SCOP: PDB HeaderStructural Classification of Proteins PDB entry 1fmk Options: [ Scop | Headers | Full Entry | PDB3D (Java) | Chime | Pfam | Seq | More opts ] Header of PDB entry 1fmk HEADER PHOSPHOTRANSFERASE 24-JAN-97 1FMK TITLE CRYSTAL STRUCTURE OF HUMAN TYROSINE-PROTEIN KINASE C-SRC COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYROSINE-PROTEIN KINASE SRC; COMPND 3 CHAIN: NULL; COMPND 4 FRAGMENT: RESIDUES 86-836, CONTAINING SH2, SH3, KINASE 2 COMPND 5 DOMAINS AND C-TERMINAL TAIL; COMPND 6 SYNONYM: C-SRC, P60-SRC; COMPND 7 EC: 2.7.1.112; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: BACULOVIRUS/INSECT CELL KEYWDS SRC, TYROSINE KINASE, PHOSPHORYLATION, SH2, SH3, KEYWDS 2 PHOSPHOTYROSINE, PROTO-ONCOGENE, PHOSPHOTRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XU,S.C.HARRISON,M.J.ECK REVDAT 1 20-AUG-97 1FMK 0 JRNL AUTH W.XU,S.C.HARRISON,M.J.ECK JRNL TITL THREE-DIMENSIONAL STRUCTURE OF THE TYROSINE KINASE JRNL TITL 2 C-SRC JRNL REF NATURE V. 385 595 1997 JRNL REFN ASTM NATUAS UK ISSN 0028-0836 0006 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.5 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.5 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.0 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 165384 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5. REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5780 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 490 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.3 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.16 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 RMSD BONDED B FACTORS (A**2) : 2.16 REMARK 4 REMARK 4 1FMK COMPLIES WITH FORMAT V. 2.2, 16-DEC-1996 REMARK 6 REMARK 6 RESIDUES 410 - 423 HAVE NOT BEEN MODELED DUE TO POOR REMARK 6 ELECTRON DENSITY. PHE 424 WAS MODELED AS ALA. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48728 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.5 REMARK 200 RESOLUTION RANGE LOW (A) : 20.0 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 66.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL 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) : 0.049 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE REMARK 200 ISOMORPHOUS HEAVY-ATOM REPLACEMENT (MIR) METHOD. THREE REMARK 200 DERIVATIVES USED FOR PHASING. REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 25.87992 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.64830 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.69102 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.64830 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.87992 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.69102 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 PHE 424 CG CD1 CE1 CZ CE2 CD2 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 GLU 332 PRO 333 0 61.14 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. SOME OF THESE MAY BE ATOMS REMARK 500 LOCATED ON SPECIAL POSITIONS IN THE CELL. ATOMS WITH REMARK 500 NON-BLANK ALTERNATE LOCATION INDICATORS ARE NOT INCLUDED REMARK 500 IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH 1256 N MET 82 3555 2.19 REMARK 500 N MET 82 O HOH 1256 3545 2.19 REMARK 999 REMARK 999 SEQUENCE REMARK 999 1FMK SWS P12931 1 - 83 NOT IN ATOMS LIST REMARK 999 REMARK 999 RESIDUES OF HUMAN C-SRC (86 - 536) ARE NUMBERED REMARK 999 CORRESPONDING TO CHICKEN C-SRC (83 - 533), FOR HISTORICAL REMARK 999 REASONS. DBREF 1FMK 82 409 SWS P12931 SRC_HUMAN 84 411 DBREF 1FMK 424 533 SWS P12931 SRC_HUMAN 426 535 SEQADV 1FMK MET 82 SWS P12931 GLY 84 CLONING ARTIFACT SEQADV 1FMK SWS P12931 ILE 413 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 GLU 414 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 ASP 415 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 ASN 416 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 GLU 417 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 TYR 418 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 THR 419 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 ALA 420 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 ARG 421 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 GLN 422 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 GLY 423 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 ALA 424 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 LYS 425 GAP IN PDB ENTRY SEQADV 1FMK SWS P12931 PHE 426 GAP IN PDB ENTRY SEQADV 1FMK PTR 527 SWS P12931 TYR 529 MODIFIED RESIDUE SEQRES 1 452 MET VAL THR THR PHE VAL ALA LEU TYR ASP TYR GLU SER SEQRES 2 452 ARG THR GLU THR ASP LEU SER PHE LYS LYS GLY GLU ARG SEQRES 3 452 LEU GLN ILE VAL ASN ASN THR GLU GLY ASP TRP TRP LEU SEQRES 4 452 ALA HIS SER LEU SER THR GLY GLN THR GLY TYR ILE PRO SEQRES 5 452 SER ASN TYR VAL ALA PRO SER ASP SER ILE GLN ALA GLU SEQRES 6 452 GLU TRP TYR PHE GLY LYS ILE THR ARG ARG GLU SER GLU SEQRES 7 452 ARG LEU LEU LEU ASN ALA GLU ASN PRO ARG GLY THR PHE SEQRES 8 452 LEU VAL ARG GLU SER GLU THR THR LYS GLY ALA TYR CYS SEQRES 9 452 LEU SER VAL SER ASP PHE ASP ASN ALA LYS GLY LEU ASN SEQRES 10 452 VAL LYS HIS TYR LYS ILE ARG LYS LEU ASP SER GLY GLY SEQRES 11 452 PHE TYR ILE THR SER ARG THR GLN PHE ASN SER LEU GLN SEQRES 12 452 GLN LEU VAL ALA TYR TYR SER LYS HIS ALA ASP GLY LEU SEQRES 13 452 CYS HIS ARG LEU THR THR VAL CYS PRO THR SER LYS PRO SEQRES 14 452 GLN THR GLN GLY LEU ALA LYS ASP ALA TRP GLU ILE PRO SEQRES 15 452 ARG GLU SER LEU ARG LEU GLU VAL LYS LEU GLY GLN GLY SEQRES 16 452 CYS PHE GLY GLU VAL TRP MET GLY THR TRP ASN GLY THR SEQRES 17 452 THR ARG VAL ALA ILE LYS THR LEU LYS PRO GLY THR MET SEQRES 18 452 SER PRO GLU ALA PHE LEU GLN GLU ALA GLN VAL MET LYS SEQRES 19 452 LYS LEU ARG HIS GLU LYS LEU VAL GLN LEU TYR ALA VAL SEQRES 20 452 VAL SER GLU GLU PRO ILE TYR ILE VAL THR GLU TYR MET SEQRES 21 452 SER LYS GLY SER LEU LEU ASP PHE LEU LYS GLY GLU THR SEQRES 22 452 GLY LYS TYR LEU ARG LEU PRO GLN LEU VAL ASP MET ALA SEQRES 23 452 ALA GLN ILE ALA SER GLY MET ALA TYR VAL GLU ARG MET SEQRES 24 452 ASN TYR VAL HIS ARG ASP LEU ARG ALA ALA ASN ILE LEU SEQRES 25 452 VAL GLY GLU ASN LEU VAL CYS LYS VAL ALA ASP PHE GLY SEQRES 26 452 LEU ALA ARG LEU ILE GLU ASP ASN GLU TYR THR ALA ARG SEQRES 27 452 GLN GLY ALA LYS PHE PRO ILE LYS TRP THR ALA PRO GLU SEQRES 28 452 ALA ALA LEU TYR GLY ARG PHE THR ILE LYS SER ASP VAL SEQRES 29 452 TRP SER PHE GLY ILE LEU LEU THR GLU LEU THR THR LYS SEQRES 30 452 GLY ARG VAL PRO TYR PRO GLY MET VAL ASN ARG GLU VAL SEQRES 31 452 LEU ASP GLN VAL GLU ARG GLY TYR ARG MET PRO CYS PRO SEQRES 32 452 PRO GLU CYS PRO GLU SER LEU HIS ASP LEU MET CYS GLN SEQRES 33 452 CYS TRP ARG LYS GLU PRO GLU GLU ARG PRO THR PHE GLU SEQRES 34 452 TYR LEU GLN ALA PHE LEU GLU ASP TYR PHE THR SER THR SEQRES 35 452 GLU PRO GLN PTR GLN PRO GLY GLU ASN LEU MODRES 1FMK PTR 527 TYR PHOSPHOTYROSINE HET PTR 527 16 HETNAM PTR PHOSPHOTYROSINE HETSYN PTR PHOSPHONOTYROSINE FORMUL 1 PTR C9 H12 N1 O6 P1 FORMUL 2 HOH *490(H2 O1) HELIX 1 1 SER 134 TYR 136 5 3 HELIX 2 2 ILE 143 ALA 145 5 3 HELIX 3 3 ARG 155 LEU 162 1 8 HELIX 4 4 LEU 223 TYR 230 1 8 HELIX 5 5 ARG 264 SER 266 5 3 HELIX 6 6 PRO 304 LYS 316 1 13 HELIX 7 7 LEU 346 LEU 350 1 5 HELIX 8 8 GLY 352 TYR 357 1 6 HELIX 9 9 LEU 360 ARG 379 1 20 HELIX 10 10 ALA 389 ASN 391 5 3 HELIX 11 11 GLU 396 LEU 398 5 3 HELIX 12 12 ILE 426 TRP 428 5 3 HELIX 13 13 PRO 431 TYR 436 1 6 HELIX 14 14 ILE 441 THR 456 1 16 HELIX 15 15 ASN 468 GLU 476 1 9 HELIX 16 16 GLU 489 CYS 498 1 10 HELIX 17 17 PRO 503 GLU 505 5 3 HELIX 18 18 PHE 509 GLU 517 1 9 SHEET 1 A 3 ARG 107 ILE 110 0 SHEET 2 A 3 THR 84 ALA 88 -1 N PHE 86 O LEU 108 SHEET 3 A 3 VAL 137 PRO 139 -1 N ALA 138 O VAL 87 SHEET 1 B 2 TRP 118 HIS 122 0 SHEET 2 B 2 THR 129 PRO 133 -1 N ILE 132 O TRP 119 SHEET 1 C 3 PHE 172 GLU 176 0 SHEET 2 C 3 TYR 184 ASP 192 -1 N SER 187 O LEU 173 SHEET 3 C 3 GLY 196 ILE 204 -1 N ILE 204 O TYR 184 SHEET 1 D 5 LEU 325 VAL 329 0 SHEET 2 D 5 ILE 334 THR 338 -1 N VAL 337 O TYR 326 SHEET 3 D 5 THR 290 LEU 297 -1 N LEU 297 O ILE 334 SHEET 4 D 5 VAL 281 TRP 286 -1 N TRP 286 O THR 290 SHEET 5 D 5 LEU 267 LYS 272 -1 N VAL 271 O MET 283 SHEET 1 E 2 ILE 392 VAL 394 0 SHEET 2 E 2 CYS 400 VAL 402 -1 N LYS 401 O LEU 393 LINK N PTR 527 C GLN 526 LINK C PTR 527 N GLN 528 CRYST1 51.759 87.380 101.295 90.00 90.00 90.00 P 21 21 21 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 0.019320 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011444 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009872 0.00000 Copyright © 1994-2002 The scop authors / scop@mrc-lmb.cam.ac.uk November 2002