HEADER SIGNALING PROTEIN 22-APR-24 9BI1 TITLE CRYSTAL STRUCTURE OF GMPPNP BOUND KRAS G12D IN COMPLEX WITH CYPA AND TITLE 2 RMC-7977 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 5 EC: 3.6.5.2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A; COMPND 10 CHAIN: B, D; COMPND 11 SYNONYM: PPIASE A,CYCLOPHILIN A,CYCLOSPORIN A-BINDING PROTEIN, COMPND 12 ROTAMASE A; COMPND 13 EC: 5.2.1.8; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: PPIA, CYPA; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GTPASE SIGNALING PROTEIN ISOMERASE, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.POURFARJAM,Y.GOLDGUR,A.CUEVAS-NAVARRO,P.LITO REVDAT 1 06-NOV-24 9BI1 0 JRNL AUTH Y.POURFARJAM,Y.GOLDGUR,A.CUEVAS-NAVARRO,P.LITO JRNL TITL CRYSTAL STRUCTURE OF GMPPNP BOUND KRAS G12D IN COMPLEX WITH JRNL TITL 2 CYPA AND RMC-7977 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???) 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 79807 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.090 REMARK 3 FREE R VALUE TEST SET COUNT : 4063 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 5.0800 - 4.0300 1.00 2801 151 0.1711 0.1988 REMARK 3 2 4.0300 - 3.5200 1.00 2774 142 0.1803 0.2317 REMARK 3 3 3.5200 - 3.2000 1.00 2765 145 0.1945 0.2371 REMARK 3 4 3.2000 - 2.9700 1.00 2735 148 0.2072 0.2380 REMARK 3 5 2.9700 - 2.8000 1.00 2748 130 0.2079 0.2470 REMARK 3 6 2.8000 - 2.6600 1.00 2722 151 0.2183 0.2577 REMARK 3 7 2.6600 - 2.5400 1.00 2726 133 0.2149 0.2782 REMARK 3 8 2.5400 - 2.4400 1.00 2709 132 0.2148 0.2449 REMARK 3 9 2.4400 - 2.3600 1.00 2702 169 0.2169 0.2540 REMARK 3 10 2.3600 - 2.2900 1.00 2698 153 0.2149 0.2400 REMARK 3 11 2.2900 - 2.2200 0.66 1789 90 0.2211 0.2364 REMARK 3 12 2.2200 - 2.1600 1.00 2684 147 0.2206 0.2986 REMARK 3 13 2.1600 - 2.1100 1.00 2703 127 0.2251 0.2601 REMARK 3 14 2.1100 - 2.0600 1.00 2680 152 0.2489 0.2742 REMARK 3 15 2.0600 - 2.0200 1.00 2710 138 0.2492 0.2998 REMARK 3 16 2.0200 - 1.9800 1.00 2691 148 0.2561 0.3234 REMARK 3 17 1.9800 - 1.9400 1.00 2693 134 0.2570 0.3054 REMARK 3 18 1.9400 - 1.9300 1.00 1065 54 0.0000 0.2608 REMARK 3 19 1.9000 - 1.8700 1.00 2573 133 0.2618 0.2927 REMARK 3 20 1.8700 - 1.8400 1.00 2682 164 0.2639 0.3187 REMARK 3 21 1.8400 - 1.8100 1.00 2646 167 0.2709 0.3324 REMARK 3 22 1.8100 - 1.7900 1.00 2677 157 0.2940 0.3117 REMARK 3 23 1.7900 - 1.7600 1.00 2684 133 0.3033 0.3410 REMARK 3 24 1.7600 - 1.7400 1.00 2700 142 0.3173 0.3889 REMARK 3 25 1.7400 - 1.7200 1.00 2650 142 0.3381 0.3664 REMARK 3 26 1.7200 - 1.6900 0.99 2684 127 0.0000 0.3537 REMARK 3 27 1.6900 - 1.6700 0.98 2611 146 0.3678 0.4206 REMARK 3 28 1.6700 - 1.6500 0.94 2538 136 0.4070 0.4366 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.130 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 : 0.016 NULL REMARK 3 ANGLE : 1.265 NULL REMARK 3 CHIRALITY : 0.066 790 REMARK 3 PLANARITY : 0.012 949 REMARK 3 DIHEDRAL : 15.890 770 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 19.6742 20.7605 21.5804 REMARK 3 T TENSOR REMARK 3 T11: 0.1924 T22: 0.1910 REMARK 3 T33: 0.1609 T12: -0.0208 REMARK 3 T13: 0.0160 T23: -0.0046 REMARK 3 L TENSOR REMARK 3 L11: 0.8686 L22: 0.9634 REMARK 3 L33: 0.5415 L12: 0.5369 REMARK 3 L13: 0.0324 L23: -0.0235 REMARK 3 S TENSOR REMARK 3 S11: 0.2308 S12: -0.1955 S13: 0.0116 REMARK 3 S21: 0.2361 S22: -0.1273 S23: 0.0306 REMARK 3 S31: -0.0152 S32: 0.0131 S33: -0.0851 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 9BI1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-APR-24. REMARK 100 THE DEPOSITION ID IS D_1000283410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 80063 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 34.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL PH 8.5, 24% PEG 10000, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 32.75950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.95100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.02600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.95100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 32.75950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.02600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, 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 GLY B 0 REMARK 465 MET B 1 REMARK 465 GLU B 165 REMARK 465 GLY D 0 REMARK 465 MET D 1 REMARK 465 GLU D 165 REMARK 465 GLU C 168 REMARK 465 LYS C 169 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 H ILE C 139 O HOH C 305 1.33 REMARK 500 HZ3 LYS A 88 O HOH A 301 1.34 REMARK 500 HE ARG A 97 O HOH A 305 1.37 REMARK 500 H ARG C 164 O HOH C 304 1.48 REMARK 500 HH12 ARG B 144 O HOH B 302 1.49 REMARK 500 HH21 ARG C 68 O HOH C 309 1.51 REMARK 500 HZ1 LYS C 16 O2G GNP C 201 1.53 REMARK 500 HH12 ARG D 69 O HOH D 305 1.55 REMARK 500 H GLY C 60 O HOH C 302 1.56 REMARK 500 HH TYR C 40 O HOH C 312 1.57 REMARK 500 HZ3 LYS A 104 O HOH A 307 1.57 REMARK 500 HZ3 LYS B 91 O HOH B 304 1.59 REMARK 500 HZ2 LYS B 91 O HOH B 305 1.59 REMARK 500 HH11 ARG C 41 O HOH C 301 1.59 REMARK 500 O HOH A 396 O HOH A 412 1.62 REMARK 500 O HOH B 301 O HOH B 423 1.67 REMARK 500 O HOH D 393 O HOH D 444 1.71 REMARK 500 O HOH B 317 O HOH B 453 1.73 REMARK 500 NH1 ARG C 41 O HOH C 301 1.74 REMARK 500 O HOH A 328 O HOH A 396 1.77 REMARK 500 O HOH C 378 O HOH C 382 1.78 REMARK 500 O2G GNP C 201 O HOH C 302 1.79 REMARK 500 OD1 ASN C 116 O HOH C 303 1.80 REMARK 500 O HOH A 349 O HOH B 417 1.82 REMARK 500 O HOH B 357 O HOH B 417 1.83 REMARK 500 O HOH D 447 O HOH D 454 1.84 REMARK 500 O VAL C 160 O HOH C 304 1.85 REMARK 500 O HOH C 333 O HOH C 404 1.85 REMARK 500 O HOH A 436 O HOH D 430 1.86 REMARK 500 O HOH A 422 O HOH D 422 1.88 REMARK 500 O HOH A 430 O HOH A 445 1.91 REMARK 500 NZ LYS A 88 O HOH A 301 1.92 REMARK 500 O HOH A 417 O HOH B 357 1.92 REMARK 500 O HOH D 384 O HOH D 424 1.93 REMARK 500 O ALA C 134 O HOH C 305 1.93 REMARK 500 O HOH A 457 O HOH A 458 1.98 REMARK 500 O HOH C 334 O HOH C 403 1.98 REMARK 500 O HOH C 343 O HOH C 387 1.99 REMARK 500 N ILE C 139 O HOH C 305 2.02 REMARK 500 O HOH B 422 O HOH B 432 2.02 REMARK 500 O HOH A 393 O HOH A 414 2.03 REMARK 500 O HOH D 349 O HOH D 436 2.03 REMARK 500 OE2 GLU B 81 O HOH B 301 2.04 REMARK 500 OD2 ASP A 153 O HOH A 302 2.05 REMARK 500 O THR C 74 O HOH C 306 2.05 REMARK 500 O HOH C 323 O HOH C 400 2.05 REMARK 500 O HOH B 402 O HOH B 435 2.05 REMARK 500 O GLY C 138 O HOH C 307 2.06 REMARK 500 NZ LYS D 31 OE2 GLU D 84 2.07 REMARK 500 O HOH A 401 O HOH A 402 2.08 REMARK 500 REMARK 500 THIS ENTRY HAS 69 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL 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. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED 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 A 325 O HOH B 481 4555 1.57 REMARK 500 O HOH A 315 O HOH D 456 1455 1.77 REMARK 500 O HOH B 488 O HOH D 308 3645 1.80 REMARK 500 O HOH A 416 O HOH D 456 1455 1.91 REMARK 500 OE1 GLN A 150 O HOH B 481 4555 1.93 REMARK 500 O HOH A 411 O HOH B 452 4555 1.97 REMARK 500 O HOH B 424 O HOH D 425 4455 1.99 REMARK 500 O HOH A 459 O HOH B 470 4555 2.01 REMARK 500 O HOH B 459 O HOH C 353 2554 2.09 REMARK 500 O HOH B 426 O HOH D 425 4455 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 MET B 61 CG - SD - CE ANGL. DEV. = -20.1 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 37 132.63 -170.51 REMARK 500 ASP A 105 54.06 39.45 REMARK 500 ARG A 149 -0.27 75.23 REMARK 500 PHE B 60 -65.09 -135.11 REMARK 500 LYS B 133 -62.64 -95.28 REMARK 500 PHE D 60 -66.11 -132.73 REMARK 500 LYS D 133 -68.72 -95.33 REMARK 500 ILE C 36 -66.37 -95.05 REMARK 500 ARG C 102 -70.94 -56.07 REMARK 500 ASP C 105 76.30 46.32 REMARK 500 LYS C 117 30.92 72.55 REMARK 500 CYS C 118 3.08 -64.88 REMARK 500 HIS C 166 -9.98 -58.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 149 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 458 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 459 DISTANCE = 6.10 ANGSTROMS REMARK 525 HOH A 460 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH A 461 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH A 462 DISTANCE = 9.36 ANGSTROMS REMARK 525 HOH B 485 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B 486 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH B 487 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH B 488 DISTANCE = 7.30 ANGSTROMS REMARK 525 HOH B 489 DISTANCE = 7.75 ANGSTROMS REMARK 525 HOH B 490 DISTANCE = 9.37 ANGSTROMS REMARK 525 HOH B 491 DISTANCE = 12.14 ANGSTROMS REMARK 525 HOH D 453 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH D 454 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH D 455 DISTANCE = 6.56 ANGSTROMS REMARK 525 HOH D 456 DISTANCE = 7.44 ANGSTROMS REMARK 525 HOH C 410 DISTANCE = 8.39 ANGSTROMS 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 THR A 35 OG1 80.3 REMARK 620 3 GNP A 201 O1G 170.2 90.0 REMARK 620 4 GNP A 201 O1B 91.1 169.8 98.7 REMARK 620 5 HOH A 318 O 85.8 87.2 92.5 97.8 REMARK 620 6 HOH A 346 O 91.3 85.1 89.2 89.5 172.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 17 OG REMARK 620 2 THR C 35 OG1 79.6 REMARK 620 3 GNP C 201 O1G 152.7 84.4 REMARK 620 4 GNP C 201 O1B 93.2 166.4 97.6 REMARK 620 5 HOH C 320 O 97.8 102.9 107.2 89.4 REMARK 620 6 HOH C 326 O 81.8 74.6 72.6 93.1 177.5 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9BGH RELATED DB: PDB REMARK 900 RELATED ID: 9BHO RELATED DB: PDB REMARK 900 RELATED ID: 9BHP RELATED DB: PDB REMARK 900 RELATED ID: 9BHQ RELATED DB: PDB DBREF 9BI1 A 1 169 UNP P01116 RASK_HUMAN 1 169 DBREF 9BI1 B 1 165 UNP P62937 PPIA_HUMAN 1 165 DBREF 9BI1 D 1 165 UNP P62937 PPIA_HUMAN 1 165 DBREF 9BI1 C 1 169 UNP P01116 RASK_HUMAN 1 169 SEQADV 9BI1 GLY A 0 UNP P01116 EXPRESSION TAG SEQADV 9BI1 ASP A 12 UNP P01116 GLY 12 VARIANT SEQADV 9BI1 GLY B 0 UNP P62937 EXPRESSION TAG SEQADV 9BI1 GLY D 0 UNP P62937 EXPRESSION TAG SEQADV 9BI1 GLY C 0 UNP P01116 EXPRESSION TAG SEQADV 9BI1 ASP C 12 UNP P01116 GLY 12 VARIANT SEQRES 1 A 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA ASP SEQRES 2 A 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 A 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 A 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 A 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 A 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 A 170 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 A 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 A 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 A 170 LYS CYS ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 A 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 A 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 A 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 A 170 LYS SEQRES 1 B 166 GLY MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL SEQRES 2 B 166 ASP GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE SEQRES 3 B 166 ALA ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA SEQRES 4 B 166 LEU SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER SEQRES 5 B 166 CYS PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY SEQRES 6 B 166 GLY ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER SEQRES 7 B 166 ILE TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU SEQRES 8 B 166 LYS HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA SEQRES 9 B 166 GLY PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR SEQRES 10 B 166 ALA LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE SEQRES 11 B 166 GLY LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET SEQRES 12 B 166 GLU ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS SEQRES 13 B 166 ILE THR ILE ALA ASP CYS GLY GLN LEU GLU SEQRES 1 D 166 GLY MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL SEQRES 2 D 166 ASP GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE SEQRES 3 D 166 ALA ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA SEQRES 4 D 166 LEU SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER SEQRES 5 D 166 CYS PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY SEQRES 6 D 166 GLY ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER SEQRES 7 D 166 ILE TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU SEQRES 8 D 166 LYS HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA SEQRES 9 D 166 GLY PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR SEQRES 10 D 166 ALA LYS THR GLU TRP LEU ASP GLY LYS HIS VAL VAL PHE SEQRES 11 D 166 GLY LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET SEQRES 12 D 166 GLU ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS SEQRES 13 D 166 ILE THR ILE ALA ASP CYS GLY GLN LEU GLU SEQRES 1 C 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA ASP SEQRES 2 C 170 GLY VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 C 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 C 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 C 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 C 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 C 170 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 C 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 C 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 C 170 LYS CYS ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 C 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 C 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 C 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 C 170 LYS HET GNP A 201 45 HET MG A 202 1 HET ZNI B 201 122 HET ZNI D 201 122 HET GNP C 201 45 HET MG C 202 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM ZNI (1R,5S,6R)-N-[(1P,7S,9S,13S,20M)-20-{5-(4- HETNAM 2 ZNI CYCLOPROPYLPIPERAZIN-1-YL)-2-[(1S)-1- HETNAM 3 ZNI METHOXYETHYL]PYRIDIN-3-YL}-21-ETHYL-17,17-DIMETHYL-8, HETNAM 4 ZNI 14-DIOXO-15-OXA-4-THIA-9,21,27,28- HETNAM 5 ZNI TETRAAZAPENTACYCLO[17.5.2.1~2,5~.1~9,13~.0~22, HETNAM 6 ZNI 26~]OCTACOSA-1(24),2,5(28),19,22,25-HEXAEN-7-YL]-3- HETNAM 7 ZNI OXABICYCLO[3.1.0]HEXANE-6-CARBOXAMIDE HETSYN ZNI RMC-7977 FORMUL 5 GNP 2(C10 H17 N6 O13 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 ZNI 2(C47 H60 N8 O6 S) FORMUL 11 HOH *619(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 GLN A 61 MET A 67 5 7 HELIX 3 AA3 ARG A 68 GLY A 75 1 8 HELIX 4 AA4 ASN A 86 ASP A 105 1 20 HELIX 5 AA5 ASP A 126 GLY A 138 1 13 HELIX 6 AA6 GLY A 151 LYS A 167 1 17 HELIX 7 AA7 VAL B 29 GLY B 42 1 14 HELIX 8 AA8 THR B 119 ASP B 123 5 5 HELIX 9 AA9 GLY B 135 ARG B 144 1 10 HELIX 10 AB1 VAL D 29 GLY D 42 1 14 HELIX 11 AB2 THR D 119 ASP D 123 5 5 HELIX 12 AB3 GLY D 135 GLU D 143 1 9 HELIX 13 AB4 ARG D 144 GLY D 146 5 3 HELIX 14 AB5 GLY C 15 ASN C 26 1 12 HELIX 15 AB6 GLN C 61 GLU C 63 5 3 HELIX 16 AB7 TYR C 64 GLY C 75 1 12 HELIX 17 AB8 ASN C 86 ASP C 105 1 20 HELIX 18 AB9 ASP C 126 GLY C 138 1 13 HELIX 19 AC1 GLY C 151 LYS C 167 1 17 SHEET 1 AA1 6 GLU A 37 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 THR A 58 -1 O ASP A 57 N ASP A 38 SHEET 3 AA1 6 GLU A 3 VAL A 9 1 N VAL A 8 O LEU A 56 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O LEU A 79 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 SHEET 1 AA2 8 ARG B 55 ILE B 57 0 SHEET 2 AA2 8 MET B 61 GLY B 64 -1 O GLN B 63 N ARG B 55 SHEET 3 AA2 8 PHE B 112 CYS B 115 -1 O ILE B 114 N CYS B 62 SHEET 4 AA2 8 ILE B 97 MET B 100 -1 N SER B 99 O PHE B 113 SHEET 5 AA2 8 VAL B 128 GLU B 134 -1 O GLY B 130 N LEU B 98 SHEET 6 AA2 8 GLU B 15 LEU B 24 -1 N SER B 21 O LYS B 133 SHEET 7 AA2 8 THR B 5 VAL B 12 -1 N ILE B 10 O GLY B 18 SHEET 8 AA2 8 ILE B 156 LEU B 164 -1 O ASP B 160 N ASP B 9 SHEET 1 AA3 8 ARG D 55 ILE D 57 0 SHEET 2 AA3 8 MET D 61 GLY D 64 -1 O GLN D 63 N ARG D 55 SHEET 3 AA3 8 PHE D 112 CYS D 115 -1 O ILE D 114 N CYS D 62 SHEET 4 AA3 8 ILE D 97 MET D 100 -1 N ILE D 97 O CYS D 115 SHEET 5 AA3 8 VAL D 128 VAL D 132 -1 O GLY D 130 N LEU D 98 SHEET 6 AA3 8 GLU D 15 LEU D 24 -1 N GLU D 23 O LYS D 131 SHEET 7 AA3 8 THR D 5 VAL D 12 -1 N ILE D 10 O LEU D 17 SHEET 8 AA3 8 ILE D 156 LEU D 164 -1 O ASP D 160 N ASP D 9 SHEET 1 AA4 6 GLU C 37 ILE C 46 0 SHEET 2 AA4 6 GLU C 49 THR C 58 -1 O LEU C 53 N LYS C 42 SHEET 3 AA4 6 THR C 2 VAL C 9 1 N TYR C 4 O ASP C 54 SHEET 4 AA4 6 GLY C 77 ALA C 83 1 O VAL C 81 N VAL C 9 SHEET 5 AA4 6 MET C 111 ASN C 116 1 O ASN C 116 N PHE C 82 SHEET 6 AA4 6 PHE C 141 GLU C 143 1 O ILE C 142 N LEU C 113 LINK OG SER A 17 MG MG A 202 1555 1555 2.07 LINK OG1 THR A 35 MG MG A 202 1555 1555 2.11 LINK O1G GNP A 201 MG MG A 202 1555 1555 2.03 LINK O1B GNP A 201 MG MG A 202 1555 1555 1.97 LINK MG MG A 202 O HOH A 318 1555 1555 2.15 LINK MG MG A 202 O HOH A 346 1555 1555 2.11 LINK OG SER C 17 MG MG C 202 1555 1555 2.03 LINK OG1 THR C 35 MG MG C 202 1555 1555 2.25 LINK O1G GNP C 201 MG MG C 202 1555 1555 1.91 LINK O1B GNP C 201 MG MG C 202 1555 1555 2.02 LINK MG MG C 202 O HOH C 320 1555 1555 2.19 LINK MG MG C 202 O HOH C 326 1555 1555 2.29 CRYST1 65.519 82.052 127.902 90.00 90.00 90.00 P 21 21 21 8 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 0.015263 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012187 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007818 0.00000