HEADER PROTEIN BINDING 18-AUG-20 7JTO TITLE CRYSTAL STRUCTURE OF PROTAC MS33 IN COMPLEX WITH THE WD REPEAT- TITLE 2 CONTAINING PROTEIN 5 AND PVHL:ELONGINC:ELONGINB COMPND MOL_ID: 1; COMPND 2 MOLECULE: WD REPEAT-CONTAINING PROTEIN 5; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: BMP2-INDUCED 3-KB GENE PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ELONGIN-B; COMPND 8 CHAIN: J; COMPND 9 SYNONYM: ELOB,ELONGIN 18 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 10 FACTOR SIII SUBUNIT B,SIII P18,TRANSCRIPTION ELONGATION FACTOR B COMPND 11 POLYPEPTIDE 2; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: ELONGIN-C; COMPND 15 CHAIN: K; COMPND 16 SYNONYM: ELOC,ELONGIN 15 KDA SUBUNIT,RNA POLYMERASE II TRANSCRIPTION COMPND 17 FACTOR SIII SUBUNIT C,SIII P15,TRANSCRIPTION ELONGATION FACTOR B COMPND 18 POLYPEPTIDE 1; COMPND 19 ENGINEERED: YES; COMPND 20 MOL_ID: 4; COMPND 21 MOLECULE: VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR; COMPND 22 CHAIN: L; COMPND 23 SYNONYM: PROTEIN G7,PVHL; COMPND 24 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: WDR5, BIG3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: ELOB, TCEB2; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PCDF DUET; SOURCE 19 MOL_ID: 3; SOURCE 20 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 21 ORGANISM_COMMON: HUMAN; SOURCE 22 ORGANISM_TAXID: 9606; SOURCE 23 GENE: ELOC, TCEB1; SOURCE 24 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 25 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 26 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 27 EXPRESSION_SYSTEM_PLASMID: PCDF DUET; SOURCE 28 MOL_ID: 4; SOURCE 29 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 30 ORGANISM_COMMON: HUMAN; SOURCE 31 ORGANISM_TAXID: 9606; SOURCE 32 GENE: VHL; SOURCE 33 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 34 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PROTAC, PROTEIN DEGRADATION, UBIQUITINATION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.KOTTUR,R.JAIN,A.K.AGGARWAL REVDAT 3 18-OCT-23 7JTO 1 REMARK REVDAT 2 13-OCT-21 7JTO 1 JRNL REVDAT 1 06-OCT-21 7JTO 0 JRNL AUTH X.YU,D.LI,J.KOTTUR,Y.SHEN,H.S.KIM,K.S.PARK,Y.H.TSAI,W.GONG, JRNL AUTH 2 J.WANG,K.SUZUKI,J.PARKER,L.HERRING,H.U.KANISKAN,L.CAI, JRNL AUTH 3 R.JAIN,J.LIU,A.K.AGGARWAL,G.G.WANG,J.JIN JRNL TITL A SELECTIVE WDR5 DEGRADER INHIBITS ACUTE MYELOID LEUKEMIA IN JRNL TITL 2 PATIENT-DERIVED MOUSE MODELS. JRNL REF SCI TRANSL MED V. 13 J1578 2021 JRNL REFN ESSN 1946-6242 JRNL PMID 34586829 JRNL DOI 10.1126/SCITRANSLMED.ABJ1578 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 83544 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 4161 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 46.9580 - 5.2799 1.00 2686 129 0.1573 0.1573 REMARK 3 2 5.2799 - 4.1916 1.00 2662 145 0.1340 0.1521 REMARK 3 3 4.1916 - 3.6620 1.00 2650 146 0.1448 0.1495 REMARK 3 4 3.6620 - 3.3273 1.00 2649 138 0.1587 0.1896 REMARK 3 5 3.3273 - 3.0889 1.00 2704 110 0.1791 0.2172 REMARK 3 6 3.0889 - 2.9068 1.00 2672 108 0.1832 0.1985 REMARK 3 7 2.9068 - 2.7612 1.00 2659 141 0.1854 0.2358 REMARK 3 8 2.7612 - 2.6410 1.00 2597 169 0.1937 0.2155 REMARK 3 9 2.6410 - 2.5394 1.00 2680 132 0.2084 0.2430 REMARK 3 10 2.5394 - 2.4518 1.00 2648 140 0.2064 0.2238 REMARK 3 11 2.4518 - 2.3751 1.00 2651 122 0.2086 0.2561 REMARK 3 12 2.3751 - 2.3072 1.00 2654 139 0.2006 0.2666 REMARK 3 13 2.3072 - 2.2465 1.00 2614 149 0.2079 0.2399 REMARK 3 14 2.2465 - 2.1917 1.00 2638 140 0.2101 0.2476 REMARK 3 15 2.1917 - 2.1418 1.00 2611 166 0.2139 0.2730 REMARK 3 16 2.1418 - 2.0963 1.00 2672 143 0.2211 0.2671 REMARK 3 17 2.0963 - 2.0543 1.00 2613 141 0.2202 0.2751 REMARK 3 18 2.0543 - 2.0156 1.00 2661 137 0.2306 0.2893 REMARK 3 19 2.0156 - 1.9796 1.00 2615 137 0.2340 0.2586 REMARK 3 20 1.9796 - 1.9460 1.00 2657 145 0.2424 0.2616 REMARK 3 21 1.9460 - 1.9146 1.00 2645 138 0.2496 0.3031 REMARK 3 22 1.9146 - 1.8852 0.99 2616 134 0.2547 0.3146 REMARK 3 23 1.8852 - 1.8574 1.00 2683 144 0.2787 0.3409 REMARK 3 24 1.8574 - 1.8313 1.00 2608 122 0.2925 0.3107 REMARK 3 25 1.8313 - 1.8065 1.00 2639 142 0.3079 0.3519 REMARK 3 26 1.8065 - 1.7831 1.00 2694 131 0.3309 0.3536 REMARK 3 27 1.7831 - 1.7608 1.00 2570 154 0.3476 0.3705 REMARK 3 28 1.7608 - 1.7396 1.00 2664 149 0.3430 0.3430 REMARK 3 29 1.7396 - 1.7193 1.00 2651 145 0.3795 0.4042 REMARK 3 30 1.7193 - 1.7000 1.00 2620 125 0.3728 0.3728 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.690 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.23 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.33 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7JTO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251369. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5-8.0 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) : 0.97928 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83626 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 93.915 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07700 REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.40500 REMARK 200 R SYM FOR SHELL (I) : 0.40500 REMARK 200 FOR SHELL : 1.900 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: PDB ENTRIES 2GNQ & 1VCB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES SODIUM, PH 7.5-8.0, 1.3 REMARK 280 -1.6 M SODIUM THIOCYANATE, 15-20% PEG3350, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293.15K 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 93.91500 REMARK 290 SMTRY3 2 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 APPLY THE FOLLOWING TO CHAINS: B, J, K, L 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 GLU B 27 REMARK 465 PHE B 28 REMARK 465 HIS B 29 REMARK 465 MET B 30 REMARK 465 VAL B 31 REMARK 465 LYS J 104 REMARK 465 MET K 16 REMARK 465 GLY K 48 REMARK 465 PRO K 49 REMARK 465 GLY K 50 REMARK 465 GLN K 51 REMARK 465 PHE K 52 REMARK 465 ALA K 53 REMARK 465 GLU K 54 REMARK 465 ASN K 55 REMARK 465 GLU K 56 REMARK 465 GLY L 52 REMARK 465 SER L 53 REMARK 465 MET L 54 REMARK 465 GLU L 55 REMARK 465 ALA L 56 REMARK 465 GLY L 57 REMARK 465 ILE L 206 REMARK 465 ALA L 207 REMARK 465 HIS L 208 REMARK 465 GLN L 209 REMARK 465 ARG L 210 REMARK 465 MET L 211 REMARK 465 GLY L 212 REMARK 465 ASP L 213 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 87 CD CE NZ REMARK 470 LYS B 159 CG CD CE NZ REMARK 470 LYS B 162 CG CD CE NZ REMARK 470 ARG B 181 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 212 CG OD1 OD2 REMARK 470 LYS B 227 CG CD CE NZ REMARK 470 LYS B 256 CG CD CE NZ REMARK 470 LYS B 272 CD CE NZ REMARK 470 GLN B 298 CG CD OE1 NE2 REMARK 470 MET J 1 CG SD CE REMARK 470 ASP J 48 CG OD1 OD2 REMARK 470 LYS J 55 CE NZ REMARK 470 GLN J 65 CG CD OE1 NE2 REMARK 470 ARG J 80 NH1 REMARK 470 MET K 17 CG SD CE REMARK 470 THR K 57 OG1 CG2 REMARK 470 ARG K 82 NE CZ NH1 NH2 REMARK 470 ASN K 85 CG OD1 ND2 REMARK 470 SER K 87 OG REMARK 470 ARG L 58 CG CD NE CZ NH1 NH2 REMARK 470 ARG L 113 CG CD NE CZ NH1 NH2 REMARK 470 LEU L 140 CG CD1 CD2 REMARK 470 ASN L 174 ND2 REMARK 470 ARG L 177 CD NE CZ NH1 NH2 REMARK 470 ARG L 182 CZ NH1 NH2 REMARK 470 GLN L 203 CD OE1 NE2 REMARK 470 ARG L 205 CG CD NE CZ NH1 NH2 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 OD1 ASP B 211 O HOH B 501 1.85 REMARK 500 O HOH B 633 O HOH B 694 1.90 REMARK 500 OG SER L 68 O HOH L 801 1.90 REMARK 500 ND2 ASN B 225 O HOH B 502 1.95 REMARK 500 O HOH K 471 O HOH K 482 1.98 REMARK 500 OH TYR L 112 O HOH L 802 2.06 REMARK 500 O HOH B 666 O HOH B 704 2.13 REMARK 500 OD2 ASP B 172 O HOH B 503 2.15 REMARK 500 O HOH B 511 O HOH B 612 2.15 REMARK 500 O HOH B 540 O HOH B 637 2.15 REMARK 500 O HOH J 320 O HOH J 373 2.15 REMARK 500 O HOH B 502 O HOH B 694 2.16 REMARK 500 O PRO L 61 O HOH L 803 2.16 REMARK 500 O HOH J 350 O HOH J 374 2.17 REMARK 500 O HOH B 613 O HOH B 742 2.17 REMARK 500 O MET J 103 O HOH J 301 2.17 REMARK 500 O PRO B 168 O HOH B 504 2.18 REMARK 500 O HOH B 598 O HOH B 612 2.18 REMARK 500 O HOH B 503 O HOH L 881 2.18 REMARK 500 O HOH J 302 O HOH J 361 2.18 REMARK 500 O HOH B 523 O HOH B 731 2.19 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 B 662 O HOH L 951 1455 2.10 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 ALA B 42 55.83 -110.93 REMARK 500 ASP B 211 -151.31 -91.90 REMARK 500 LEU B 234 37.16 -78.44 REMARK 500 ASN B 257 89.80 -155.75 REMARK 500 LEU B 321 -158.60 -81.63 REMARK 500 LEU B 321 -156.15 -81.63 REMARK 500 HIS J 10 -117.12 57.88 REMARK 500 ASP J 47 -128.28 55.06 REMARK 500 ASP J 82 -112.01 58.58 REMARK 500 ARG L 79 42.03 -91.22 REMARK 500 SER L 111 -154.32 -131.91 REMARK 500 SER L 111 -154.32 -133.01 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 NA L 703 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP L 126 OD2 REMARK 620 2 HOH L 849 O 107.3 REMARK 620 3 HOH L 882 O 97.5 117.8 REMARK 620 4 HOH L 890 O 142.9 107.6 77.2 REMARK 620 N 1 2 3 DBREF 7JTO B 31 334 UNP P61964 WDR5_HUMAN 31 334 DBREF 7JTO J 1 104 UNP Q15370 ELOB_HUMAN 1 104 DBREF 7JTO K 17 112 UNP Q15369 ELOC_HUMAN 1 96 DBREF 7JTO L 54 213 UNP P40337 VHL_HUMAN 1 160 SEQADV 7JTO GLU B 27 UNP P61964 EXPRESSION TAG SEQADV 7JTO PHE B 28 UNP P61964 EXPRESSION TAG SEQADV 7JTO HIS B 29 UNP P61964 EXPRESSION TAG SEQADV 7JTO MET B 30 UNP P61964 EXPRESSION TAG SEQADV 7JTO MET K 16 UNP Q15369 INITIATING METHIONINE SEQADV 7JTO GLY L 52 UNP P40337 EXPRESSION TAG SEQADV 7JTO SER L 53 UNP P40337 EXPRESSION TAG SEQRES 1 B 308 GLU PHE HIS MET VAL LYS PRO ASN TYR ALA LEU LYS PHE SEQRES 2 B 308 THR LEU ALA GLY HIS THR LYS ALA VAL SER SER VAL LYS SEQRES 3 B 308 PHE SER PRO ASN GLY GLU TRP LEU ALA SER SER SER ALA SEQRES 4 B 308 ASP LYS LEU ILE LYS ILE TRP GLY ALA TYR ASP GLY LYS SEQRES 5 B 308 PHE GLU LYS THR ILE SER GLY HIS LYS LEU GLY ILE SER SEQRES 6 B 308 ASP VAL ALA TRP SER SER ASP SER ASN LEU LEU VAL SER SEQRES 7 B 308 ALA SER ASP ASP LYS THR LEU LYS ILE TRP ASP VAL SER SEQRES 8 B 308 SER GLY LYS CYS LEU LYS THR LEU LYS GLY HIS SER ASN SEQRES 9 B 308 TYR VAL PHE CYS CYS ASN PHE ASN PRO GLN SER ASN LEU SEQRES 10 B 308 ILE VAL SER GLY SER PHE ASP GLU SER VAL ARG ILE TRP SEQRES 11 B 308 ASP VAL LYS THR GLY LYS CYS LEU LYS THR LEU PRO ALA SEQRES 12 B 308 HIS SER ASP PRO VAL SER ALA VAL HIS PHE ASN ARG ASP SEQRES 13 B 308 GLY SER LEU ILE VAL SER SER SER TYR ASP GLY LEU CYS SEQRES 14 B 308 ARG ILE TRP ASP THR ALA SER GLY GLN CYS LEU LYS THR SEQRES 15 B 308 LEU ILE ASP ASP ASP ASN PRO PRO VAL SER PHE VAL LYS SEQRES 16 B 308 PHE SER PRO ASN GLY LYS TYR ILE LEU ALA ALA THR LEU SEQRES 17 B 308 ASP ASN THR LEU LYS LEU TRP ASP TYR SER LYS GLY LYS SEQRES 18 B 308 CYS LEU LYS THR TYR THR GLY HIS LYS ASN GLU LYS TYR SEQRES 19 B 308 CYS ILE PHE ALA ASN PHE SER VAL THR GLY GLY LYS TRP SEQRES 20 B 308 ILE VAL SER GLY SER GLU ASP ASN LEU VAL TYR ILE TRP SEQRES 21 B 308 ASN LEU GLN THR LYS GLU ILE VAL GLN LYS LEU GLN GLY SEQRES 22 B 308 HIS THR ASP VAL VAL ILE SER THR ALA CYS HIS PRO THR SEQRES 23 B 308 GLU ASN ILE ILE ALA SER ALA ALA LEU GLU ASN ASP LYS SEQRES 24 B 308 THR ILE LYS LEU TRP LYS SER ASP CYS SEQRES 1 J 104 MET ASP VAL PHE LEU MET ILE ARG ARG HIS LYS THR THR SEQRES 2 J 104 ILE PHE THR ASP ALA LYS GLU SER SER THR VAL PHE GLU SEQRES 3 J 104 LEU LYS ARG ILE VAL GLU GLY ILE LEU LYS ARG PRO PRO SEQRES 4 J 104 ASP GLU GLN ARG LEU TYR LYS ASP ASP GLN LEU LEU ASP SEQRES 5 J 104 ASP GLY LYS THR LEU GLY GLU CYS GLY PHE THR SER GLN SEQRES 6 J 104 THR ALA ARG PRO GLN ALA PRO ALA THR VAL GLY LEU ALA SEQRES 7 J 104 PHE ARG ALA ASP ASP THR PHE GLU ALA LEU CYS ILE GLU SEQRES 8 J 104 PRO PHE SER SER PRO PRO GLU LEU PRO ASP VAL MET LYS SEQRES 1 K 97 MET MET TYR VAL LYS LEU ILE SER SER ASP GLY HIS GLU SEQRES 2 K 97 PHE ILE VAL LYS ARG GLU HIS ALA LEU THR SER GLY THR SEQRES 3 K 97 ILE LYS ALA MET LEU SER GLY PRO GLY GLN PHE ALA GLU SEQRES 4 K 97 ASN GLU THR ASN GLU VAL ASN PHE ARG GLU ILE PRO SER SEQRES 5 K 97 HIS VAL LEU SER LYS VAL CYS MET TYR PHE THR TYR LYS SEQRES 6 K 97 VAL ARG TYR THR ASN SER SER THR GLU ILE PRO GLU PHE SEQRES 7 K 97 PRO ILE ALA PRO GLU ILE ALA LEU GLU LEU LEU MET ALA SEQRES 8 K 97 ALA ASN PHE LEU ASP CYS SEQRES 1 L 162 GLY SER MET GLU ALA GLY ARG PRO ARG PRO VAL LEU ARG SEQRES 2 L 162 SER VAL ASN SER ARG GLU PRO SER GLN VAL ILE PHE CYS SEQRES 3 L 162 ASN ARG SER PRO ARG VAL VAL LEU PRO VAL TRP LEU ASN SEQRES 4 L 162 PHE ASP GLY GLU PRO GLN PRO TYR PRO THR LEU PRO PRO SEQRES 5 L 162 GLY THR GLY ARG ARG ILE HIS SER TYR ARG GLY HIS LEU SEQRES 6 L 162 TRP LEU PHE ARG ASP ALA GLY THR HIS ASP GLY LEU LEU SEQRES 7 L 162 VAL ASN GLN THR GLU LEU PHE VAL PRO SER LEU ASN VAL SEQRES 8 L 162 ASP GLY GLN PRO ILE PHE ALA ASN ILE THR LEU PRO VAL SEQRES 9 L 162 TYR THR LEU LYS GLU ARG CYS LEU GLN VAL VAL ARG SER SEQRES 10 L 162 LEU VAL LYS PRO GLU ASN TYR ARG ARG LEU ASP ILE VAL SEQRES 11 L 162 ARG SER LEU TYR GLU ASP LEU GLU ASP HIS PRO ASN VAL SEQRES 12 L 162 GLN LYS ASP LEU GLU ARG LEU THR GLN GLU ARG ILE ALA SEQRES 13 L 162 HIS GLN ARG MET GLY ASP HET SCN B 401 3 HET SCN B 402 3 HET EDO B 403 4 HET SCN B 404 3 HET EDO B 405 4 HET VKA B 406 86 HET SCN J 201 3 HET GOL K 301 6 HET EDO K 302 4 HET EDO L 701 4 HET EDO L 702 4 HET NA L 703 1 HETNAM SCN THIOCYANATE ION HETNAM EDO 1,2-ETHANEDIOL HETNAM VKA 3-METHYL-N-(11-{[2-(4-{[4'-(4-METHYLPIPERAZIN-1-YL)-3'- HETNAM 2 VKA {[6-OXO-4-(TRIFLUOROMETHYL)-5,6-DIHYDROPYRIDINE-3- HETNAM 3 VKA CARBONYL]AMINO}[1,1'-BIPHENYL]-3-YL]METHYL}PIPERAZIN- HETNAM 4 VKA 1-YL)ETHYL]AMINO}-11-OXOUNDECANOYL)-L-VALYL-(4R)-4- HETNAM 5 VKA HYDROXY-N-{[4-(4-METHYL-1,3-THIAZOL-5-YL) HETNAM 6 VKA PHENYL]METHYL}-L-PROLINAMIDE HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL HETSYN VKA PROTAC MS33 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SCN 4(C N S 1-) FORMUL 7 EDO 5(C2 H6 O2) FORMUL 10 VKA C64 H84 F3 N11 O7 S FORMUL 12 GOL C3 H8 O3 FORMUL 16 NA NA 1+ FORMUL 17 HOH *624(H2 O) HELIX 1 AA1 THR J 23 LYS J 36 1 14 HELIX 2 AA2 PRO J 38 ASP J 40 5 3 HELIX 3 AA3 LEU J 57 GLY J 61 5 5 HELIX 4 AA4 ARG K 33 LEU K 37 1 5 HELIX 5 AA5 SER K 39 SER K 47 1 9 HELIX 6 AA6 PRO K 66 THR K 84 1 19 HELIX 7 AA7 ALA K 96 ASP K 111 1 16 HELIX 8 AA8 THR L 157 VAL L 170 1 14 HELIX 9 AA9 LYS L 171 LEU L 178 5 8 HELIX 10 AB1 VAL L 181 ASP L 190 1 10 HELIX 11 AB2 ASN L 193 ARG L 205 1 13 SHEET 1 AA1 4 ALA B 36 LEU B 41 0 SHEET 2 AA1 4 ILE B 327 LYS B 331 -1 O ILE B 327 N LEU B 41 SHEET 3 AA1 4 ILE B 315 ALA B 320 -1 N ILE B 316 O TRP B 330 SHEET 4 AA1 4 VAL B 304 CYS B 309 -1 N ALA B 308 O ALA B 317 SHEET 1 AA2 4 VAL B 48 PHE B 53 0 SHEET 2 AA2 4 TRP B 59 SER B 64 -1 O ALA B 61 N LYS B 52 SHEET 3 AA2 4 LEU B 68 GLY B 73 -1 O LYS B 70 N SER B 62 SHEET 4 AA2 4 PHE B 79 SER B 84 -1 O GLU B 80 N ILE B 71 SHEET 1 AA3 4 ILE B 90 TRP B 95 0 SHEET 2 AA3 4 LEU B 101 SER B 106 -1 O ALA B 105 N SER B 91 SHEET 3 AA3 4 LEU B 111 ASP B 115 -1 O TRP B 114 N LEU B 102 SHEET 4 AA3 4 LYS B 120 LEU B 125 -1 O LYS B 120 N ASP B 115 SHEET 1 AA4 4 VAL B 132 PHE B 137 0 SHEET 2 AA4 4 LEU B 143 SER B 148 -1 O VAL B 145 N ASN B 136 SHEET 3 AA4 4 VAL B 153 ASP B 157 -1 O TRP B 156 N ILE B 144 SHEET 4 AA4 4 CYS B 163 LEU B 167 -1 O LEU B 167 N VAL B 153 SHEET 1 AA5 4 VAL B 174 PHE B 179 0 SHEET 2 AA5 4 LEU B 185 SER B 190 -1 O VAL B 187 N HIS B 178 SHEET 3 AA5 4 CYS B 195 ASP B 199 -1 O TRP B 198 N ILE B 186 SHEET 4 AA5 4 CYS B 205 LEU B 209 -1 O LYS B 207 N ILE B 197 SHEET 1 AA6 4 VAL B 217 PHE B 222 0 SHEET 2 AA6 4 TYR B 228 THR B 233 -1 O LEU B 230 N LYS B 221 SHEET 3 AA6 4 THR B 237 ASP B 242 -1 O LYS B 239 N ALA B 231 SHEET 4 AA6 4 LYS B 247 TYR B 252 -1 O LYS B 247 N ASP B 242 SHEET 1 AA7 4 ALA B 264 SER B 267 0 SHEET 2 AA7 4 TRP B 273 GLY B 277 -1 O TRP B 273 N SER B 267 SHEET 3 AA7 4 VAL B 283 ASN B 287 -1 O TYR B 284 N SER B 276 SHEET 4 AA7 4 ILE B 293 LEU B 297 -1 O VAL B 294 N ILE B 285 SHEET 1 AA8 4 GLN J 49 LEU J 50 0 SHEET 2 AA8 4 GLN J 42 LYS J 46 -1 N LYS J 46 O GLN J 49 SHEET 3 AA8 4 ALA J 73 ALA J 81 -1 O GLY J 76 N TYR J 45 SHEET 4 AA8 4 THR J 84 PHE J 85 -1 O THR J 84 N ALA J 81 SHEET 1 AA9 8 GLN J 49 LEU J 50 0 SHEET 2 AA9 8 GLN J 42 LYS J 46 -1 N LYS J 46 O GLN J 49 SHEET 3 AA9 8 ALA J 73 ALA J 81 -1 O GLY J 76 N TYR J 45 SHEET 4 AA9 8 ASP J 2 ARG J 9 1 N MET J 6 O VAL J 75 SHEET 5 AA9 8 THR J 12 LYS J 19 -1 O THR J 16 N LEU J 5 SHEET 6 AA9 8 GLU K 28 LYS K 32 1 O ILE K 30 N THR J 13 SHEET 7 AA9 8 TYR K 18 ILE K 22 -1 N LEU K 21 O PHE K 29 SHEET 8 AA9 8 GLU K 59 ASN K 61 1 O VAL K 60 N ILE K 22 SHEET 1 AB1 4 GLY L 106 TYR L 112 0 SHEET 2 AB1 4 PRO L 71 ASN L 78 -1 N VAL L 74 O ILE L 109 SHEET 3 AB1 4 ILE L 147 THR L 152 1 O ILE L 147 N ILE L 75 SHEET 4 AB1 4 LEU L 129 VAL L 130 -1 N LEU L 129 O THR L 152 SHEET 1 AB2 3 PRO L 95 PRO L 97 0 SHEET 2 AB2 3 VAL L 84 LEU L 89 -1 N TRP L 88 O GLN L 96 SHEET 3 AB2 3 LEU L 116 ASP L 121 -1 O LEU L 118 N VAL L 87 LINK OD2 ASP L 126 NA NA L 703 1555 1555 2.64 LINK NA NA L 703 O HOH L 849 1555 1555 2.89 LINK NA NA L 703 O HOH L 882 1555 1555 3.10 LINK NA NA L 703 O HOH L 890 1555 1555 2.67 CRYST1 47.380 187.830 49.150 90.00 116.96 90.00 P 1 21 1 2 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 0.021106 0.000000 0.010735 0.00000 SCALE2 0.000000 0.005324 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022827 0.00000