PDB Short entry for 1KZP HEADER TRANSFERASE/TRANSFERASE SUBSTRATE 07-FEB-02 1KZP TITLE PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A FARNESYLATED K-RAS4B TITLE 2 PEPTIDE PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN FARNESYLTRANSFERASE ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAAX FARNESYLTRANSFERASE ALPHA SUBUNIT, RAS PROTEINS COMPND 5 PRENYLTRANSFERASE ALPHA, FTASE-ALPHA; COMPND 6 EC: 2.5.1.21; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: CAAX FARNESYLTRANSFERASE BETA SUBUNIT, RAS PROTEINS COMPND 12 PRENYLTRANSFERASE BETA, FTASE-BETA; COMPND 13 EC: 2.5.1.21; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: FARNESYLATED K-RAS4B PEPTIDE PRODUCT; COMPND 17 CHAIN: C; COMPND 18 SYNONYM: TRANSFORMING PROTEIN P21B; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 6 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 8 EXPRESSION_SYSTEM_ATCC_NUMBER: 63134; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 12 ORGANISM_COMMON: NORWAY RAT; SOURCE 13 ORGANISM_TAXID: 10116; SOURCE 14 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 15 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 17 EXPRESSION_SYSTEM_ATCC_NUMBER: 63134; SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 OTHER_DETAILS: THE PROTEIN WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 22 OF THE PROTEIN IS NATURALLY FOUND IN HOMO SAPIENS. KEYWDS FTASE, PFT, PFTASE, FT, FPT, FARNESYLTRANSFERASE, FARNESYL KEYWDS 2 TRANSFERASE, FARNESYL PROTEIN TRANSFERASE, CAAX, RAS CANCER, KEYWDS 3 TRANSFERASE-TRANSFERASE SUBSTRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.B.LONG,P.J.CASEY,L.S.BEESE REVDAT 4 16-AUG-23 1KZP 1 REMARK LINK REVDAT 3 13-JUL-11 1KZP 1 VERSN REVDAT 2 24-FEB-09 1KZP 1 VERSN REVDAT 1 16-OCT-02 1KZP 0 JRNL AUTH S.B.LONG,P.J.CASEY,L.S.BEESE JRNL TITL REACTION PATH OF PROTEIN FARNESYLTRANSFERASE AT ATOMIC JRNL TITL 2 RESOLUTION JRNL REF NATURE V. 419 645 2002 JRNL REFN ISSN 0028-0836 JRNL PMID 12374986 JRNL DOI 10.1038/NATURE00986 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.B.LONG,P.J.CASEY,L.S.BEESE REMARK 1 TITL THE BASIS FOR K-RAS4B BINDING SPECIFICITY TO PROTEIN REMARK 1 TITL 2 FARNESYLTRANSFERASE REVEALED BY 2 A RESOLUTION TERNARY REMARK 1 TITL 3 COMPLEX STRUCTURES REMARK 1 REF STRUCTURE V. 8 209 2000 REMARK 1 REFN ISSN 0969-2126 REMARK 1 DOI 10.1016/S0969-2126(00)00096-4 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.W.PARK,S.R.BODULURI,J.F.MOOMAW,P.J.CASEY,L.S.BEESE REMARK 1 TITL CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE AT 2.25 A REMARK 1 TITL 2 RESOLUTION REMARK 1 REF SCIENCE V. 275 1800 1997 REMARK 1 REFN ISSN 0036-8075 REMARK 1 DOI 10.1126/SCIENCE.275.5307.1800 REMARK 1 REFERENCE 3 REMARK 1 AUTH S.B.LONG,P.J.CASEY,L.S.BEESE REMARK 1 TITL CO-CRYSTAL STRUCTURE OF PROTEIN FARNESYLTRANSFERASE REMARK 1 TITL 2 COMPLEXED WITH A FARNESYL DIPHOSPHATE SUBSTRATE REMARK 1 REF BIOCHEMISTRY V. 37 9612 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 DOI 10.1021/BI980708E REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.5 REMARK 3 NUMBER OF REFLECTIONS : 61433 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : FROM STARTING MODEL: PDB REMARK 3 ENTRY 1D8D REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3073 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.004 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6119 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 334 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5983 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 421 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.36400 REMARK 3 B22 (A**2) : -1.36400 REMARK 3 B33 (A**2) : 6.84100 REMARK 3 B12 (A**2) : -0.03000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.24 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.340 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.650 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.610 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.950 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.510 ; 2.500 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : PARAM19.SOL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KZP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-02. REMARK 100 THE DEPOSITION ID IS D_1000015512. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.70 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 RUH3R REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI FILTER REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67840 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.930 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.62 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.63700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.470 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: PDB ENTRY 1D8D REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, AMMONIUM ACETATE, MAGNESIUM REMARK 280 CHLORIDE, DTT, TRIS-HCL, PH 5.70, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 23.12033 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 46.24067 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 34.68050 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 57.80083 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 11.56017 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 300 REMARK: THE BIOLOGICAL UNIT OF PROTEIN FARNESYLTRANSFERASE (FTASE) REMARK 300 IS A HETERODIMER OF ALPHA AND BETA SUBUNITS. THERE IS ONE FTASE REMARK 300 HETERODIMER PER ASYMMETRIC UNIT. 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: 8390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -65.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 465 GLU A 5 REMARK 465 GLY A 6 REMARK 465 VAL A 7 REMARK 465 GLY A 8 REMARK 465 GLU A 9 REMARK 465 SER A 10 REMARK 465 ALA A 11 REMARK 465 PRO A 12 REMARK 465 GLY A 13 REMARK 465 GLY A 14 REMARK 465 GLU A 15 REMARK 465 PRO A 16 REMARK 465 GLY A 17 REMARK 465 GLN A 18 REMARK 465 PRO A 19 REMARK 465 GLU A 20 REMARK 465 GLN A 21 REMARK 465 PRO A 22 REMARK 465 PRO A 23 REMARK 465 PRO A 24 REMARK 465 PRO A 25 REMARK 465 PRO A 26 REMARK 465 PRO A 27 REMARK 465 PRO A 28 REMARK 465 PRO A 29 REMARK 465 PRO A 30 REMARK 465 ALA A 31 REMARK 465 GLN A 32 REMARK 465 GLN A 33 REMARK 465 PRO A 34 REMARK 465 GLN A 35 REMARK 465 GLU A 36 REMARK 465 GLU A 37 REMARK 465 GLU A 38 REMARK 465 MET A 39 REMARK 465 ALA A 40 REMARK 465 ALA A 41 REMARK 465 GLU A 42 REMARK 465 ALA A 43 REMARK 465 GLY A 44 REMARK 465 GLU A 45 REMARK 465 ALA A 46 REMARK 465 ALA A 47 REMARK 465 ALA A 48 REMARK 465 SER A 49 REMARK 465 PRO A 50 REMARK 465 MET A 51 REMARK 465 ASP A 52 REMARK 465 ASP A 53 REMARK 465 GLY A 54 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 SER B 3 REMARK 465 SER B 4 REMARK 465 SER B 5 REMARK 465 SER B 6 REMARK 465 PHE B 7 REMARK 465 THR B 8 REMARK 465 TYR B 9 REMARK 465 TYR B 10 REMARK 465 CYS B 11 REMARK 465 PRO B 12 REMARK 465 PRO B 13 REMARK 465 SER B 14 REMARK 465 SER B 15 REMARK 465 SER B 16 REMARK 465 GLU B 424 REMARK 465 GLU B 425 REMARK 465 CYS B 426 REMARK 465 GLU B 427 REMARK 465 ASP B 428 REMARK 465 ALA B 429 REMARK 465 VAL B 430 REMARK 465 THR B 431 REMARK 465 SER B 432 REMARK 465 ASP B 433 REMARK 465 PRO B 434 REMARK 465 ALA B 435 REMARK 465 THR B 436 REMARK 465 ASP B 437 REMARK 465 LYS C 1 REMARK 465 LYS C 2 REMARK 465 LYS C 3 REMARK 465 SER C 4 REMARK 465 LYS C 5 REMARK 465 THR C 6 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 LYS C 7 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LEU B 308 CA - CB - CG ANGL. DEV. = -16.1 DEGREES 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 GLU A 71 1.10 -62.90 REMARK 500 ASN A 127 87.59 -156.47 REMARK 500 LYS A 164 54.29 -109.22 REMARK 500 ASN A 199 109.41 -59.54 REMARK 500 LEU A 215 50.48 -104.08 REMARK 500 THR A 247 -92.88 -113.64 REMARK 500 PRO A 304 -79.40 -68.12 REMARK 500 HIS A 306 32.10 -151.31 REMARK 500 GLN A 326 67.33 28.44 REMARK 500 GLU A 347 -62.67 -131.54 REMARK 500 ASP A 349 56.10 -158.41 REMARK 500 SER B 39 19.14 59.05 REMARK 500 GLN B 74 62.34 -68.45 REMARK 500 ASP B 91 2.17 -68.48 REMARK 500 SER B 326 -10.97 -141.77 REMARK 500 MET B 329 49.04 -80.88 REMARK 500 PRO B 421 124.55 -37.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 297 OD1 REMARK 620 2 ASP B 297 OD2 57.2 REMARK 620 3 CYS B 299 SG 94.2 108.0 REMARK 620 4 HIS B 362 NE2 89.7 123.8 119.5 REMARK 620 5 CYS C 8 SG 140.7 87.4 114.3 98.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAR C 12 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACY B 3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF FARNESYLATED K-RAS4B REMARK 800 PEPTIDE PRODUCT REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KZO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF RAT PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH REMARK 900 FARNESYLATED K-RAS4B PEPTIDE PRODUCT AND FARNESYL DIPHOSPHATE REMARK 900 SUBSTRATE BOUND SIMULTANEOUSLY REMARK 900 RELATED ID: 1D8D RELATED DB: PDB REMARK 900 PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH A K-RAS4B PEPTIDE REMARK 900 SUBSTRATE AND FARNESYL DIPHOSPHATE ANALOG REMARK 900 RELATED ID: 1FT1 RELATED DB: PDB REMARK 900 UNLIGANDED PROTEIN FARENESYLTRANSFERASE REMARK 900 RELATED ID: 1FT2 RELATED DB: PDB REMARK 900 PROTEIN FARNESYLTRANSFERASE COMPLEXED WITH THE FARNESYL DIPHOSPHATE REMARK 900 SUBSTRATE REMARK 900 RELATED ID: 1KZR RELATED DB: PDB REMARK 900 TRANSITION STATE MODEL OF THE PROTEIN FARNESYLTRANSFERASE REACTION REMARK 900 BASED ON CRYSTAL STRUCTURES OF PROTEIN FARNESYLTRANSFERASE WITH REMARK 900 BOUND SUBSTRATES AND PRODUCTS REMARK 900 RELATED ID: 1JCQ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN PROTEIN FARNESYLTRANSFERASE COMPLEXED REMARK 900 WITH FARNESYL DIPHOSPHATE AND THE PEPTIDOMIMETIC INHIBITOR L-739,750 DBREF 1KZP A 1 377 UNP Q04631 PFTA_RAT 1 377 DBREF 1KZP B 1 437 UNP Q02293 PFTB_RAT 1 437 DBREF 1KZP C 1 11 UNP P01118 RASL_HUMAN 178 188 SEQRES 1 A 377 MET ALA ALA THR GLU GLY VAL GLY GLU SER ALA PRO GLY SEQRES 2 A 377 GLY GLU PRO GLY GLN PRO GLU GLN PRO PRO PRO PRO PRO SEQRES 3 A 377 PRO PRO PRO PRO ALA GLN GLN PRO GLN GLU GLU GLU MET SEQRES 4 A 377 ALA ALA GLU ALA GLY GLU ALA ALA ALA SER PRO MET ASP SEQRES 5 A 377 ASP GLY PHE LEU SER LEU ASP SER PRO THR TYR VAL LEU SEQRES 6 A 377 TYR ARG ASP ARG ALA GLU TRP ALA ASP ILE ASP PRO VAL SEQRES 7 A 377 PRO GLN ASN ASP GLY PRO SER PRO VAL VAL GLN ILE ILE SEQRES 8 A 377 TYR SER GLU LYS PHE ARG ASP VAL TYR ASP TYR PHE ARG SEQRES 9 A 377 ALA VAL LEU GLN ARG ASP GLU ARG SER GLU ARG ALA PHE SEQRES 10 A 377 LYS LEU THR ARG ASP ALA ILE GLU LEU ASN ALA ALA ASN SEQRES 11 A 377 TYR THR VAL TRP HIS PHE ARG ARG VAL LEU LEU ARG SER SEQRES 12 A 377 LEU GLN LYS ASP LEU GLN GLU GLU MET ASN TYR ILE ILE SEQRES 13 A 377 ALA ILE ILE GLU GLU GLN PRO LYS ASN TYR GLN VAL TRP SEQRES 14 A 377 HIS HIS ARG ARG VAL LEU VAL GLU TRP LEU LYS ASP PRO SEQRES 15 A 377 SER GLN GLU LEU GLU PHE ILE ALA ASP ILE LEU ASN GLN SEQRES 16 A 377 ASP ALA LYS ASN TYR HIS ALA TRP GLN HIS ARG GLN TRP SEQRES 17 A 377 VAL ILE GLN GLU PHE ARG LEU TRP ASP ASN GLU LEU GLN SEQRES 18 A 377 TYR VAL ASP GLN LEU LEU LYS GLU ASP VAL ARG ASN ASN SEQRES 19 A 377 SER VAL TRP ASN GLN ARG HIS PHE VAL ILE SER ASN THR SEQRES 20 A 377 THR GLY TYR SER ASP ARG ALA VAL LEU GLU ARG GLU VAL SEQRES 21 A 377 GLN TYR THR LEU GLU MET ILE LYS LEU VAL PRO HIS ASN SEQRES 22 A 377 GLU SER ALA TRP ASN TYR LEU LYS GLY ILE LEU GLN ASP SEQRES 23 A 377 ARG GLY LEU SER ARG TYR PRO ASN LEU LEU ASN GLN LEU SEQRES 24 A 377 LEU ASP LEU GLN PRO SER HIS SER SER PRO TYR LEU ILE SEQRES 25 A 377 ALA PHE LEU VAL ASP ILE TYR GLU ASP MET LEU GLU ASN SEQRES 26 A 377 GLN CYS ASP ASN LYS GLU ASP ILE LEU ASN LYS ALA LEU SEQRES 27 A 377 GLU LEU CYS GLU ILE LEU ALA LYS GLU LYS ASP THR ILE SEQRES 28 A 377 ARG LYS GLU TYR TRP ARG TYR ILE GLY ARG SER LEU GLN SEQRES 29 A 377 SER LYS HIS SER ARG GLU SER ASP ILE PRO ALA SER VAL SEQRES 1 B 437 MET ALA SER SER SER SER PHE THR TYR TYR CYS PRO PRO SEQRES 2 B 437 SER SER SER PRO VAL TRP SER GLU PRO LEU TYR SER LEU SEQRES 3 B 437 ARG PRO GLU HIS ALA ARG GLU ARG LEU GLN ASP ASP SER SEQRES 4 B 437 VAL GLU THR VAL THR SER ILE GLU GLN ALA LYS VAL GLU SEQRES 5 B 437 GLU LYS ILE GLN GLU VAL PHE SER SER TYR LYS PHE ASN SEQRES 6 B 437 HIS LEU VAL PRO ARG LEU VAL LEU GLN ARG GLU LYS HIS SEQRES 7 B 437 PHE HIS TYR LEU LYS ARG GLY LEU ARG GLN LEU THR ASP SEQRES 8 B 437 ALA TYR GLU CYS LEU ASP ALA SER ARG PRO TRP LEU CYS SEQRES 9 B 437 TYR TRP ILE LEU HIS SER LEU GLU LEU LEU ASP GLU PRO SEQRES 10 B 437 ILE PRO GLN ILE VAL ALA THR ASP VAL CYS GLN PHE LEU SEQRES 11 B 437 GLU LEU CYS GLN SER PRO ASP GLY GLY PHE GLY GLY GLY SEQRES 12 B 437 PRO GLY GLN TYR PRO HIS LEU ALA PRO THR TYR ALA ALA SEQRES 13 B 437 VAL ASN ALA LEU CYS ILE ILE GLY THR GLU GLU ALA TYR SEQRES 14 B 437 ASN VAL ILE ASN ARG GLU LYS LEU LEU GLN TYR LEU TYR SEQRES 15 B 437 SER LEU LYS GLN PRO ASP GLY SER PHE LEU MET HIS VAL SEQRES 16 B 437 GLY GLY GLU VAL ASP VAL ARG SER ALA TYR CYS ALA ALA SEQRES 17 B 437 SER VAL ALA SER LEU THR ASN ILE ILE THR PRO ASP LEU SEQRES 18 B 437 PHE GLU GLY THR ALA GLU TRP ILE ALA ARG CYS GLN ASN SEQRES 19 B 437 TRP GLU GLY GLY ILE GLY GLY VAL PRO GLY MET GLU ALA SEQRES 20 B 437 HIS GLY GLY TYR THR PHE CYS GLY LEU ALA ALA LEU VAL SEQRES 21 B 437 ILE LEU LYS LYS GLU ARG SER LEU ASN LEU LYS SER LEU SEQRES 22 B 437 LEU GLN TRP VAL THR SER ARG GLN MET ARG PHE GLU GLY SEQRES 23 B 437 GLY PHE GLN GLY ARG CYS ASN LYS LEU VAL ASP GLY CYS SEQRES 24 B 437 TYR SER PHE TRP GLN ALA GLY LEU LEU PRO LEU LEU HIS SEQRES 25 B 437 ARG ALA LEU HIS ALA GLN GLY ASP PRO ALA LEU SER MET SEQRES 26 B 437 SER HIS TRP MET PHE HIS GLN GLN ALA LEU GLN GLU TYR SEQRES 27 B 437 ILE LEU MET CYS CYS GLN CYS PRO ALA GLY GLY LEU LEU SEQRES 28 B 437 ASP LYS PRO GLY LYS SER ARG ASP PHE TYR HIS THR CYS SEQRES 29 B 437 TYR CYS LEU SER GLY LEU SER ILE ALA GLN HIS PHE GLY SEQRES 30 B 437 SER GLY ALA MET LEU HIS ASP VAL VAL MET GLY VAL PRO SEQRES 31 B 437 GLU ASN VAL LEU GLN PRO THR HIS PRO VAL TYR ASN ILE SEQRES 32 B 437 GLY PRO ASP LYS VAL ILE GLN ALA THR THR HIS PHE LEU SEQRES 33 B 437 GLN LYS PRO VAL PRO GLY PHE GLU GLU CYS GLU ASP ALA SEQRES 34 B 437 VAL THR SER ASP PRO ALA THR ASP SEQRES 1 C 11 LYS LYS LYS SER LYS THR LYS CYS VAL ILE MET HET ZN B1001 1 HET ACY B3002 4 HET ACY B3003 4 HET FAR C 12 15 HETNAM ZN ZINC ION HETNAM ACY ACETIC ACID HETNAM FAR FARNESYL FORMUL 4 ZN ZN 2+ FORMUL 5 ACY 2(C2 H4 O2) FORMUL 7 FAR C15 H26 FORMUL 8 HOH *421(H2 O) HELIX 1 1 LEU A 65 ALA A 73 5 9 HELIX 2 2 SER A 93 ARG A 109 1 17 HELIX 3 3 SER A 113 ASN A 127 1 15 HELIX 4 4 ASN A 130 LEU A 144 1 15 HELIX 5 5 ASP A 147 GLN A 162 1 16 HELIX 6 6 ASN A 165 LYS A 180 1 16 HELIX 7 7 GLN A 184 ASP A 196 1 13 HELIX 8 8 ASN A 199 ARG A 214 1 16 HELIX 9 9 ASN A 218 ASP A 230 1 13 HELIX 10 10 ASN A 233 THR A 247 1 15 HELIX 11 11 ASP A 252 VAL A 270 1 19 HELIX 12 12 ASN A 273 GLN A 285 1 13 HELIX 13 13 GLY A 288 ARG A 291 5 4 HELIX 14 14 TYR A 292 ASP A 301 1 10 HELIX 15 15 SER A 308 ASN A 325 1 18 HELIX 16 16 ASN A 329 GLU A 347 1 19 HELIX 17 17 ASP A 349 ILE A 351 5 3 HELIX 18 18 ARG A 352 SER A 368 1 17 HELIX 19 19 LEU B 23 ARG B 34 5 12 HELIX 20 20 THR B 42 HIS B 66 1 25 HELIX 21 21 GLN B 74 LEU B 86 1 13 HELIX 22 22 THR B 90 ASP B 97 5 8 HELIX 23 23 SER B 99 LEU B 114 1 16 HELIX 24 24 PRO B 119 GLN B 134 1 16 HELIX 25 25 HIS B 149 GLY B 164 1 16 HELIX 26 26 THR B 165 ILE B 172 1 8 HELIX 27 27 ASN B 173 LYS B 185 1 13 HELIX 28 28 ASP B 200 THR B 214 1 15 HELIX 29 29 GLY B 224 CYS B 232 1 9 HELIX 30 30 HIS B 248 LYS B 263 1 16 HELIX 31 31 LYS B 264 LEU B 268 5 5 HELIX 32 32 ASN B 269 ARG B 280 1 12 HELIX 33 33 CYS B 299 GLN B 304 1 6 HELIX 34 34 GLY B 306 GLN B 318 1 13 HELIX 35 35 HIS B 331 CYS B 343 1 13 HELIX 36 36 ASP B 359 GLN B 374 1 16 HELIX 37 37 VAL B 389 VAL B 393 5 5 HELIX 38 38 GLY B 404 LEU B 416 1 13 SHEET 1 A 2 GLN A 89 ILE A 90 0 SHEET 2 A 2 GLN B 88 LEU B 89 1 O LEU B 89 N GLN A 89 SHEET 1 B 2 HIS B 375 SER B 378 0 SHEET 2 B 2 MET B 381 ASP B 384 -1 O HIS B 383 N PHE B 376 LINK SG CYS C 8 C1 FAR C 12 1555 1555 1.81 LINK OD1 ASP B 297 ZN ZN B1001 1555 1555 2.42 LINK OD2 ASP B 297 ZN ZN B1001 1555 1555 2.06 LINK SG CYS B 299 ZN ZN B1001 1555 1555 2.27 LINK NE2 HIS B 362 ZN ZN B1001 1555 1555 2.18 LINK ZN ZN B1001 SG CYS C 8 1555 1555 2.66 SITE 1 AC1 5 ASP B 297 CYS B 299 HIS B 362 CYS C 8 SITE 2 AC1 5 FAR C 12 SITE 1 AC2 13 TYR A 166 TYR B 205 HIS B 248 GLY B 250 SITE 2 AC2 13 CYS B 254 ASP B 297 CYS B 299 TYR B 300 SITE 3 AC2 13 TRP B 303 TYR B 361 ZN B1001 CYS C 8 SITE 4 AC2 13 ILE C 10 SITE 1 AC3 6 LEU B 89 THR B 90 TYR B 93 HOH B1183 SITE 2 AC3 6 HOH B1449 ACY B3003 SITE 1 AC4 5 TYR B 81 TYR B 93 ARG B 358 HOH B1449 SITE 2 AC4 5 ACY B3002 SITE 1 AC5 23 TYR A 166 GLN A 167 HOH A1167 HOH A1310 SITE 2 AC5 23 ALA B 98 SER B 99 TRP B 102 PRO B 152 SITE 3 AC5 23 ARG B 202 ASP B 297 TYR B 361 HIS B 362 SITE 4 AC5 23 ZN B1001 HOH B1163 FAR C 12 HOH C1184 SITE 5 AC5 23 HOH C1246 HOH C1318 HOH C1338 HOH C1511 SITE 6 AC5 23 HOH C1516 HOH C1559 HOH C1562 CRYST1 171.239 171.239 69.361 90.00 90.00 120.00 P 61 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 0.005840 0.003372 0.000000 0.00000 SCALE2 0.000000 0.006743 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014417 0.00000