HEADER LIGASE 04-SEP-19 6SQO TITLE CRYSTAL STRUCTURE OF HUMAN MDM2 RING DOMAIN HOMODIMER BOUND TO UBCH5B- TITLE 2 UB COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE MDM2; COMPND 3 CHAIN: A, D; COMPND 4 SYNONYM: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,RING-TYPE E3 COMPND 5 UBIQUITIN TRANSFERASE MDM2,P53-BINDING PROTEIN MDM2; COMPND 6 EC: 2.3.2.27; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CONSTRUCT CONTAINS MDM2 RESIDUES 419-491. RESIDUES COMPND 9 419-427 ARE ABSENT DUE TO LACK OF ELECTRON DENSITY. GS AT THE N- COMPND 10 TERMINUS RESULTED FROM CLONING.; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2 D2; COMPND 13 CHAIN: B, E; COMPND 14 SYNONYM: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D2,E2 COMPND 15 UBIQUITIN-CONJUGATING ENZYME D2,UBIQUITIN CARRIER PROTEIN D2, COMPND 16 UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2,UBIQUITIN-CONJUGATING ENZYME COMPND 17 E2-17 KDA 2,UBIQUITIN-PROTEIN LIGASE D2,P53-REGULATED UBIQUITIN- COMPND 18 CONJUGATING ENZYME 1; COMPND 19 EC: 2.3.2.23,2.3.2.24; COMPND 20 ENGINEERED: YES; COMPND 21 MUTATION: YES; COMPND 22 OTHER_DETAILS: K85 SIDECHAINS FROM CHAINS B AND E FORM AN ISOPEPTIDE COMPND 23 BOND WITH THE C-TERMINUS OF G76 IN CHAINS C AND F, RESPECTIVELY.; COMPND 24 MOL_ID: 3; COMPND 25 MOLECULE: UBIQUITIN-40S RIBOSOMAL PROTEIN S27A; COMPND 26 CHAIN: C, F; COMPND 27 ENGINEERED: YES; COMPND 28 OTHER_DETAILS: GSGGS LINKER AT THE N-TERMINUS RESULTED FROM CLONING. COMPND 29 G76 IN CHAINS C AND F ARE COVALENTLY LINKED TO K85 SIDE CHAIN IN COMPND 30 CHAINS B AND E, RESPECTIVELY. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: MDM2; 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: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B; 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: RPS27A; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITIN LIGASE, E3, MDM2, MDMX, E2, PHOSPHORYLATION, P53, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR H.M.MAGNUSSEN,S.F.AHMED,D.T.HUANG REVDAT 3 24-JAN-24 6SQO 1 REMARK REVDAT 2 13-MAY-20 6SQO 1 JRNL REVDAT 1 06-MAY-20 6SQO 0 JRNL AUTH H.M.MAGNUSSEN,S.F.AHMED,G.J.SIBBET,V.A.HRISTOVA,K.NOMURA, JRNL AUTH 2 A.K.HOCK,L.J.ARCHIBALD,A.G.JAMIESON,D.FUSHMAN,K.H.VOUSDEN, JRNL AUTH 3 A.M.WEISSMAN,D.T.HUANG JRNL TITL STRUCTURAL BASIS FOR DNA DAMAGE-INDUCED PHOSPHOREGULATION OF JRNL TITL 2 MDM2 RING DOMAIN. JRNL REF NAT COMMUN V. 11 2094 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32350255 JRNL DOI 10.1038/S41467-020-15783-Y REMARK 2 REMARK 2 RESOLUTION. 1.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2142: ???) 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) : 1.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 112.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 129794 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.173 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL 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 : 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 6SQO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1292104139. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 129794 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410 REMARK 200 RESOLUTION RANGE LOW (A) : 112.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.900 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.41 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5MNJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SPG, PH 7.0, 10% (W/V) PEG SMEAR REMARK 280 BROAD, 0.15 M NH4NO3, VAPOR DIFFUSION, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 23.51233 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 47.02467 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.26850 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.78083 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 11.75617 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10850 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, 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 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 LEU A 432 CG CD1 CD2 REMARK 470 LYS A 454 CG CD CE NZ REMARK 470 LYS B 66 CG CD CE NZ REMARK 470 GLU C 24 CG CD OE1 OE2 REMARK 470 LYS C 63 CG CD CE NZ REMARK 470 LEU D 432 CG CD1 CD2 REMARK 470 LYS D 454 CG CD CE NZ REMARK 470 LYS D 470 CG CD CE NZ REMARK 470 ASP E 16 CG OD1 OD2 REMARK 470 GLU F 18 CG CD OE1 OE2 REMARK 470 ASN F 60 CG OD1 ND2 REMARK 470 LYS F 63 CG CD CE NZ 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 NZ LYS E 85 C GLY F 76 1.34 REMARK 500 NZ LYS B 85 C GLY C 76 1.34 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 ASP B 16 69.26 -161.71 REMARK 500 ARG B 90 -110.80 -135.90 REMARK 500 ASP B 130 79.02 -155.51 REMARK 500 ASP B 130 79.17 -155.51 REMARK 500 CYS D 438 126.28 -39.08 REMARK 500 ARG E 90 -121.02 -125.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 461 DISTANCE = 6.09 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 438 SG REMARK 620 2 CYS A 441 SG 107.2 REMARK 620 3 CYS A 461 SG 113.9 114.7 REMARK 620 4 CYS A 464 SG 110.5 109.6 100.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 452 NE2 REMARK 620 2 HIS A 457 ND1 100.7 REMARK 620 3 CYS A 475 SG 120.0 116.2 REMARK 620 4 CYS A 478 SG 96.1 110.8 111.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 438 SG REMARK 620 2 CYS D 441 SG 107.3 REMARK 620 3 CYS D 461 SG 113.4 114.5 REMARK 620 4 CYS D 464 SG 110.5 109.7 101.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 452 NE2 REMARK 620 2 HIS D 457 ND1 103.3 REMARK 620 3 CYS D 475 SG 118.1 115.8 REMARK 620 4 CYS D 478 SG 95.3 112.2 110.3 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 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL E 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NO3 E 202 DBREF 6SQO A 430 491 UNP Q00987 MDM2_HUMAN 430 491 DBREF 6SQO B 2 147 UNP P62837 UB2D2_HUMAN 2 147 DBREF 6SQO C 1 76 UNP J3QTR3 J3QTR3_HUMAN 1 76 DBREF 6SQO D 430 491 UNP Q00987 MDM2_HUMAN 430 491 DBREF 6SQO E 2 147 UNP P62837 UB2D2_HUMAN 2 147 DBREF 6SQO F 1 76 UNP J3QTR3 J3QTR3_HUMAN 1 76 SEQADV 6SQO ARG B 22 UNP P62837 SER 22 ENGINEERED MUTATION SEQADV 6SQO LYS B 85 UNP P62837 CYS 85 ENGINEERED MUTATION SEQADV 6SQO SER C 0 UNP J3QTR3 EXPRESSION TAG SEQADV 6SQO ARG E 22 UNP P62837 SER 22 ENGINEERED MUTATION SEQADV 6SQO LYS E 85 UNP P62837 CYS 85 ENGINEERED MUTATION SEQADV 6SQO SER F 0 UNP J3QTR3 EXPRESSION TAG SEQRES 1 A 62 LEU PRO LEU ASN ALA ILE GLU PRO CYS VAL ILE CYS GLN SEQRES 2 A 62 GLY ARG PRO LYS ASN GLY CYS ILE VAL HIS GLY LYS THR SEQRES 3 A 62 GLY HIS LEU MET ALA CYS PHE THR CYS ALA LYS LYS LEU SEQRES 4 A 62 LYS LYS ARG ASN LYS PRO CYS PRO VAL CYS ARG GLN PRO SEQRES 5 A 62 ILE GLN MET ILE VAL LEU THR TYR PHE PRO SEQRES 1 B 146 ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU ALA SEQRES 2 B 146 ARG ASP PRO PRO ALA GLN CYS ARG ALA GLY PRO VAL GLY SEQRES 3 B 146 ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY PRO SEQRES 4 B 146 ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU THR SEQRES 5 B 146 ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO LYS SEQRES 6 B 146 VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE ASN SEQRES 7 B 146 SER ASN GLY SER ILE LYS LEU ASP ILE LEU ARG SER GLN SEQRES 8 B 146 TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU SER SEQRES 9 B 146 ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO SEQRES 10 B 146 LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP ARG SEQRES 11 B 146 GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN LYS SEQRES 12 B 146 TYR ALA MET SEQRES 1 C 77 SER MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR SEQRES 2 C 77 ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN SEQRES 3 C 77 VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO SEQRES 4 C 77 ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU SEQRES 5 C 77 ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SEQRES 6 C 77 SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY SEQRES 1 D 62 LEU PRO LEU ASN ALA ILE GLU PRO CYS VAL ILE CYS GLN SEQRES 2 D 62 GLY ARG PRO LYS ASN GLY CYS ILE VAL HIS GLY LYS THR SEQRES 3 D 62 GLY HIS LEU MET ALA CYS PHE THR CYS ALA LYS LYS LEU SEQRES 4 D 62 LYS LYS ARG ASN LYS PRO CYS PRO VAL CYS ARG GLN PRO SEQRES 5 D 62 ILE GLN MET ILE VAL LEU THR TYR PHE PRO SEQRES 1 E 146 ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU ALA SEQRES 2 E 146 ARG ASP PRO PRO ALA GLN CYS ARG ALA GLY PRO VAL GLY SEQRES 3 E 146 ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY PRO SEQRES 4 E 146 ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU THR SEQRES 5 E 146 ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO LYS SEQRES 6 E 146 VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE ASN SEQRES 7 E 146 SER ASN GLY SER ILE LYS LEU ASP ILE LEU ARG SER GLN SEQRES 8 E 146 TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU SER SEQRES 9 E 146 ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP PRO SEQRES 10 E 146 LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP ARG SEQRES 11 E 146 GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN LYS SEQRES 12 E 146 TYR ALA MET SEQRES 1 F 77 SER MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR SEQRES 2 F 77 ILE THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN SEQRES 3 F 77 VAL LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO SEQRES 4 F 77 ASP GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU SEQRES 5 F 77 ASP GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SEQRES 6 F 77 SER THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HET ZN A 501 1 HET ZN A 502 1 HET CL A 503 1 HET CL B 201 1 HET NO3 B 202 4 HET ZN D 501 1 HET ZN D 502 1 HET CL D 503 1 HET CL E 201 1 HET NO3 E 202 4 HETNAM ZN ZINC ION HETNAM CL CHLORIDE ION HETNAM NO3 NITRATE ION FORMUL 7 ZN 4(ZN 2+) FORMUL 9 CL 4(CL 1-) FORMUL 11 NO3 2(N O3 1-) FORMUL 17 HOH *546(H2 O) HELIX 1 AA1 PRO A 431 GLU A 436 5 6 HELIX 2 AA2 CYS A 461 ARG A 471 1 11 HELIX 3 AA3 LEU B 3 ASP B 16 1 14 HELIX 4 AA4 LEU B 86 ARG B 90 5 5 HELIX 5 AA5 THR B 98 CYS B 111 1 14 HELIX 6 AA6 VAL B 120 ASP B 130 1 11 HELIX 7 AA7 ASP B 130 ALA B 146 1 17 HELIX 8 AA8 THR C 22 GLY C 35 1 14 HELIX 9 AA9 PRO C 37 ASP C 39 5 3 HELIX 10 AB1 PRO D 431 GLU D 436 5 6 HELIX 11 AB2 CYS D 461 ARG D 471 1 11 HELIX 12 AB3 LEU E 3 ASP E 16 1 14 HELIX 13 AB4 LEU E 86 ARG E 90 5 5 HELIX 14 AB5 THR E 98 CYS E 111 1 14 HELIX 15 AB6 VAL E 120 ASP E 130 1 11 HELIX 16 AB7 ASP E 130 ALA E 146 1 17 HELIX 17 AB8 THR F 22 GLY F 35 1 14 HELIX 18 AB9 PRO F 37 ASP F 39 5 3 SHEET 1 AA1 7 GLY A 448 HIS A 452 0 SHEET 2 AA1 7 THR A 455 ALA A 460 -1 O THR A 455 N HIS A 452 SHEET 3 AA1 7 MET D 484 TYR D 489 1 O TYR D 489 N LEU A 458 SHEET 4 AA1 7 GLY D 448 HIS D 452 -1 N VAL D 451 O MET D 484 SHEET 5 AA1 7 THR D 455 ALA D 460 -1 O THR D 455 N HIS D 452 SHEET 6 AA1 7 MET A 484 TYR A 489 1 N TYR A 489 O LEU D 458 SHEET 7 AA1 7 GLY A 448 HIS A 452 -1 N VAL A 451 O MET A 484 SHEET 1 AA2 4 CYS B 21 VAL B 26 0 SHEET 2 AA2 4 ASP B 29 MET B 38 -1 O GLN B 34 N GLY B 24 SHEET 3 AA2 4 VAL B 49 HIS B 55 -1 O PHE B 50 N ILE B 37 SHEET 4 AA2 4 LYS B 66 PHE B 69 -1 O ALA B 68 N THR B 53 SHEET 1 AA3 5 THR C 12 VAL C 17 0 SHEET 2 AA3 5 MET C 1 LYS C 6 -1 N MET C 1 O VAL C 17 SHEET 3 AA3 5 THR C 66 LEU C 71 1 O LEU C 67 N PHE C 4 SHEET 4 AA3 5 GLN C 41 PHE C 45 -1 N ARG C 42 O VAL C 70 SHEET 5 AA3 5 LYS C 48 GLN C 49 -1 O LYS C 48 N PHE C 45 SHEET 1 AA4 4 CYS E 21 VAL E 26 0 SHEET 2 AA4 4 ASP E 29 MET E 38 -1 O HIS E 32 N VAL E 26 SHEET 3 AA4 4 VAL E 49 HIS E 55 -1 O PHE E 50 N ILE E 37 SHEET 4 AA4 4 LYS E 66 PHE E 69 -1 O LYS E 66 N HIS E 55 SHEET 1 AA5 5 THR F 12 VAL F 17 0 SHEET 2 AA5 5 MET F 1 LYS F 6 -1 N MET F 1 O VAL F 17 SHEET 3 AA5 5 THR F 66 LEU F 71 1 O LEU F 67 N PHE F 4 SHEET 4 AA5 5 GLN F 41 PHE F 45 -1 N ARG F 42 O VAL F 70 SHEET 5 AA5 5 LYS F 48 GLN F 49 -1 O LYS F 48 N PHE F 45 LINK SG CYS A 438 ZN ZN A 501 1555 1555 2.38 LINK SG CYS A 441 ZN ZN A 501 1555 1555 2.34 LINK NE2 HIS A 452 ZN ZN A 502 1555 1555 2.07 LINK ND1 HIS A 457 ZN ZN A 502 1555 1555 2.03 LINK SG CYS A 461 ZN ZN A 501 1555 1555 2.29 LINK SG CYS A 464 ZN ZN A 501 1555 1555 2.36 LINK SG CYS A 475 ZN ZN A 502 1555 1555 2.29 LINK SG CYS A 478 ZN ZN A 502 1555 1555 2.32 LINK SG CYS D 438 ZN ZN D 501 1555 1555 2.34 LINK SG CYS D 441 ZN ZN D 501 1555 1555 2.33 LINK NE2 HIS D 452 ZN ZN D 502 1555 1555 2.08 LINK ND1 HIS D 457 ZN ZN D 502 1555 1555 2.03 LINK SG CYS D 461 ZN ZN D 501 1555 1555 2.32 LINK SG CYS D 464 ZN ZN D 501 1555 1555 2.28 LINK SG CYS D 475 ZN ZN D 502 1555 1555 2.31 LINK SG CYS D 478 ZN ZN D 502 1555 1555 2.34 CISPEP 1 TYR B 60 PRO B 61 0 4.05 CISPEP 2 TYR E 60 PRO E 61 0 4.23 SITE 1 AC1 4 CYS A 438 CYS A 441 CYS A 461 CYS A 464 SITE 1 AC2 4 HIS A 452 HIS A 457 CYS A 475 CYS A 478 SITE 1 AC3 1 ILE A 485 SITE 1 AC4 4 HOH A 622 ALA B 2 LEU B 3 LYS B 4 SITE 1 AC5 2 ARG B 136 GLU B 140 SITE 1 AC6 4 CYS D 438 CYS D 441 CYS D 461 CYS D 464 SITE 1 AC7 4 HIS D 452 HIS D 457 CYS D 475 CYS D 478 SITE 1 AC8 1 ILE D 485 SITE 1 AC9 4 ALA E 2 LEU E 3 LYS E 4 HOH E 422 SITE 1 AD1 5 LYS E 85 ARG E 90 LYS E 133 ARG E 136 SITE 2 AD1 5 HOH E 322 CRYST1 129.709 129.709 70.537 90.00 90.00 120.00 P 61 12 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 0.007710 0.004451 0.000000 0.00000 SCALE2 0.000000 0.008902 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014177 0.00000