HEADER LIGASE/LIGASE INHIBITOR 24-AUG-05 2AST TITLE CRYSTAL STRUCTURE OF SKP1-SKP2-CKS1 IN COMPLEX WITH A P27 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-PHASE KINASE-ASSOCIATED PROTEIN 1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYCLIN A/CDK2-ASSOCIATED PROTEIN P19, P19A, P19SKP1, RNA COMPND 5 POLYMERASE II ELONGATION FACTOR-LIKE PROTEIN, ORGAN OF CORTI PROTEIN COMPND 6 2, OCP-II PROTEIN, OCP-2, TRANSCRIPTION ELONGATION FACTOR B, SIII; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: S-PHASE KINASE-ASSOCIATED PROTEIN 2; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: F-BOX PROTEIN SKP2, CYCLIN A/CDK2-ASSOCIATED PROTEIN P45, COMPND 12 P45SKP2, F-BOX/LRR-REPEAT PROTEIN 1; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: CYCLIN-DEPENDENT KINASES REGULATORY SUBUNIT 1; COMPND 16 CHAIN: C; COMPND 17 SYNONYM: CKS-1; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 4; COMPND 20 MOLECULE: CYCLIN-DEPENDENT KINASE INHIBITOR 1B; COMPND 21 CHAIN: D; COMPND 22 SYNONYM: CYCLIN-DEPENDENT KINASE INHIBITOR P27, P27KIP1; COMPND 23 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: SKP1A, EMC19, OCP2, SKP1, TCEB1L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: SKP2, FBXL1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX4T1; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 23 ORGANISM_COMMON: HUMAN; SOURCE 24 ORGANISM_TAXID: 9606; SOURCE 25 GENE: CKS1, CKS1B; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 27 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 28 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 29 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 30 EXPRESSION_SYSTEM_PLASMID: PGEX4T3; SOURCE 31 MOL_ID: 4; SOURCE 32 SYNTHETIC: YES; SOURCE 33 OTHER_DETAILS: CHEMICAL SYNTHESIS, THIS SEQUENCE OCCURS NATURALLY IN SOURCE 34 HUMANS. KEYWDS SCF-SUBSTRATE COMPLEX, LRR, CELL CYCLE, PROTEIN TURNOVER COMPLEX, KEYWDS 2 LIGASE-LIGASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR B.HAO,N.ZHANG,B.A.SCHULMAN,G.WU,M.PAGANO,N.P.PAVLETICH REVDAT 5 23-AUG-23 2AST 1 REMARK REVDAT 4 20-OCT-21 2AST 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2AST 1 VERSN REVDAT 2 24-FEB-09 2AST 1 VERSN REVDAT 1 18-OCT-05 2AST 0 JRNL AUTH B.HAO,N.ZHENG,B.A.SCHULMAN,G.WU,J.J.MILLER,M.PAGANO, JRNL AUTH 2 N.P.PAVLETICH JRNL TITL STRUCTURAL BASIS OF THE CKS1-DEPENDENT RECOGNITION OF JRNL TITL 2 P27(KIP1) BY THE SCF(SKP2) UBIQUITIN LIGASE. JRNL REF MOL.CELL V. 20 9 2005 JRNL REFN ISSN 1097-2765 JRNL PMID 16209941 JRNL DOI 10.1016/J.MOLCEL.2005.09.003 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 52996 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.221 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2826 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3831 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 195 REMARK 3 BIN FREE R VALUE : 0.3150 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4377 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 265 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.49000 REMARK 3 B22 (A**2) : -0.49000 REMARK 3 B33 (A**2) : 0.74000 REMARK 3 B12 (A**2) : -0.25000 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): 0.174 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.109 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.448 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4483 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6074 ; 1.085 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 540 ; 5.151 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 203 ;37.743 ;25.074 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 815 ;14.907 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;19.929 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 696 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3324 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2049 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3019 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 327 ; 0.135 ; 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): 38 ; 0.195 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.153 ; 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): 2846 ; 2.008 ; 1.800 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4441 ; 3.120 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1872 ; 2.760 ; 2.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1633 ; 4.186 ; 4.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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: NULL REMARK 4 REMARK 4 2AST COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-05. REMARK 100 THE DEPOSITION ID IS D_1000034271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-05 REMARK 200 TEMPERATURE (KELVIN) : 173 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : YALE MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55849 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 35.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.00 REMARK 200 R MERGE FOR SHELL (I) : 0.42200 REMARK 200 R SYM FOR SHELL (I) : 0.42200 REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1FQV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 75.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG8K, 5% BENZAMIDINE, PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 65.86667 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 32.93333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.93333 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 65.86667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 TOTAL BURIED SURFACE AREA: 6200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25720 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 13570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 50260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -79.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 65.86667 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 52370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -63.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 65.86667 REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 74.35000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -128.77798 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 32.93333 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 74.35000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 -128.77798 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 32.93333 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 A 1038F REMARK 465 GLU A 1038E REMARK 465 GLY A 1038D REMARK 465 ASP A 1038C REMARK 465 ASP A 1038B REMARK 465 ASP A 1038A REMARK 465 PRO A 1071 REMARK 465 PRO A 1072 REMARK 465 GLU A 1073 REMARK 465 ASP A 1074 REMARK 465 ASP A 1075 REMARK 465 GLU A 1076 REMARK 465 ASN A 1077 REMARK 465 LYS A 1078 REMARK 465 GLU A 1079 REMARK 465 LYS A 1080 REMARK 465 ARG A 1081 REMARK 465 ARG B 2089 REMARK 465 GLU B 2090 REMARK 465 ASN B 2091 REMARK 465 PHE B 2092 REMARK 465 PRO B 2093 REMARK 465 GLY B 2094 REMARK 465 LYS B 2420 REMARK 465 PRO B 2421 REMARK 465 SER B 2422 REMARK 465 CYS B 2423 REMARK 465 LEU B 2424 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 PRO A1064 CB CG CD 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 ASN B 2403 N LYS B 2405 2.14 REMARK 500 O HOH B 123 O HOH B 195 2.18 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 GLU A1148 N - CA - CB ANGL. DEV. = 11.3 DEGREES REMARK 500 SER B2135 C - N - CA ANGL. DEV. = 18.4 DEGREES REMARK 500 SER B2135 N - CA - CB ANGL. DEV. = 12.4 DEGREES REMARK 500 LYS B2404 O - C - N ANGL. DEV. = -16.5 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 LEU A1034 112.79 67.25 REMARK 500 MET A1036 113.70 73.52 REMARK 500 ASP A1083 107.64 67.19 REMARK 500 ASP A1084 110.39 96.21 REMARK 500 PRO A1086 152.10 -49.27 REMARK 500 ASN A1140 74.17 54.45 REMARK 500 PHE A1145 88.24 55.81 REMARK 500 GLU A1147 -24.75 66.99 REMARK 500 ASP B2133 -71.26 -40.57 REMARK 500 GLU B2134 -54.55 159.12 REMARK 500 CYS B2165 48.59 -146.73 REMARK 500 ASP B2171 43.47 -87.55 REMARK 500 LEU B2218 -158.56 -113.42 REMARK 500 ARG B2294 -134.39 48.47 REMARK 500 LYS B2295 -21.10 -39.10 REMARK 500 LEU B2342 35.64 -140.28 REMARK 500 ASN B2403 47.42 25.99 REMARK 500 LYS B2404 -19.87 26.53 REMARK 500 LYS B2405 -73.02 -105.31 REMARK 500 ASN B2406 108.32 37.13 REMARK 500 ASP C3014 -164.07 -112.99 REMARK 500 SER D4183 110.69 51.38 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 BEN C 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BEN B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF CYCLIN-DEPENDENT REMARK 800 KINASE INHIBITOR 1B REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ASS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE SKP1-SKP2-CKS1 COMPLEX REMARK 900 RELATED ID: 1FQV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SKP1-SKP2 DBREF 2AST A 1002 1160 UNP P63208 SKP1_HUMAN 1 159 DBREF 2AST B 2089 2424 UNP Q13309 SKP2_HUMAN 89 424 DBREF 2AST C 3005 3073 UNP P61024 CKS1_HUMAN 5 73 DBREF 2AST D 4181 4190 UNP P46527 CDN1B_HUMAN 181 190 SEQADV 2AST ALA A 1002 UNP P63208 PRO 1 ENGINEERED MUTATION SEQRES 1 A 159 ALA SER ILE LYS LEU GLN SER SER ASP GLY GLU ILE PHE SEQRES 2 A 159 GLU VAL ASP VAL GLU ILE ALA LYS GLN SER VAL THR ILE SEQRES 3 A 159 LYS THR MET LEU GLU ASP LEU GLY MET ASP ASP GLU GLY SEQRES 4 A 159 ASP ASP ASP PRO VAL PRO LEU PRO ASN VAL ASN ALA ALA SEQRES 5 A 159 ILE LEU LYS LYS VAL ILE GLN TRP CYS THR HIS HIS LYS SEQRES 6 A 159 ASP ASP PRO PRO PRO PRO GLU ASP ASP GLU ASN LYS GLU SEQRES 7 A 159 LYS ARG THR ASP ASP ILE PRO VAL TRP ASP GLN GLU PHE SEQRES 8 A 159 LEU LYS VAL ASP GLN GLY THR LEU PHE GLU LEU ILE LEU SEQRES 9 A 159 ALA ALA ASN TYR LEU ASP ILE LYS GLY LEU LEU ASP VAL SEQRES 10 A 159 THR CYS LYS THR VAL ALA ASN MET ILE LYS GLY LYS THR SEQRES 11 A 159 PRO GLU GLU ILE ARG LYS THR PHE ASN ILE LYS ASN ASP SEQRES 12 A 159 PHE THR GLU GLU GLU GLU ALA GLN VAL ARG LYS GLU ASN SEQRES 13 A 159 GLN TRP CYS SEQRES 1 B 336 ARG GLU ASN PHE PRO GLY VAL SER TRP ASP SER LEU PRO SEQRES 2 B 336 ASP GLU LEU LEU LEU GLY ILE PHE SER CYS LEU CYS LEU SEQRES 3 B 336 PRO GLU LEU LEU LYS VAL SER GLY VAL CYS LYS ARG TRP SEQRES 4 B 336 TYR ARG LEU ALA SER ASP GLU SER LEU TRP GLN THR LEU SEQRES 5 B 336 ASP LEU THR GLY LYS ASN LEU HIS PRO ASP VAL THR GLY SEQRES 6 B 336 ARG LEU LEU SER GLN GLY VAL ILE ALA PHE ARG CYS PRO SEQRES 7 B 336 ARG SER PHE MET ASP GLN PRO LEU ALA GLU HIS PHE SER SEQRES 8 B 336 PRO PHE ARG VAL GLN HIS MET ASP LEU SER ASN SER VAL SEQRES 9 B 336 ILE GLU VAL SER THR LEU HIS GLY ILE LEU SER GLN CYS SEQRES 10 B 336 SER LYS LEU GLN ASN LEU SER LEU GLU GLY LEU ARG LEU SEQRES 11 B 336 SER ASP PRO ILE VAL ASN THR LEU ALA LYS ASN SER ASN SEQRES 12 B 336 LEU VAL ARG LEU ASN LEU SER GLY CYS SER GLY PHE SER SEQRES 13 B 336 GLU PHE ALA LEU GLN THR LEU LEU SER SER CYS SER ARG SEQRES 14 B 336 LEU ASP GLU LEU ASN LEU SER TRP CYS PHE ASP PHE THR SEQRES 15 B 336 GLU LYS HIS VAL GLN VAL ALA VAL ALA HIS VAL SER GLU SEQRES 16 B 336 THR ILE THR GLN LEU ASN LEU SER GLY TYR ARG LYS ASN SEQRES 17 B 336 LEU GLN LYS SER ASP LEU SER THR LEU VAL ARG ARG CYS SEQRES 18 B 336 PRO ASN LEU VAL HIS LEU ASP LEU SER ASP SER VAL MET SEQRES 19 B 336 LEU LYS ASN ASP CYS PHE GLN GLU PHE PHE GLN LEU ASN SEQRES 20 B 336 TYR LEU GLN HIS LEU SER LEU SER ARG CYS TYR ASP ILE SEQRES 21 B 336 ILE PRO GLU THR LEU LEU GLU LEU GLY GLU ILE PRO THR SEQRES 22 B 336 LEU LYS THR LEU GLN VAL PHE GLY ILE VAL PRO ASP GLY SEQRES 23 B 336 THR LEU GLN LEU LEU LYS GLU ALA LEU PRO HIS LEU GLN SEQRES 24 B 336 ILE ASN CYS SER HIS PHE THR THR ILE ALA ARG PRO THR SEQRES 25 B 336 ILE GLY ASN LYS LYS ASN GLN GLU ILE TRP GLY ILE LYS SEQRES 26 B 336 CYS ARG LEU THR LEU GLN LYS PRO SER CYS LEU SEQRES 1 C 69 GLN ILE TYR TYR SER ASP LYS TYR ASP ASP GLU GLU PHE SEQRES 2 C 69 GLU TYR ARG HIS VAL MET LEU PRO LYS ASP ILE ALA LYS SEQRES 3 C 69 LEU VAL PRO LYS THR HIS LEU MET SER GLU SER GLU TRP SEQRES 4 C 69 ARG ASN LEU GLY VAL GLN GLN SER GLN GLY TRP VAL HIS SEQRES 5 C 69 TYR MET ILE HIS GLU PRO GLU PRO HIS ILE LEU LEU PHE SEQRES 6 C 69 ARG ARG PRO LEU SEQRES 1 D 10 ALA GLY SER VAL GLU GLN TPO PRO LYS LYS MODRES 2AST TPO D 4187 THR PHOSPHOTHREONINE HET TPO D4187 11 HET BEN B1002 9 HET BEN C1001 9 HETNAM TPO PHOSPHOTHREONINE HETNAM BEN BENZAMIDINE HETSYN TPO PHOSPHONOTHREONINE FORMUL 4 TPO C4 H10 N O6 P FORMUL 5 BEN 2(C7 H8 N2) FORMUL 7 HOH *265(H2 O) HELIX 1 1 VAL A 1018 GLN A 1023 1 6 HELIX 2 2 SER A 1024 LEU A 1031 1 8 HELIX 3 3 ASN A 1045 HIS A 1059 1 15 HELIX 4 4 PRO A 1086 LEU A 1093 1 8 HELIX 5 5 ASP A 1096 ASP A 1111 1 16 HELIX 6 6 ILE A 1112 LYS A 1128 1 17 HELIX 7 7 THR A 1131 PHE A 1139 1 9 HELIX 8 8 GLU A 1148 ASN A 1157 1 10 HELIX 9 9 PRO B 2101 SER B 2110 1 10 HELIX 10 10 CYS B 2113 VAL B 2120 1 8 HELIX 11 11 CYS B 2124 SER B 2132 1 9 HELIX 12 12 HIS B 2148 GLN B 2158 1 11 HELIX 13 13 GLU B 2194 SER B 2203 1 10 HELIX 14 14 SER B 2219 ALA B 2227 1 9 HELIX 15 15 SER B 2244 CYS B 2255 1 12 HELIX 16 16 THR B 2270 VAL B 2281 1 12 HELIX 17 17 TYR B 2293 LEU B 2297 5 5 HELIX 18 18 GLN B 2298 CYS B 2309 1 12 HELIX 19 19 LYS B 2324 LEU B 2334 5 11 HELIX 20 20 ILE B 2349 ILE B 2359 5 11 HELIX 21 21 THR B 2375 LEU B 2383 1 9 HELIX 22 22 PRO C 3025 LYS C 3030 1 6 HELIX 23 23 SER C 3039 GLY C 3047 1 9 SHEET 1 A 3 ILE A1013 ASP A1017 0 SHEET 2 A 3 SER A1003 GLN A1007 -1 N ILE A1004 O VAL A1016 SHEET 3 A 3 VAL A1039 PRO A1040 1 O VAL A1039 N GLN A1007 SHEET 1 B12 GLN B2387 ILE B2388 0 SHEET 2 B12 THR B2364 GLN B2366 1 N LEU B2365 O GLN B2387 SHEET 3 B12 HIS B2339 SER B2341 1 N LEU B2340 O GLN B2366 SHEET 4 B12 HIS B2314 ASP B2316 1 N LEU B2315 O HIS B2339 SHEET 5 B12 GLN B2287 ASN B2289 1 N LEU B2288 O ASP B2316 SHEET 6 B12 GLU B2260 ASN B2262 1 N LEU B2261 O GLN B2287 SHEET 7 B12 ARG B2234 ASN B2236 1 N LEU B2235 O GLU B2260 SHEET 8 B12 ASN B2210 SER B2212 1 N LEU B2211 O ASN B2236 SHEET 9 B12 HIS B2185 ASP B2187 1 N MET B2186 O ASN B2210 SHEET 10 B12 ALA B2162 ARG B2164 1 N PHE B2163 O HIS B2185 SHEET 11 B12 THR B2139 ASP B2141 1 N LEU B2140 O ARG B2164 SHEET 12 B12 LEU B2416 THR B2417 1 O LEU B2416 N ASP B2141 SHEET 1 C 2 PHE B2169 MET B2170 0 SHEET 2 C 2 VAL B2192 ILE B2193 1 O VAL B2192 N MET B2170 SHEET 1 D 3 TYR C3007 TYR C3008 0 SHEET 2 D 3 PHE C3017 MET C3023 -1 O MET C3023 N TYR C3007 SHEET 3 D 3 TYR C3012 ASP C3013 -1 N TYR C3012 O TYR C3019 SHEET 1 E 4 TYR C3007 TYR C3008 0 SHEET 2 E 4 PHE C3017 MET C3023 -1 O MET C3023 N TYR C3007 SHEET 3 E 4 ILE C3066 PRO C3072 -1 O PHE C3069 N ARG C3020 SHEET 4 E 4 VAL C3055 ILE C3059 -1 N VAL C3055 O ARG C3070 LINK C GLN D4186 N TPO D4187 1555 1555 1.33 LINK C TPO D4187 N PRO D4188 1555 1555 1.35 SITE 1 AC1 7 PHE B2169 VAL B2192 HOH C 100 HOH C 182 SITE 2 AC1 7 HOH C 247 MET C3058 ARG C3070 SITE 1 AC2 10 HOH B 67 HOH B 74 HOH B 263 ALA B2227 SITE 2 AC2 10 SER B2230 SER B2254 HIS C3021 HIS C3060 SITE 3 AC2 10 GLU C3063 ILE C3066 SITE 1 AC3 14 HOH B 13 ARG B2294 TYR B2346 ASP B2347 SITE 2 AC3 14 TYR C3008 ASP C3010 LYS C3011 ARG C3020 SITE 3 AC3 14 ARG C3044 GLN C3049 GLN C3050 SER C3051 SITE 4 AC3 14 GLN C3052 TRP C3054 CRYST1 148.700 148.700 98.800 90.00 90.00 120.00 P 32 2 1 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 0.006725 0.003883 0.000000 0.00000 SCALE2 0.000000 0.007765 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010121 0.00000