PDB Short entry for 3DPL HEADER LIGASE 08-JUL-08 3DPL TITLE STRUCTURAL INSIGHTS INTO NEDD8 ACTIVATION OF CULLIN-RING LIGASES: TITLE 2 CONFORMATIONAL CONTROL OF CONJUGATION. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CULLIN-5; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: RESIDUES 401-780; COMPND 5 SYNONYM: CUL-5, VASOPRESSIN-ACTIVATED CALCIUM-MOBILIZING RECEPTOR, COMPND 6 VACM-1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RING-BOX PROTEIN 1; COMPND 11 CHAIN: R; COMPND 12 SYNONYM: RBX1, REGULATOR OF CULLIN-1, RING FINGER PROTEIN 75, PROTEIN COMPND 13 ZYP; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: CUL5, VACM1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX4T1; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: RBX1, RNF75, ROC1; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)GOLD; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PRSF-DUET KEYWDS UBIQUITIN, NEDD8, CULLIN, HOST-VIRUS INTERACTION, RECEPTOR, UBL KEYWDS 2 CONJUGATION, UBL CONJUGATION PATHWAY, ACETYLATION, CYTOPLASM, DNA KEYWDS 3 DAMAGE, DNA REPAIR, METAL-BINDING, NUCLEUS, ZINC, ZINC-FINGER, KEYWDS 4 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR D.M.DUDA,B.A.SCHULMAN REVDAT 3 20-OCT-21 3DPL 1 REMARK SEQADV REVDAT 2 24-FEB-09 3DPL 1 VERSN REVDAT 1 30-SEP-08 3DPL 0 JRNL AUTH D.M.DUDA,L.A.BORG,D.C.SCOTT,H.W.HUNT,M.HAMMEL,B.A.SCHULMAN JRNL TITL STRUCTURAL INSIGHTS INTO NEDD8 ACTIVATION OF CULLIN-RING JRNL TITL 2 LIGASES: CONFORMATIONAL CONTROL OF CONJUGATION. JRNL REF CELL(CAMBRIDGE,MASS.) V. 134 995 2008 JRNL REFN ISSN 0092-8674 JRNL PMID 18805092 JRNL DOI 10.1016/J.CELL.2008.07.022 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1323701.740 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 17724 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 SET) : 0.244 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 915 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2186 REMARK 3 BIN R VALUE (WORKING SET) : 0.3520 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 128 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.036 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3856 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 73 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 37.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.14800 REMARK 3 B22 (A**2) : -5.81400 REMARK 3 B33 (A**2) : -6.33400 REMARK 3 B12 (A**2) : 0.00000 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.42 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.48 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.51 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.382 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 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) : 1.551 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.756 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.129 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.426 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.31 REMARK 3 BSOL : 27.95 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3DPL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-08. REMARK 100 THE DEPOSITION ID IS D_1000048330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 OPTICS : CRYOGENICALLY COOLED FIRST REMARK 200 CRYSTAL AND SAGITALLY BENT REMARK 200 SECOND CRYSTAL HORIZONTALLY REMARK 200 FOCUSING REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18719 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.15600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2% PEG 3350, 0.1M HEPES, 0.2M L REMARK 280 -PROLINE, PH 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K 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 31.48250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.55800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.75500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.55800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.48250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.75500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, R 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 C 399 REMARK 465 SER C 400 REMARK 465 LYS C 518 REMARK 465 LEU C 519 REMARK 465 GLY R 3 REMARK 465 SER R 4 REMARK 465 MET R 5 REMARK 465 ASP R 6 REMARK 465 VAL R 7 REMARK 465 ASP R 8 REMARK 465 THR R 9 REMARK 465 PRO R 10 REMARK 465 SER R 11 REMARK 465 GLY R 12 REMARK 465 THR R 13 REMARK 465 ASN R 14 REMARK 465 SER R 15 REMARK 465 GLY R 16 REMARK 465 ALA R 17 REMARK 465 GLY R 18 REMARK 465 THR R 64 REMARK 465 SER R 65 REMARK 465 GLU R 66 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 MET C 723 O ARG C 726 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 PRO C 652 C - N - CA ANGL. DEV. = -9.1 DEGREES REMARK 500 CYS R 53 CA - CB - SG ANGL. DEV. = 9.3 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 SER C 402 94.61 36.85 REMARK 500 LYS C 424 34.97 -86.26 REMARK 500 GLU C 471 -73.21 -64.93 REMARK 500 VAL C 483 4.10 -54.31 REMARK 500 HIS C 514 60.05 -117.58 REMARK 500 PRO C 522 92.04 -66.18 REMARK 500 ALA C 523 -76.42 1.72 REMARK 500 GLU C 550 -8.85 -54.70 REMARK 500 LYS C 564 0.26 -64.49 REMARK 500 HIS C 574 64.66 -105.80 REMARK 500 ASN C 586 -145.40 -71.83 REMARK 500 ARG C 609 62.27 -168.65 REMARK 500 ALA C 639 50.07 -147.79 REMARK 500 LYS C 642 -21.81 74.00 REMARK 500 GLU C 651 -116.87 -79.03 REMARK 500 GLN C 670 7.90 -68.65 REMARK 500 ASN C 677 40.32 89.91 REMARK 500 ALA C 678 2.17 57.18 REMARK 500 MET C 745 -58.56 -120.75 REMARK 500 SER C 771 64.07 -117.71 REMARK 500 ASP C 772 120.67 176.99 REMARK 500 ASN C 774 -103.53 -108.69 REMARK 500 THR C 775 118.27 -1.20 REMARK 500 LYS R 20 -169.86 -113.33 REMARK 500 ASP R 36 -76.28 -25.01 REMARK 500 ILE R 37 -97.43 9.04 REMARK 500 VAL R 39 57.63 -64.55 REMARK 500 CYS R 42 150.77 -48.37 REMARK 500 CYS R 45 -127.47 -81.28 REMARK 500 ARG R 46 0.72 -173.81 REMARK 500 ILE R 54 -42.69 -24.04 REMARK 500 GLN R 57 -3.69 -56.53 REMARK 500 GLN R 60 31.35 -91.98 REMARK 500 SER R 62 -156.44 -172.42 REMARK 500 CYS R 68 93.77 -47.23 REMARK 500 ASP R 97 -158.15 -96.16 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 R 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS R 42 SG REMARK 620 2 HIS R 80 ND1 124.9 REMARK 620 3 CYS R 83 SG 93.5 140.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN R 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS R 53 SG REMARK 620 2 CYS R 56 SG 102.7 REMARK 620 3 CYS R 68 SG 52.2 53.8 REMARK 620 4 HIS R 82 ND1 113.2 119.2 119.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN R 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS R 75 SG REMARK 620 2 HIS R 77 ND1 117.3 REMARK 620 3 CYS R 94 SG 113.0 109.2 REMARK 620 4 ASP R 97 OD1 130.1 90.9 92.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN R 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN R 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN R 203 DBREF 3DPL C 401 780 UNP Q93034 CUL5_HUMAN 401 780 DBREF 3DPL R 5 108 UNP P62877 RBX1_HUMAN 5 108 SEQADV 3DPL GLY C 399 UNP Q93034 EXPRESSION TAG SEQADV 3DPL SER C 400 UNP Q93034 EXPRESSION TAG SEQADV 3DPL GLU C 407 UNP Q93034 LEU 407 ENGINEERED MUTATION SEQADV 3DPL LYS C 439 UNP Q93034 LEU 439 ENGINEERED MUTATION SEQADV 3DPL LYS C 440 UNP Q93034 VAL 440 ENGINEERED MUTATION SEQADV 3DPL GLY R 3 UNP P62877 EXPRESSION TAG SEQADV 3DPL SER R 4 UNP P62877 EXPRESSION TAG SEQRES 1 C 382 GLY SER GLU SER LYS CYS PRO GLU GLU LEU ALA ASN TYR SEQRES 2 C 382 CYS ASP MET LEU LEU ARG LYS THR PRO LEU SER LYS LYS SEQRES 3 C 382 LEU THR SER GLU GLU ILE GLU ALA LYS LEU LYS GLU VAL SEQRES 4 C 382 LEU LYS LYS LEU LYS TYR VAL GLN ASN LYS ASP VAL PHE SEQRES 5 C 382 MET ARG TYR HIS LYS ALA HIS LEU THR ARG ARG LEU ILE SEQRES 6 C 382 LEU ASP ILE SER ALA ASP SER GLU ILE GLU GLU ASN MET SEQRES 7 C 382 VAL GLU TRP LEU ARG GLU VAL GLY MET PRO ALA ASP TYR SEQRES 8 C 382 VAL ASN LYS LEU ALA ARG MET PHE GLN ASP ILE LYS VAL SEQRES 9 C 382 SER GLU ASP LEU ASN GLN ALA PHE LYS GLU MET HIS LYS SEQRES 10 C 382 ASN ASN LYS LEU ALA LEU PRO ALA ASP SER VAL ASN ILE SEQRES 11 C 382 LYS ILE LEU ASN ALA GLY ALA TRP SER ARG SER SER GLU SEQRES 12 C 382 LYS VAL PHE VAL SER LEU PRO THR GLU LEU GLU ASP LEU SEQRES 13 C 382 ILE PRO GLU VAL GLU GLU PHE TYR LYS LYS ASN HIS SER SEQRES 14 C 382 GLY ARG LYS LEU HIS TRP HIS HIS LEU MET SER ASN GLY SEQRES 15 C 382 ILE ILE THR PHE LYS ASN GLU VAL GLY GLN TYR ASP LEU SEQRES 16 C 382 GLU VAL THR THR PHE GLN LEU ALA VAL LEU PHE ALA TRP SEQRES 17 C 382 ASN GLN ARG PRO ARG GLU LYS ILE SER PHE GLU ASN LEU SEQRES 18 C 382 LYS LEU ALA THR GLU LEU PRO ASP ALA GLU LEU ARG ARG SEQRES 19 C 382 THR LEU TRP SER LEU VAL ALA PHE PRO LYS LEU LYS ARG SEQRES 20 C 382 GLN VAL LEU LEU TYR GLU PRO GLN VAL ASN SER PRO LYS SEQRES 21 C 382 ASP PHE THR GLU GLY THR LEU PHE SER VAL ASN GLN GLU SEQRES 22 C 382 PHE SER LEU ILE LYS ASN ALA LYS VAL GLN LYS ARG GLY SEQRES 23 C 382 LYS ILE ASN LEU ILE GLY ARG LEU GLN LEU THR THR GLU SEQRES 24 C 382 ARG MET ARG GLU GLU GLU ASN GLU GLY ILE VAL GLN LEU SEQRES 25 C 382 ARG ILE LEU ARG THR GLN GLU ALA ILE ILE GLN ILE MET SEQRES 26 C 382 LYS MET ARG LYS LYS ILE SER ASN ALA GLN LEU GLN THR SEQRES 27 C 382 GLU LEU VAL GLU ILE LEU LYS ASN MET PHE LEU PRO GLN SEQRES 28 C 382 LYS LYS MET ILE LYS GLU GLN ILE GLU TRP LEU ILE GLU SEQRES 29 C 382 HIS LYS TYR ILE ARG ARG ASP GLU SER ASP ILE ASN THR SEQRES 30 C 382 PHE ILE TYR MET ALA SEQRES 1 R 106 GLY SER MET ASP VAL ASP THR PRO SER GLY THR ASN SER SEQRES 2 R 106 GLY ALA GLY LYS LYS ARG PHE GLU VAL LYS LYS TRP ASN SEQRES 3 R 106 ALA VAL ALA LEU TRP ALA TRP ASP ILE VAL VAL ASP ASN SEQRES 4 R 106 CYS ALA ILE CYS ARG ASN HIS ILE MET ASP LEU CYS ILE SEQRES 5 R 106 GLU CYS GLN ALA ASN GLN ALA SER ALA THR SER GLU GLU SEQRES 6 R 106 CYS THR VAL ALA TRP GLY VAL CYS ASN HIS ALA PHE HIS SEQRES 7 R 106 PHE HIS CYS ILE SER ARG TRP LEU LYS THR ARG GLN VAL SEQRES 8 R 106 CYS PRO LEU ASP ASN ARG GLU TRP GLU PHE GLN LYS TYR SEQRES 9 R 106 GLY HIS HET ZN R 201 1 HET ZN R 202 1 HET ZN R 203 1 HETNAM ZN ZINC ION FORMUL 3 ZN 3(ZN 2+) FORMUL 6 HOH *73(H2 O) HELIX 1 1 CYS C 404 ARG C 417 1 14 HELIX 2 2 THR C 419 LYS C 424 1 6 HELIX 3 3 THR C 426 LYS C 439 1 14 HELIX 4 4 LYS C 440 VAL C 444 5 5 HELIX 5 5 ASN C 446 LEU C 464 1 19 HELIX 6 6 ASP C 469 VAL C 483 1 15 HELIX 7 7 PRO C 486 HIS C 514 1 29 HELIX 8 8 PRO C 522 ASP C 524 5 3 HELIX 9 9 ALA C 533 SER C 537 1 5 HELIX 10 10 PRO C 548 ASP C 553 1 6 HELIX 11 11 LEU C 554 LYS C 564 1 11 HELIX 12 12 HIS C 575 MET C 577 5 3 HELIX 13 13 THR C 597 PHE C 604 1 8 HELIX 14 14 ALA C 605 ASN C 607 5 3 HELIX 15 15 PHE C 616 GLU C 624 1 9 HELIX 16 16 PRO C 626 ALA C 639 1 14 HELIX 17 17 SER C 656 PHE C 660 5 5 HELIX 18 18 THR C 696 LYS C 724 1 29 HELIX 19 19 SER C 730 LEU C 742 1 13 HELIX 20 20 GLN C 749 HIS C 763 1 15 HELIX 21 21 GLU R 55 GLN R 60 1 6 HELIX 22 22 PHE R 81 LYS R 89 1 9 SHEET 1 A 3 VAL C 526 ASN C 532 0 SHEET 2 A 3 PHE R 22 TRP R 35 1 O TRP R 27 N ASN C 527 SHEET 3 A 3 ARG C 569 TRP C 573 -1 N HIS C 572 O LEU R 32 SHEET 1 B 5 VAL C 526 ASN C 532 0 SHEET 2 B 5 PHE R 22 TRP R 35 1 O TRP R 27 N ASN C 527 SHEET 3 B 5 ASN C 579 LYS C 585 -1 N THR C 583 O GLU R 23 SHEET 4 B 5 GLN C 590 THR C 596 -1 O TYR C 591 N PHE C 584 SHEET 5 B 5 ARG C 683 ASN C 687 1 O ILE C 686 N GLU C 594 SHEET 1 C 3 ILE C 614 SER C 615 0 SHEET 2 C 3 LEU C 665 VAL C 668 -1 O PHE C 666 N ILE C 614 SHEET 3 C 3 LEU C 648 TYR C 650 -1 N LEU C 649 O SER C 667 SHEET 1 D 2 LEU C 674 ILE C 675 0 SHEET 2 D 2 VAL C 680 GLN C 681 -1 O GLN C 681 N LEU C 674 SHEET 1 E 3 LYS C 728 ILE C 729 0 SHEET 2 E 3 ASP C 772 TYR C 778 -1 O PHE C 776 N ILE C 729 SHEET 3 E 3 ILE C 766 ASP C 769 -1 N ARG C 767 O ILE C 777 SHEET 1 F 3 ALA R 78 HIS R 80 0 SHEET 2 F 3 VAL R 70 GLY R 73 -1 N ALA R 71 O PHE R 79 SHEET 3 F 3 PHE R 103 LYS R 105 -1 O LYS R 105 N TRP R 72 SSBOND 1 CYS R 42 CYS R 45 1555 1555 2.05 SSBOND 2 CYS R 45 CYS R 83 1555 1555 2.04 SSBOND 3 CYS R 53 CYS R 68 1555 1555 2.04 SSBOND 4 CYS R 56 CYS R 68 1555 1555 2.04 LINK SG CYS R 42 ZN ZN R 201 1555 1555 2.26 LINK SG CYS R 53 ZN ZN R 203 1555 1555 2.47 LINK SG CYS R 56 ZN ZN R 203 1555 1555 2.38 LINK SG CYS R 68 ZN ZN R 203 1555 1555 2.10 LINK SG CYS R 75 ZN ZN R 202 1555 1555 2.38 LINK ND1 HIS R 77 ZN ZN R 202 1555 1555 2.12 LINK ND1 HIS R 80 ZN ZN R 201 1555 1555 2.22 LINK ND1 HIS R 82 ZN ZN R 203 1555 1555 2.32 LINK SG CYS R 83 ZN ZN R 201 1555 1555 2.64 LINK SG CYS R 94 ZN ZN R 202 1555 1555 2.39 LINK OD1 ASP R 97 ZN ZN R 202 1555 1555 2.10 SITE 1 AC1 4 CYS R 42 CYS R 45 HIS R 80 CYS R 83 SITE 1 AC2 4 CYS R 75 HIS R 77 CYS R 94 ASP R 97 SITE 1 AC3 4 CYS R 53 CYS R 56 CYS R 68 HIS R 82 CRYST1 62.965 65.510 141.116 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.015882 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015265 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007086 0.00000