HEADER PROTEIN BINDING 04-JAN-18 6C16 TITLE UBIQUITIN VARIANT (UBV.FBL10.1) BOUND TO A HUMAN SKP1-FBL11 FRAGMENT TITLE 2 COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-PHASE KINASE-ASSOCIATED PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYCLIN-A/CDK2-ASSOCIATED PROTEIN P19,P19A,ORGAN OF CORTI COMPND 5 PROTEIN 2,OCP-2,ORGAN OF CORTI PROTEIN II,OCP-II,RNA POLYMERASE II COMPND 6 ELONGATION FACTOR-LIKE PROTEIN,SIII,TRANSCRIPTION ELONGATION FACTOR B COMPND 7 POLYPEPTIDE 1-LIKE,P19SKP1; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A; COMPND 11 CHAIN: C, F; COMPND 12 SYNONYM: CXXC-TYPE ZINC FINGER PROTEIN 8,F-BOX AND LEUCINE-RICH COMPND 13 REPEAT PROTEIN 11,F-BOX PROTEIN FBL7,F-BOX PROTEIN LILINA,F-BOX/LRR- COMPND 14 REPEAT PROTEIN 11,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION COMPND 15 PROTEIN 1A,[HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A; COMPND 16 EC: 1.14.11.27; COMPND 17 ENGINEERED: YES; COMPND 18 MOL_ID: 3; COMPND 19 MOLECULE: POLYUBIQUITIN-B; COMPND 20 CHAIN: D, H; COMPND 21 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: SKP1, EMC19, OCP2, SKP1A, TCEB1L; 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: KDM2A, CXXC8, FBL7, FBXL11, JHDM1A, KIAA1004; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: UBB; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITINATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR N.MANCZYK,F.SICHERI REVDAT 5 04-OCT-23 6C16 1 REMARK REVDAT 4 08-JAN-20 6C16 1 REMARK REVDAT 3 19-SEP-18 6C16 1 JRNL REVDAT 2 08-AUG-18 6C16 1 JRNL REVDAT 1 18-JUL-18 6C16 0 JRNL AUTH M.GORELIK,N.MANCZYK,A.PAVLENCO,I.KURINOV,S.S.SIDHU,F.SICHERI JRNL TITL A STRUCTURE-BASED STRATEGY FOR ENGINEERING SELECTIVE JRNL TITL 2 UBIQUITIN VARIANT INHIBITORS OF SKP1-CUL1-F-BOX UBIQUITIN JRNL TITL 3 LIGASES. JRNL REF STRUCTURE V. 26 1226 2018 JRNL REFN ISSN 1878-4186 JRNL PMID 30033217 JRNL DOI 10.1016/J.STR.2018.06.004 REMARK 2 REMARK 2 RESOLUTION. 3.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.12_2829: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 8658 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.263 REMARK 3 R VALUE (WORKING SET) : 0.260 REMARK 3 FREE R VALUE : 0.317 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.360 REMARK 3 FREE R VALUE TEST SET COUNT : 464 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 19.8180 - 4.7025 0.99 2770 145 0.2296 0.2869 REMARK 3 2 4.7025 - 3.7407 0.99 2716 160 0.2770 0.3329 REMARK 3 3 3.7407 - 3.2703 0.98 2708 159 0.3393 0.3824 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.570 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.470 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 : 0.003 3587 REMARK 3 ANGLE : 0.615 4932 REMARK 3 CHIRALITY : 0.043 621 REMARK 3 PLANARITY : 0.006 639 REMARK 3 DIHEDRAL : 21.926 1134 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 6C16 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231888. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 93.15 REMARK 200 PH : 4.5 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) : 0.979 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 : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8718 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.270 REMARK 200 RESOLUTION RANGE LOW (A) : 19.820 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.17900 REMARK 200 FOR THE DATA SET : 5.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.06800 REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1UBQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MALIC ACID PH 4.5, 0.15 M SODIUM REMARK 280 CHLORIDE, 27% (W/V) PEG3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 59.79100 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, H 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 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13340 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F 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 A -1 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 MET A 36 REMARK 465 ASP A 37 REMARK 465 ASP A 38 REMARK 465 GLU A 39 REMARK 465 GLY A 40 REMARK 465 ASP A 41 REMARK 465 PRO A 71 REMARK 465 PRO A 72 REMARK 465 GLU A 73 REMARK 465 ASP A 74 REMARK 465 ASP A 75 REMARK 465 GLU A 76 REMARK 465 ASN A 77 REMARK 465 LYS A 78 REMARK 465 GLU A 79 REMARK 465 LYS A 80 REMARK 465 ARG A 81 REMARK 465 ILE A 141 REMARK 465 LYS A 142 REMARK 465 ASN A 143 REMARK 465 GLU A 156 REMARK 465 ASN A 157 REMARK 465 GLN A 158 REMARK 465 TRP A 159 REMARK 465 CYS A 160 REMARK 465 GLU A 161 REMARK 465 GLU A 162 REMARK 465 LYS A 163 REMARK 465 GLY B -1 REMARK 465 GLY B 35 REMARK 465 MET B 36 REMARK 465 ASP B 37 REMARK 465 ASP B 38 REMARK 465 GLU B 39 REMARK 465 GLY B 40 REMARK 465 PRO B 70 REMARK 465 PRO B 71 REMARK 465 PRO B 72 REMARK 465 GLU B 73 REMARK 465 ASP B 74 REMARK 465 ASP B 75 REMARK 465 GLU B 76 REMARK 465 ASN B 77 REMARK 465 LYS B 78 REMARK 465 LYS B 142 REMARK 465 ASN B 143 REMARK 465 ASP B 144 REMARK 465 PHE B 145 REMARK 465 GLN B 158 REMARK 465 TRP B 159 REMARK 465 CYS B 160 REMARK 465 GLU B 161 REMARK 465 GLU B 162 REMARK 465 LYS B 163 REMARK 465 GLY C 886 REMARK 465 ALA C 887 REMARK 465 GLY C 888 REMARK 465 ASP C 889 REMARK 465 GLU C 890 REMARK 465 SER C 891 REMARK 465 LYS C 927 REMARK 465 ARG C 928 REMARK 465 LEU C 929 REMARK 465 TRP C 930 REMARK 465 THR C 931 REMARK 465 LYS C 932 REMARK 465 GLY D -2 REMARK 465 SER D -1 REMARK 465 GLY D 0 REMARK 465 GLY D 74 REMARK 465 ARG D 75 REMARK 465 ARG D 76 REMARK 465 GLY F 886 REMARK 465 ALA F 887 REMARK 465 GLY F 888 REMARK 465 ASP F 889 REMARK 465 TRP F 930 REMARK 465 THR F 931 REMARK 465 LYS F 932 REMARK 465 GLY H -2 REMARK 465 GLY H 74 REMARK 465 ARG H 75 REMARK 465 ARG H 76 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 SER A 3 OG REMARK 470 LYS A 5 CG CD CE NZ REMARK 470 SER A 8 OG REMARK 470 ASP A 17 CG OD1 OD2 REMARK 470 GLU A 19 CG CD OE1 OE2 REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 SER A 24 OG REMARK 470 ASP A 33 CG OD1 OD2 REMARK 470 ASP A 42 CG OD1 OD2 REMARK 470 VAL A 45 CG1 CG2 REMARK 470 ASN A 49 CG OD1 ND2 REMARK 470 VAL A 50 CG1 CG2 REMARK 470 ASN A 51 CG OD1 ND2 REMARK 470 LYS A 56 CG CD CE NZ REMARK 470 LYS A 57 CG CD CE NZ REMARK 470 LYS A 66 CG CD CE NZ REMARK 470 THR A 82 OG1 CG2 REMARK 470 ASP A 83 CG OD1 OD2 REMARK 470 ILE A 85 CG1 CG2 CD1 REMARK 470 VAL A 87 CG1 CG2 REMARK 470 GLU A 91 CG CD OE1 OE2 REMARK 470 LYS A 94 CG CD CE NZ REMARK 470 GLN A 97 CG CD OE1 NE2 REMARK 470 GLU A 102 CG CD OE1 OE2 REMARK 470 ILE A 112 CG1 CG2 CD1 REMARK 470 LYS A 113 CG CD CE NZ REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 ASN A 125 CG OD1 ND2 REMARK 470 ILE A 127 CG1 CG2 CD1 REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 LYS A 130 CG CD CE NZ REMARK 470 GLU A 133 CG CD OE1 OE2 REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 ILE A 135 CG1 CG2 CD1 REMARK 470 ARG A 136 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 ASN A 140 CG OD1 ND2 REMARK 470 ASP A 144 CG OD1 OD2 REMARK 470 THR A 146 OG1 CG2 REMARK 470 GLU A 147 CG CD OE1 OE2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 GLU A 150 CG CD OE1 OE2 REMARK 470 GLN A 152 CG CD OE1 NE2 REMARK 470 VAL A 153 CG1 CG2 REMARK 470 ARG A 154 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 155 CG CD CE NZ REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 5 CG CD CE NZ REMARK 470 SER B 9 OG REMARK 470 GLU B 15 CG CD OE1 OE2 REMARK 470 ASP B 17 CG OD1 OD2 REMARK 470 VAL B 18 CG1 CG2 REMARK 470 GLU B 19 CG CD OE1 OE2 REMARK 470 LYS B 22 CG CD CE NZ REMARK 470 LYS B 28 CG CD CE NZ REMARK 470 THR B 29 OG1 CG2 REMARK 470 LEU B 34 CG CD1 CD2 REMARK 470 ASP B 41 CG OD1 OD2 REMARK 470 ASP B 42 CG OD1 OD2 REMARK 470 VAL B 50 CG1 CG2 REMARK 470 LYS B 56 CG CD CE NZ REMARK 470 LYS B 57 CG CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU B 79 CG CD OE1 OE2 REMARK 470 LYS B 80 CG CD CE NZ REMARK 470 ARG B 81 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 83 CG OD1 OD2 REMARK 470 ILE B 85 CG1 CG2 CD1 REMARK 470 VAL B 87 CG1 CG2 REMARK 470 GLU B 91 CG CD OE1 OE2 REMARK 470 GLN B 97 CG CD OE1 NE2 REMARK 470 THR B 99 OG1 CG2 REMARK 470 LYS B 113 CG CD CE NZ REMARK 470 LYS B 121 CG CD CE NZ REMARK 470 MET B 126 CG SD CE REMARK 470 ILE B 127 CG1 CG2 CD1 REMARK 470 LYS B 128 CG CD CE NZ REMARK 470 GLU B 133 CG CD OE1 OE2 REMARK 470 GLU B 134 CG CD OE1 OE2 REMARK 470 ARG B 136 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 137 CG CD CE NZ REMARK 470 ASN B 140 CG OD1 ND2 REMARK 470 THR B 146 OG1 CG2 REMARK 470 GLU B 147 CG CD OE1 OE2 REMARK 470 GLU B 148 CG CD OE1 OE2 REMARK 470 GLU B 149 CG CD OE1 OE2 REMARK 470 GLU B 150 CG CD OE1 OE2 REMARK 470 GLN B 152 CG CD OE1 NE2 REMARK 470 VAL B 153 CG1 CG2 REMARK 470 ARG B 154 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 155 CG CD CE NZ REMARK 470 GLU B 156 CG CD OE1 OE2 REMARK 470 ASN B 157 CG OD1 ND2 REMARK 470 TRP C 892 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP C 892 CZ3 CH2 REMARK 470 MET C 893 CG SD CE REMARK 470 MET C 899 CG SD CE REMARK 470 PHE C 902 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG C 903 CG CD NE CZ NH1 NH2 REMARK 470 LEU C 905 CG CD1 CD2 REMARK 470 SER C 906 OG REMARK 470 ARG C 907 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 908 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 909 CG CD OE1 OE2 REMARK 470 CYS C 911 SG REMARK 470 CYS C 913 SG REMARK 470 CYS C 917 SG REMARK 470 LYS C 918 CG CD CE NZ REMARK 470 LYS C 922 CG CD CE NZ REMARK 470 CYS C 925 SG REMARK 470 ASP C 926 CG OD1 OD2 REMARK 470 MET D 1 CG SD CE REMARK 470 PHE D 4 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG D 9 CG CD NE CZ NH1 NH2 REMARK 470 ARG D 11b CG CD NE CZ NH1 NH2 REMARK 470 LEU D 11d CG CD1 CD2 REMARK 470 GLU D 16 CG CD OE1 OE2 REMARK 470 SER D 20 OG REMARK 470 GLU D 24 CG CD OE1 OE2 REMARK 470 ASN D 25 CG OD1 ND2 REMARK 470 LYS D 29 CG CD CE NZ REMARK 470 LYS D 33 CG CD CE NZ REMARK 470 GLU D 34 CG CD OE1 OE2 REMARK 470 ILE D 36 CG1 CG2 CD1 REMARK 470 ASP D 39 CG OD1 OD2 REMARK 470 GLN D 40 CG CD OE1 NE2 REMARK 470 ILE D 44 CG1 CG2 CD1 REMARK 470 SER D 46 OG REMARK 470 ARG D 47 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 48 CG CD CE NZ REMARK 470 ARG D 54 CG CD NE CZ NH1 NH2 REMARK 470 LEU D 56 CG CD1 CD2 REMARK 470 GLN D 62 CG CD OE1 NE2 REMARK 470 LYS D 63 CG CD CE NZ REMARK 470 GLU D 64 CG CD OE1 OE2 REMARK 470 VAL D 72 CG1 CG2 REMARK 470 PHE D 73 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU F 890 CG CD OE1 OE2 REMARK 470 SER F 891 OG REMARK 470 TRP F 892 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP F 892 CZ3 CH2 REMARK 470 GLN F 894 CG CD OE1 NE2 REMARK 470 ARG F 895 CG CD NE CZ NH1 NH2 REMARK 470 GLU F 896 CG CD OE1 OE2 REMARK 470 ARG F 903 CG CD NE CZ NH1 NH2 REMARK 470 LEU F 905 CG CD1 CD2 REMARK 470 ARG F 907 CG CD NE CZ NH1 NH2 REMARK 470 ARG F 908 CG CD NE CZ NH1 NH2 REMARK 470 GLU F 909 CG CD OE1 OE2 REMARK 470 LEU F 910 CG CD1 CD2 REMARK 470 CYS F 911 SG REMARK 470 GLU F 912 CG CD OE1 OE2 REMARK 470 MET F 914 CG SD CE REMARK 470 ARG F 915 CG CD NE CZ NH1 NH2 REMARK 470 VAL F 916 CG1 CG2 REMARK 470 CYS F 917 SG REMARK 470 LYS F 918 CG CD CE NZ REMARK 470 THR F 919 OG1 CG2 REMARK 470 TYR F 921 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS F 922 CG CD CE NZ REMARK 470 ASP F 926 CG OD1 OD2 REMARK 470 LYS F 927 CG CD CE NZ REMARK 470 ARG F 928 CG CD NE CZ NH1 NH2 REMARK 470 LEU F 929 CG CD1 CD2 REMARK 470 SER H -1 OG REMARK 470 LYS H 6 CG CD CE NZ REMARK 470 ARG H 11b CG CD NE CZ NH1 NH2 REMARK 470 LEU H 11e CG CD1 CD2 REMARK 470 LYS H 33 CG CD CE NZ REMARK 470 ILE H 36 CG1 CG2 CD1 REMARK 470 ASP H 39 CG OD1 OD2 REMARK 470 GLN H 40 CG CD OE1 NE2 REMARK 470 ARG H 47 CG CD NE CZ NH1 NH2 REMARK 470 LYS H 48 CG CD CE NZ REMARK 470 ARG H 49 CG CD NE CZ NH1 NH2 REMARK 470 SER H 57 OG REMARK 470 ASN H 60 CG OD1 ND2 REMARK 470 ILE H 61 CG1 CG2 CD1 REMARK 470 LYS H 63 CG CD CE NZ REMARK 470 GLU H 64 CG CD OE1 OE2 REMARK 470 VAL H 72 CG1 CG2 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 OE1 GLU H 51 NH1 ARG H 54 2.07 REMARK 500 NZ LYS B 130 OG1 THR B 138 2.09 REMARK 500 O VAL B 118 OG1 THR B 122 2.15 REMARK 500 NE2 GLN B 23 O HIS B 65 2.19 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 PRO A 70 C - N - CA ANGL. DEV. = -11.5 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 ASN A 49 -1.12 66.60 REMARK 500 REMARK 500 REMARK: NULL DBREF 6C16 A 1 163 UNP P63208 SKP1_HUMAN 1 163 DBREF 6C16 B 1 163 UNP P63208 SKP1_HUMAN 1 163 DBREF 6C16 C 888 932 UNP Q9Y2K7 KDM2A_HUMAN 888 932 DBREF 6C16 D 1 76 UNP P0CG47 UBB_HUMAN 77 152 DBREF 6C16 F 888 932 UNP Q9Y2K7 KDM2A_HUMAN 888 932 DBREF 6C16 H 1 76 UNP P0CG47 UBB_HUMAN 77 152 SEQADV 6C16 GLY A -1 UNP P63208 EXPRESSION TAG SEQADV 6C16 ALA A 0 UNP P63208 EXPRESSION TAG SEQADV 6C16 GLY B -1 UNP P63208 EXPRESSION TAG SEQADV 6C16 ALA B 0 UNP P63208 EXPRESSION TAG SEQADV 6C16 GLY C 886 UNP Q9Y2K7 EXPRESSION TAG SEQADV 6C16 ALA C 887 UNP Q9Y2K7 EXPRESSION TAG SEQADV 6C16 GLY D -2 UNP P0CG47 EXPRESSION TAG SEQADV 6C16 SER D -1 UNP P0CG47 EXPRESSION TAG SEQADV 6C16 GLY D 0 UNP P0CG47 EXPRESSION TAG SEQADV 6C16 PHE D 8 UNP P0CG47 THR 85 ENGINEERED MUTATION SEQADV 6C16 ARG D 9 UNP P0CG47 GLY 86 ENGINEERED MUTATION SEQADV 6C16 ASP D 10 UNP P0CG47 LYS 87 ENGINEERED MUTATION SEQADV 6C16 ARG D 11 UNP P0CG47 INSERTION SEQADV 6C16 LEU D 11A UNP P0CG47 INSERTION SEQADV 6C16 ARG D 11B UNP P0CG47 INSERTION SEQADV 6C16 ASN D 11C UNP P0CG47 INSERTION SEQADV 6C16 LEU D 11E UNP P0CG47 INSERTION SEQADV 6C16 PRO D 11F UNP P0CG47 INSERTION SEQADV 6C16 GLN D 11G UNP P0CG47 INSERTION SEQADV 6C16 VAL D 42 UNP P0CG47 ARG 118 ENGINEERED MUTATION SEQADV 6C16 SER D 46 UNP P0CG47 ALA 122 ENGINEERED MUTATION SEQADV 6C16 ARG D 47 UNP P0CG47 GLY 123 ENGINEERED MUTATION SEQADV 6C16 ARG D 49 UNP P0CG47 GLN 125 ENGINEERED MUTATION SEQADV 6C16 ARG D 68 UNP P0CG47 HIS 144 ENGINEERED MUTATION SEQADV 6C16 VAL D 72 UNP P0CG47 ARG 148 ENGINEERED MUTATION SEQADV 6C16 PHE D 73 UNP P0CG47 LEU 149 ENGINEERED MUTATION SEQADV 6C16 GLY D 74 UNP P0CG47 ARG 150 ENGINEERED MUTATION SEQADV 6C16 ARG D 75 UNP P0CG47 GLY 151 ENGINEERED MUTATION SEQADV 6C16 ARG D 76 UNP P0CG47 GLY 152 ENGINEERED MUTATION SEQADV 6C16 GLY F 886 UNP Q9Y2K7 EXPRESSION TAG SEQADV 6C16 ALA F 887 UNP Q9Y2K7 EXPRESSION TAG SEQADV 6C16 GLY H -2 UNP P0CG47 EXPRESSION TAG SEQADV 6C16 SER H -1 UNP P0CG47 EXPRESSION TAG SEQADV 6C16 GLY H 0 UNP P0CG47 EXPRESSION TAG SEQADV 6C16 PHE H 8 UNP P0CG47 THR 85 ENGINEERED MUTATION SEQADV 6C16 ARG H 9 UNP P0CG47 GLY 86 ENGINEERED MUTATION SEQADV 6C16 ASP H 10 UNP P0CG47 LYS 87 ENGINEERED MUTATION SEQADV 6C16 ARG H 11 UNP P0CG47 INSERTION SEQADV 6C16 LEU H 11A UNP P0CG47 INSERTION SEQADV 6C16 ARG H 11B UNP P0CG47 INSERTION SEQADV 6C16 ASN H 11C UNP P0CG47 INSERTION SEQADV 6C16 LEU H 11E UNP P0CG47 INSERTION SEQADV 6C16 PRO H 11F UNP P0CG47 INSERTION SEQADV 6C16 GLN H 11G UNP P0CG47 INSERTION SEQADV 6C16 VAL H 42 UNP P0CG47 ARG 118 ENGINEERED MUTATION SEQADV 6C16 SER H 46 UNP P0CG47 ALA 122 ENGINEERED MUTATION SEQADV 6C16 ARG H 47 UNP P0CG47 GLY 123 ENGINEERED MUTATION SEQADV 6C16 ARG H 49 UNP P0CG47 GLN 125 ENGINEERED MUTATION SEQADV 6C16 ARG H 68 UNP P0CG47 HIS 144 ENGINEERED MUTATION SEQADV 6C16 VAL H 72 UNP P0CG47 ARG 148 ENGINEERED MUTATION SEQADV 6C16 PHE H 73 UNP P0CG47 LEU 149 ENGINEERED MUTATION SEQADV 6C16 GLY H 74 UNP P0CG47 ARG 150 ENGINEERED MUTATION SEQADV 6C16 ARG H 75 UNP P0CG47 GLY 151 ENGINEERED MUTATION SEQADV 6C16 ARG H 76 UNP P0CG47 GLY 152 ENGINEERED MUTATION SEQRES 1 A 165 GLY ALA MET PRO SER ILE LYS LEU GLN SER SER ASP GLY SEQRES 2 A 165 GLU ILE PHE GLU VAL ASP VAL GLU ILE ALA LYS GLN SER SEQRES 3 A 165 VAL THR ILE LYS THR MET LEU GLU ASP LEU GLY MET ASP SEQRES 4 A 165 ASP GLU GLY ASP ASP ASP PRO VAL PRO LEU PRO ASN VAL SEQRES 5 A 165 ASN ALA ALA ILE LEU LYS LYS VAL ILE GLN TRP CYS THR SEQRES 6 A 165 HIS HIS LYS ASP ASP PRO PRO PRO PRO GLU ASP ASP GLU SEQRES 7 A 165 ASN LYS GLU LYS ARG THR ASP ASP ILE PRO VAL TRP ASP SEQRES 8 A 165 GLN GLU PHE LEU LYS VAL ASP GLN GLY THR LEU PHE GLU SEQRES 9 A 165 LEU ILE LEU ALA ALA ASN TYR LEU ASP ILE LYS GLY LEU SEQRES 10 A 165 LEU ASP VAL THR CYS LYS THR VAL ALA ASN MET ILE LYS SEQRES 11 A 165 GLY LYS THR PRO GLU GLU ILE ARG LYS THR PHE ASN ILE SEQRES 12 A 165 LYS ASN ASP PHE THR GLU GLU GLU GLU ALA GLN VAL ARG SEQRES 13 A 165 LYS GLU ASN GLN TRP CYS GLU GLU LYS SEQRES 1 B 165 GLY ALA MET PRO SER ILE LYS LEU GLN SER SER ASP GLY SEQRES 2 B 165 GLU ILE PHE GLU VAL ASP VAL GLU ILE ALA LYS GLN SER SEQRES 3 B 165 VAL THR ILE LYS THR MET LEU GLU ASP LEU GLY MET ASP SEQRES 4 B 165 ASP GLU GLY ASP ASP ASP PRO VAL PRO LEU PRO ASN VAL SEQRES 5 B 165 ASN ALA ALA ILE LEU LYS LYS VAL ILE GLN TRP CYS THR SEQRES 6 B 165 HIS HIS LYS ASP ASP PRO PRO PRO PRO GLU ASP ASP GLU SEQRES 7 B 165 ASN LYS GLU LYS ARG THR ASP ASP ILE PRO VAL TRP ASP SEQRES 8 B 165 GLN GLU PHE LEU LYS VAL ASP GLN GLY THR LEU PHE GLU SEQRES 9 B 165 LEU ILE LEU ALA ALA ASN TYR LEU ASP ILE LYS GLY LEU SEQRES 10 B 165 LEU ASP VAL THR CYS LYS THR VAL ALA ASN MET ILE LYS SEQRES 11 B 165 GLY LYS THR PRO GLU GLU ILE ARG LYS THR PHE ASN ILE SEQRES 12 B 165 LYS ASN ASP PHE THR GLU GLU GLU GLU ALA GLN VAL ARG SEQRES 13 B 165 LYS GLU ASN GLN TRP CYS GLU GLU LYS SEQRES 1 C 47 GLY ALA GLY ASP GLU SER TRP MET GLN ARG GLU VAL TRP SEQRES 2 C 47 MET SER VAL PHE ARG TYR LEU SER ARG ARG GLU LEU CYS SEQRES 3 C 47 GLU CYS MET ARG VAL CYS LYS THR TRP TYR LYS TRP CYS SEQRES 4 C 47 CYS ASP LYS ARG LEU TRP THR LYS SEQRES 1 D 86 GLY SER GLY MET GLN ILE PHE VAL LYS THR PHE ARG ASP SEQRES 2 D 86 ARG LEU ARG ASN LEU LEU PRO GLN THR ILE THR LEU GLU SEQRES 3 D 86 VAL GLU PRO SER ASP THR ILE GLU ASN VAL LYS ALA LYS SEQRES 4 D 86 ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN GLN VAL SEQRES 5 D 86 LEU ILE PHE SER ARG LYS ARG LEU GLU ASP GLY ARG THR SEQRES 6 D 86 LEU SER ASP TYR ASN ILE GLN LYS GLU SER THR LEU ARG SEQRES 7 D 86 LEU VAL LEU VAL PHE GLY ARG ARG SEQRES 1 F 47 GLY ALA GLY ASP GLU SER TRP MET GLN ARG GLU VAL TRP SEQRES 2 F 47 MET SER VAL PHE ARG TYR LEU SER ARG ARG GLU LEU CYS SEQRES 3 F 47 GLU CYS MET ARG VAL CYS LYS THR TRP TYR LYS TRP CYS SEQRES 4 F 47 CYS ASP LYS ARG LEU TRP THR LYS SEQRES 1 H 86 GLY SER GLY MET GLN ILE PHE VAL LYS THR PHE ARG ASP SEQRES 2 H 86 ARG LEU ARG ASN LEU LEU PRO GLN THR ILE THR LEU GLU SEQRES 3 H 86 VAL GLU PRO SER ASP THR ILE GLU ASN VAL LYS ALA LYS SEQRES 4 H 86 ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP GLN GLN VAL SEQRES 5 H 86 LEU ILE PHE SER ARG LYS ARG LEU GLU ASP GLY ARG THR SEQRES 6 H 86 LEU SER ASP TYR ASN ILE GLN LYS GLU SER THR LEU ARG SEQRES 7 H 86 LEU VAL LEU VAL PHE GLY ARG ARG HELIX 1 AA1 ASP A 17 LYS A 22 1 6 HELIX 2 AA2 SER A 24 LEU A 31 1 8 HELIX 3 AA3 ASN A 51 HIS A 65 1 15 HELIX 4 AA4 PRO A 86 LEU A 93 1 8 HELIX 5 AA5 ASP A 96 LEU A 110 1 15 HELIX 6 AA6 ILE A 112 LYS A 128 1 17 HELIX 7 AA7 THR A 131 ASN A 140 1 10 HELIX 8 AA8 THR A 146 LYS A 155 1 10 HELIX 9 AA9 VAL B 18 LYS B 22 1 5 HELIX 10 AB1 SER B 24 LEU B 31 1 8 HELIX 11 AB2 ASN B 51 HIS B 65 1 15 HELIX 12 AB3 PRO B 86 LEU B 93 1 8 HELIX 13 AB4 ASP B 96 LEU B 110 1 15 HELIX 14 AB5 ILE B 112 LYS B 128 1 17 HELIX 15 AB6 THR B 131 ASN B 140 1 10 HELIX 16 AB7 GLU B 147 ASN B 157 1 11 HELIX 17 AB8 MET C 893 LEU C 905 1 13 HELIX 18 AB9 SER C 906 MET C 914 1 9 HELIX 19 AC1 CYS C 917 CYS C 925 1 9 HELIX 20 AC2 THR D 22 ASP D 32 1 11 HELIX 21 AC3 SER D 57 ILE D 61 5 5 HELIX 22 AC4 MET F 893 ARG F 903 1 11 HELIX 23 AC5 SER F 906 MET F 914 1 9 HELIX 24 AC6 CYS F 917 CYS F 925 1 9 HELIX 25 AC7 THR H 22 GLU H 34 1 13 HELIX 26 AC8 PRO H 37 ASP H 39 5 3 SHEET 1 AA1 3 ILE A 13 VAL A 16 0 SHEET 2 AA1 3 ILE A 4 GLN A 7 -1 N ILE A 4 O VAL A 16 SHEET 3 AA1 3 VAL A 45 PRO A 46 1 O VAL A 45 N LYS A 5 SHEET 1 AA2 3 ILE B 13 ASP B 17 0 SHEET 2 AA2 3 SER B 3 GLN B 7 -1 N ILE B 4 O VAL B 16 SHEET 3 AA2 3 VAL B 45 PRO B 46 1 O VAL B 45 N LYS B 5 SHEET 1 AA3 2 GLN D 2 LYS D 6 0 SHEET 2 AA3 2 THR D 12 GLU D 16 -1 O LEU D 15 N ILE D 3 SHEET 1 AA4 3 LYS D 48 ARG D 49 0 SHEET 2 AA4 3 GLN D 41 PHE D 45 -1 N PHE D 45 O LYS D 48 SHEET 3 AA4 3 ARG D 68 LEU D 71 -1 O VAL D 70 N VAL D 42 SHEET 1 AA5 2 MET H 1 LYS H 6 0 SHEET 2 AA5 2 THR H 12 VAL H 17 -1 O VAL H 17 N MET H 1 SHEET 1 AA6 2 GLN H 41 ILE H 44 0 SHEET 2 AA6 2 ARG H 68 LEU H 71 -1 O VAL H 70 N VAL H 42 CRYST1 38.241 119.582 63.707 90.00 98.45 90.00 P 1 21 1 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 0.026150 0.000000 0.003886 0.00000 SCALE2 0.000000 0.008362 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015869 0.00000