GLN A 590 REMARK 465 GLU A 591 REMARK 465 GLY A 592 REMARK 465 ASP A 593 REMARK 465 GLU A 594 REMARK 465 GLU A 595 REMARK 465 LEU A 596 REMARK 465 TYR A 597 REMARK 465 PHE A 598 REMARK 465 HIS A 599 REMARK 465 PHE A 600 REMARK 465 LYS A 601 REMARK 465 PHE A 602 REMARK 465 PRO A 603 REMARK 465 GLY A 604 REMARK 465 THR A 605 REMARK 465 LYS A 606 REMARK 465 GLY A 642 REMARK 465 LEU A 779 REMARK 465 SER A 780 REMARK 465 ARG A 781 REMARK 465 VAL A 782 REMARK 465 ILE A 783 REMARK 465 GLU A 784 REMARK 465 ASP A 785 REMARK 465 ASP A 786 REMARK 465 PRO A 787 REMARK 465 GLU A 788 REMARK 465 ALA A 789 REMARK 465 VAL A 790 REMARK 465 TYR A 791 REMARK 465 THR A 792 REMARK 465 THR A 793 REMARK 465 THR A 794 REMARK 465 GLY A 795 REMARK 465 GLY A 796 REMARK 465 LYS A 797 REMARK 465 ILE A 798 REMARK 465 HIS A 903 REMARK 465 HIS A 904 REMARK 465 HIS A 905 REMARK 465 HIS A 906
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 A 615 CG CD OE1 OE2 REMARK 470 ARG A 619 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 643 CG CD OE1 OE2 REMARK 470 LYS A 657 CG CD CE NZ REMARK 470 ARG A 658 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 673 CD OE1 OE2 REMARK 470 LYS A 674 CG CD CE NZ REMARK 470 GLU A 715 CD OE1 OE2 REMARK 470 ILE A 733 CD1 REMARK 470 LYS A 875 CD CE NZ REMARK 470 HIS A 902 CG ND1 CD2 CE1 NE2
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 PHE A 644 -34.54 77.46 REMARK 500 ARG A 757 -17.24 83.87 REMARK 500 TRP A 838 -119.61 49.51 REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IHZ A 1001
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2REI RELATED DB: PDB REMARK 900 KINASE DOMAIN OF HUMAN EPHRIN TYPE-A RECEPTOR 7 (EPHA7)
DBREF 3DKO A 590 899 UNP Q15375 EPHA7_HUMAN 590 899
SEQADV 3DKO MET A 589 UNP Q15375 EXPRESSION TAG SEQADV 3DKO ALA A 900 UNP Q15375 EXPRESSION TAG SEQADV 3DKO HIS A 901 UNP Q15375 EXPRESSION TAG SEQADV 3DKO HIS A 902 UNP Q15375 EXPRESSION TAG SEQADV 3DKO HIS A 903 UNP Q15375 EXPRESSION TAG SEQADV 3DKO HIS A 904 UNP Q15375 EXPRESSION TAG SEQADV 3DKO HIS A 905 UNP Q15375 EXPRESSION TAG SEQADV 3DKO HIS A 906 UNP Q15375 EXPRESSION TAG
SEQRES 1 A 318 MET GLN GLU GLY ASP GLU GLU LEU TYR PHE HIS PHE LYS SEQRES 2 A 318 PHE PRO GLY THR LYS THR TYR ILE ASP PRO GLU THR TYR SEQRES 3 A 318 GLU ASP PRO ASN ARG ALA VAL HIS GLN PHE ALA LYS GLU SEQRES 4 A 318 LEU ASP ALA SER CYS ILE LYS ILE GLU ARG VAL ILE GLY SEQRES 5 A 318 ALA GLY GLU PHE GLY GLU VAL CYS SER GLY ARG LEU LYS SEQRES 6 A 318 LEU PRO GLY LYS ARG ASP VAL ALA VAL ALA ILE LYS THR SEQRES 7 A 318 LEU LYS VAL GLY TYR THR GLU LYS GLN ARG ARG ASP PHE SEQRES 8 A 318 LEU CYS GLU ALA SER ILE MET GLY GLN PHE ASP HIS PRO SEQRES 9 A 318 ASN VAL VAL HIS LEU GLU GLY VAL VAL THR ARG GLY LYS SEQRES 10 A 318 PRO VAL MET ILE VAL ILE GLU PHE MET GLU ASN GLY ALA SEQRES 11 A 318 LEU ASP ALA PHE LEU ARG LYS HIS ASP GLY GLN PHE THR SEQRES 12 A 318 VAL ILE GLN LEU VAL GLY MET LEU ARG GLY ILE ALA ALA SEQRES 13 A 318 GLY MET ARG TYR LEU ALA ASP MET GLY TYR VAL HIS ARG SEQRES 14 A 318 ASP LEU ALA ALA ARG ASN ILE LEU VAL ASN SER ASN LEU SEQRES 15 A 318 VAL CYS LYS VAL SER ASP PHE GLY LEU SER ARG VAL ILE SEQRES 16 A 318 GLU ASP ASP PRO GLU ALA VAL TYR THR THR THR GLY GLY SEQRES 17 A 318 LYS ILE PRO VAL ARG TRP THR ALA PRO GLU ALA ILE GLN SEQRES 18 A 318 TYR ARG LYS PHE THR SER ALA SER ASP VAL TRP SER TYR SEQRES 19 A 318 GLY ILE VAL MET TRP GLU VAL MET SER TYR GLY GLU ARG SEQRES 20 A 318 PRO TYR TRP ASP MET SER ASN GLN ASP VAL ILE LYS ALA SEQRES 21 A 318 ILE GLU GLU GLY TYR ARG LEU PRO ALA PRO MET ASP CYS SEQRES 22 A 318 PRO ALA GLY LEU HIS GLN LEU MET LEU ASP CYS TRP GLN SEQRES 23 A 318 LYS GLU ARG ALA GLU ARG PRO LYS PHE GLU GLN ILE VAL SEQRES 24 A 318 GLY ILE LEU ASP LYS MET ILE ARG ASN PRO ASN SER ALA SEQRES 25 A 318 HIS HIS HIS HIS HIS HIS
HET IHZ A1001 30
HETNAM IHZ 5-[(2-METHYL-5-{[3-(TRIFLUOROMETHYL) HETNAM 2 IHZ PHENYL]CARBAMOYL}PHENYL)AMINO]PYRIDINE-3-CARBOXAMIDE
FORMUL 2 IHZ C21 H17 F3 N4 O2 FORMUL 3 HOH *154(H2 O)
HELIX 1 1 ASP A 610 TYR A 614 5 5 HELIX 2 2 ASP A 616 ALA A 625 1 10 HELIX 3 3 ASP A 629 SER A 631 5 3 HELIX 4 4 THR A 672 GLY A 687 1 16 HELIX 5 5 LEU A 719 HIS A 726 1 8 HELIX 6 6 THR A 731 MET A 752 1 22 HELIX 7 7 ALA A 760 ARG A 762 5 3 HELIX 8 8 PRO A 799 THR A 803 5 5 HELIX 9 9 ALA A 804 ARG A 811 1 8 HELIX 10 10 THR A 814 SER A 831 1 18 HELIX 11 11 SER A 841 GLU A 851 1 11 HELIX 12 12 PRO A 862 TRP A 873 1 12 HELIX 13 13 GLU A 876 ARG A 880 5 5 HELIX 14 14 LYS A 882 ASN A 896 1 15 HELIX 15 15 PRO A 897 HIS A 901 5 5
SHEET 1 A 5 ILE A 633 GLY A 640 0 SHEET 2 A 5 VAL A 647 LEU A 652 -1 O VAL A 647 N ILE A 639 SHEET 3 A 5 VAL A 660 THR A 666 -1 O ILE A 664 N CYS A 648 SHEET 4 A 5 MET A 708 GLU A 712 -1 O ILE A 711 N ALA A 663 SHEET 5 A 5 LEU A 697 VAL A 701 -1 N GLY A 699 O VAL A 710 SHEET 1 B 3 GLY A 717 ALA A 718 0 SHEET 2 B 3 ILE A 764 VAL A 766 -1 O VAL A 766 N GLY A 717 SHEET 3 B 3 CYS A 772 VAL A 774 -1 O LYS A 773 N LEU A 765
SITE 1 AC1 13 ALA A 663 GLU A 682 MET A 686 PHE A 689 SITE 2 AC1 13 ILE A 711 GLU A 712 MET A 714 TYR A 754 SITE 3 AC1 13 LEU A 765 SER A 775 ASP A 776 PHE A 777 SITE 4 AC1 13 HOH A1133
CRYST1 52.658 52.658 217.059 90.00 90.00 120.00 P 65 6
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 0.018990 0.010964 0.000000 0.00000
SCALE2 0.000000 0.021928 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004607 0.00000