PDB Short entry for 2C6B HEADER LIGASE 08-NOV-05 2C6B TITLE SOLUTION STRUCTURE OF THE C4 ZINC-FINGER DOMAIN OF HDM2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-PROTEIN LIGASE E3 MDM2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HUMAN MDM2, P53-BINDING PROTEIN MDM2, ONCOPROTEIN MDM2, COMPND 5 DOUBLE MINUTE 2 PROTEIN, HDM2; COMPND 6 EC: 6.3.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: MODIFIED PRSETA KEYWDS ZINC FINGER, HUMAN MDM2, LIGASE, PHOSPHORYLATION, ALTERNATIVE KEYWDS 2 SPLICING, METAL-BINDING, NUCLEAR PROTEIN, PROTO- ONCOGENE, UBL KEYWDS 3 CONJUGATION PATHWAY, ZINC EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR G.W.YU,M.D.ALLEN,A.ANDREEVA,A.R.FERSHT,M.BYCROFT REVDAT 4 24-JAN-18 2C6B 1 SOURCE REVDAT 3 24-FEB-09 2C6B 1 VERSN REVDAT 2 01-FEB-06 2C6B 1 JRNL REVDAT 1 04-JAN-06 2C6B 0 JRNL AUTH G.W.YU,M.D.ALLEN,A.ANDREEVA,A.R.FERSHT,M.BYCROFT JRNL TITL SOLUTION STRUCTURE OF THE C4 ZINC FINGER DOMAIN OF HDM2. JRNL REF PROTEIN SCI. V. 15 384 2006 JRNL REFN ISSN 0961-8368 JRNL PMID 16385008 JRNL DOI 10.1110/PS.051927306 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. 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,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 2C6B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-NOV-05. REMARK 100 THE DEPOSITION ID IS D_1290026298. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG, AZARA, CNS REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS > 0.25A REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NONE REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 400 REMARK 400 COMPOUND REMARK 400 UBIQUITIN-PROTEIN LIGASE E3 MDM2 FUNCTIONS BY INHIBITING REMARK 400 P53- AND P73-MEDIATED CELL CYCLE ARREST AND APOPTOSIS REMARK 400 BY BINDING ITS TRANSCRIPTIONAL ACTIVATION DOMAIN. 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 1 GLU A 293 103.91 58.75 REMARK 500 1 GLU A 296 -72.16 -61.72 REMARK 500 1 TYR A 302 174.05 -50.92 REMARK 500 1 ASN A 309 63.99 62.67 REMARK 500 1 SER A 317 48.99 -81.50 REMARK 500 1 ARG A 321 -66.47 -98.28 REMARK 500 1 TRP A 323 70.09 67.00 REMARK 500 1 ARG A 326 173.33 -56.78 REMARK 500 2 PHE A 291 -78.54 -104.02 REMARK 500 2 GLU A 293 77.38 -157.38 REMARK 500 2 ASN A 309 62.28 60.62 REMARK 500 2 SER A 317 45.19 -91.11 REMARK 500 2 ARG A 321 -78.55 -88.12 REMARK 500 2 TRP A 323 62.47 62.22 REMARK 500 2 LEU A 325 140.11 63.79 REMARK 500 2 TRP A 329 -93.79 -139.97 REMARK 500 2 ASP A 333 62.08 -115.81 REMARK 500 3 GLU A 296 -82.45 60.68 REMARK 500 3 SER A 317 48.47 -90.30 REMARK 500 3 ARG A 321 -62.40 -99.01 REMARK 500 3 TRP A 323 61.19 61.67 REMARK 500 3 LEU A 325 137.89 63.65 REMARK 500 3 TRP A 329 -46.42 -145.69 REMARK 500 4 GLU A 293 -169.87 -59.26 REMARK 500 4 ASP A 294 -54.03 -174.41 REMARK 500 4 ILE A 297 154.31 60.25 REMARK 500 4 SER A 317 38.75 -93.54 REMARK 500 4 LEU A 325 144.90 66.39 REMARK 500 5 ASP A 294 57.57 -142.23 REMARK 500 5 ILE A 297 152.06 61.55 REMARK 500 5 TYR A 302 160.98 -49.84 REMARK 500 5 SER A 317 49.43 -86.31 REMARK 500 5 ARG A 321 -64.57 -93.81 REMARK 500 5 LEU A 325 139.94 67.44 REMARK 500 5 PRO A 331 -176.92 -55.41 REMARK 500 5 ASP A 333 91.93 -59.18 REMARK 500 5 LYS A 334 36.04 -147.88 REMARK 500 6 GLU A 292 169.95 58.37 REMARK 500 6 ILE A 297 153.84 60.37 REMARK 500 6 SER A 317 46.77 -80.65 REMARK 500 6 TRP A 323 64.85 74.48 REMARK 500 6 ARG A 326 168.76 -46.58 REMARK 500 7 ILE A 297 152.96 60.85 REMARK 500 7 TYR A 302 168.51 -48.47 REMARK 500 7 SER A 317 48.76 -80.38 REMARK 500 7 ARG A 321 -74.21 -92.15 REMARK 500 7 TRP A 323 73.51 66.99 REMARK 500 8 GLU A 292 42.13 -97.11 REMARK 500 8 ILE A 297 152.76 60.70 REMARK 500 8 TYR A 302 171.04 -51.69 REMARK 500 REMARK 500 THIS ENTRY HAS 148 RAMACHANDRAN OUTLIERS. 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 A 336 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 305 SG REMARK 620 2 CYS A 322 SG 98.3 REMARK 620 3 CYS A 308 SG 106.8 118.0 REMARK 620 4 CYS A 319 SG 116.7 116.8 100.8 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 336 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1RV1 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN MDM2 WITH AN IMIDAZOLINEINHIBITOR REMARK 900 RELATED ID: 1T4E RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH A BENZODIAZEPINEINHIBITOR REMARK 900 RELATED ID: 1T4F RELATED DB: PDB REMARK 900 STRUCTURE OF HUMAN MDM2 IN COMPLEX WITH AN OPTIMIZED P53PEPTIDE REMARK 900 RELATED ID: 1YCR RELATED DB: PDB REMARK 900 MDM2 BOUND TO THE TRANSACTIVATION DOMAIN OF P53 REMARK 900 RELATED ID: 1Z1M RELATED DB: PDB REMARK 900 NMR STRUCTURE OF UNLIGANDED MDM2 REMARK 900 RELATED ID: 2C6A RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE C4 ZINC-FINGER DOMAIN OF HDM2 DBREF 2C6B A 290 335 UNP Q00987 MDM2_HUMAN 290 335 SEQRES 1 A 46 SER PHE GLU GLU ASP PRO GLU ILE SER LEU ALA ASP TYR SEQRES 2 A 46 TRP LYS CYS THR SER CYS ASN GLU MET ASN PRO PRO LEU SEQRES 3 A 46 PRO SER HIS CYS ASN ARG CYS TRP ALA LEU ARG GLU ASN SEQRES 4 A 46 TRP LEU PRO GLU ASP LYS GLY HET ZN A 336 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ SHEET 1 AA 2 TRP A 303 LYS A 304 0 SHEET 2 AA 2 MET A 311 ASN A 312 -1 O ASN A 312 N TRP A 303 LINK ZN ZN A 336 SG CYS A 305 1555 1555 2.35 LINK ZN ZN A 336 SG CYS A 322 1555 1555 2.35 LINK ZN ZN A 336 SG CYS A 308 1555 1555 2.29 LINK ZN ZN A 336 SG CYS A 319 1555 1555 2.29 CISPEP 1 LEU A 315 PRO A 316 1 0.07 CISPEP 2 LEU A 315 PRO A 316 2 0.12 CISPEP 3 LEU A 315 PRO A 316 3 0.13 CISPEP 4 LEU A 315 PRO A 316 4 0.03 CISPEP 5 LEU A 315 PRO A 316 5 -0.03 CISPEP 6 LEU A 315 PRO A 316 6 -0.06 CISPEP 7 LEU A 315 PRO A 316 7 0.10 CISPEP 8 LEU A 315 PRO A 316 8 0.15 CISPEP 9 LEU A 315 PRO A 316 9 0.23 CISPEP 10 LEU A 315 PRO A 316 10 0.08 CISPEP 11 LEU A 315 PRO A 316 11 0.14 CISPEP 12 LEU A 315 PRO A 316 12 0.07 CISPEP 13 LEU A 315 PRO A 316 13 0.16 CISPEP 14 LEU A 315 PRO A 316 14 0.01 CISPEP 15 LEU A 315 PRO A 316 15 0.08 CISPEP 16 LEU A 315 PRO A 316 16 -0.07 CISPEP 17 LEU A 315 PRO A 316 17 -0.12 CISPEP 18 LEU A 315 PRO A 316 18 0.08 CISPEP 19 LEU A 315 PRO A 316 19 0.15 CISPEP 20 LEU A 315 PRO A 316 20 0.05 SITE 1 AC1 4 CYS A 305 CYS A 308 CYS A 319 CYS A 322 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000