PDB Short entry for 2HDP HEADER LIGASE 20-JUN-06 2HDP TITLE SOLUTION STRUCTURE OF HDM2 RING FINGER DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-PROTEIN LIGASE E3 MDM2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RING FINGER DOMAIN; COMPND 5 SYNONYM: P53-BINDING PROTEIN MDM2; 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 GENE: MDM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)(DNAY); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS RING FINGER DOMAIN, HOMODIMER, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.KOSTIC,T.MATT,M.YAMOUT-MARTINEZ,H.J.DYSON,P.E.WRIGHT REVDAT 3 09-MAR-22 2HDP 1 REMARK LINK REVDAT 2 24-FEB-09 2HDP 1 VERSN REVDAT 1 21-NOV-06 2HDP 0 JRNL AUTH M.KOSTIC,T.MATT,M.A.MARTINEZ-YAMOUT,H.J.DYSON,P.E.WRIGHT JRNL TITL SOLUTION STRUCTURE OF THE HDM2 C2H2C4 RING, A DOMAIN JRNL TITL 2 CRITICAL FOR UBIQUITINATION OF P53. JRNL REF J.MOL.BIOL. V. 363 433 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16965791 JRNL DOI 10.1016/J.JMB.2006.08.027 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.1, AMBER 8 REMARK 3 AUTHORS : GUENTERT, P. (CYANA), CASE, D. A. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS BASED ON A TOTAL OF REMARK 3 1150 RESTRAINTS, INCLUDING 48 INTERMOLECULAR AND 112 DIHEDRAL REMARK 3 ANGLE. REMARK 4 REMARK 4 2HDP COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1000038232. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.1 REMARK 210 IONIC STRENGTH : 0.15 M NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1 MM HDM2 RING DOMAIN, U-15N, REMARK 210 20 MM TRIS, PH 7.1, 0.15M NACL, REMARK 210 0.25M ARG, 0.5 MM TCEP, 5 UM REMARK 210 ZNSO4, 90% H2O, 10% D2O; 0.1 MM REMARK 210 HDM2 RING DOMAIN, U-15N,13C, 20 REMARK 210 MM TRIS, PH 7.1, 0.15M NACL, 0.5 REMARK 210 MM TCEP, 5 UM ZNSO4, 90% H2O, 10% REMARK 210 D2O; 0.1 MM HDM2 RING DOMAIN, REMARK 210 UNLABLED REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_1H15N_NOESY-HSQC; REMARK 210 3D_1H15N_TOCSY-HSQC; HNCA; 13C- REMARK 210 HSQC; 2D NOESY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1, NMRVIEW 5 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 5 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 11 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 13 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 18 ARG A 471 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG B 444 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 20 ARG A 444 NE - CZ - NH1 ANGL. DEV. = 3.3 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 1 ASN A 433 29.71 -63.59 REMARK 500 1 GLU A 436 70.43 50.76 REMARK 500 1 PRO A 437 -169.79 -76.63 REMARK 500 1 ILE A 440 -49.61 -131.11 REMARK 500 1 GLN A 442 -9.21 -160.29 REMARK 500 1 PRO A 445 -8.05 -54.48 REMARK 500 1 MET A 459 54.27 90.72 REMARK 500 1 CYS A 475 129.52 -31.14 REMARK 500 1 VAL A 477 -59.59 -126.09 REMARK 500 1 LEU A 487 99.95 -69.94 REMARK 500 1 ASN B 433 -10.61 57.12 REMARK 500 1 ALA B 434 49.02 -73.74 REMARK 500 1 CYS B 438 178.06 -54.59 REMARK 500 1 GLN B 442 13.50 57.87 REMARK 500 1 LYS B 446 32.03 -65.47 REMARK 500 1 MET B 459 30.72 78.48 REMARK 500 1 CYS B 475 128.36 -30.72 REMARK 500 1 VAL B 477 -58.49 -127.68 REMARK 500 2 ILE A 435 -53.94 -129.92 REMARK 500 2 GLU A 436 -53.38 113.86 REMARK 500 2 PRO A 437 -82.20 -55.25 REMARK 500 2 ILE A 440 -46.34 -133.26 REMARK 500 2 GLN A 442 -14.04 -153.89 REMARK 500 2 MET A 459 56.89 75.46 REMARK 500 2 VAL A 477 -59.21 -131.46 REMARK 500 2 LEU B 430 -53.32 -144.75 REMARK 500 2 CYS B 438 -174.52 -63.02 REMARK 500 2 MET B 459 67.37 64.65 REMARK 500 2 CYS B 475 125.33 -22.45 REMARK 500 2 LEU B 487 99.82 -66.91 REMARK 500 3 LEU A 430 -59.88 -129.96 REMARK 500 3 ALA A 434 12.93 56.96 REMARK 500 3 GLU A 436 64.20 38.29 REMARK 500 3 ILE A 440 -47.33 -132.12 REMARK 500 3 GLN A 442 -12.02 -155.44 REMARK 500 3 MET A 459 66.35 85.54 REMARK 500 3 PRO A 474 -85.57 -71.80 REMARK 500 3 VAL A 477 -72.30 -116.36 REMARK 500 3 ILE B 440 -48.37 -134.69 REMARK 500 3 MET B 459 53.87 94.65 REMARK 500 3 ASN B 472 8.13 59.80 REMARK 500 3 PRO B 474 -81.80 -69.33 REMARK 500 3 VAL B 477 -75.90 -119.68 REMARK 500 3 LEU B 487 99.93 -69.61 REMARK 500 4 ILE A 435 75.50 -101.91 REMARK 500 4 CYS A 438 -167.91 -57.33 REMARK 500 4 ILE A 440 -60.10 -93.30 REMARK 500 4 LYS A 446 28.14 -67.60 REMARK 500 4 PRO A 474 -76.45 -68.00 REMARK 500 4 VAL A 477 -71.99 -113.44 REMARK 500 REMARK 500 THIS ENTRY HAS 284 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 18 ARG B 444 0.08 SIDE CHAIN REMARK 500 19 ARG B 444 0.08 SIDE CHAIN 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 B 492 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 438 SG REMARK 620 2 CYS A 441 SG 111.1 REMARK 620 3 CYS A 461 SG 113.6 110.9 REMARK 620 4 CYS A 464 SG 105.8 109.9 105.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 493 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 452 NE2 REMARK 620 2 HIS A 457 ND1 113.5 REMARK 620 3 CYS A 475 SG 112.0 102.1 REMARK 620 4 CYS A 478 SG 107.4 111.9 109.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 492 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 438 SG REMARK 620 2 CYS B 441 SG 114.1 REMARK 620 3 CYS B 461 SG 109.8 106.7 REMARK 620 4 CYS B 464 SG 105.8 109.0 111.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 493 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 452 NE2 REMARK 620 2 HIS B 457 ND1 113.8 REMARK 620 3 CYS B 475 SG 111.9 102.4 REMARK 620 4 CYS B 478 SG 108.4 110.8 109.4 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 B 492 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 493 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 492 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 493 DBREF 2HDP A 429 491 UNP Q00987 MDM2_HUMAN 429 491 DBREF 2HDP B 429 491 UNP Q00987 MDM2_HUMAN 429 491 SEQRES 1 A 63 SER LEU PRO LEU ASN ALA ILE GLU PRO CYS VAL ILE CYS SEQRES 2 A 63 GLN GLY ARG PRO LYS ASN GLY CYS ILE VAL HIS GLY LYS SEQRES 3 A 63 THR GLY HIS LEU MET ALA CYS PHE THR CYS ALA LYS LYS SEQRES 4 A 63 LEU LYS LYS ARG ASN LYS PRO CYS PRO VAL CYS ARG GLN SEQRES 5 A 63 PRO ILE GLN MET ILE VAL LEU THR TYR PHE PRO SEQRES 1 B 63 SER LEU PRO LEU ASN ALA ILE GLU PRO CYS VAL ILE CYS SEQRES 2 B 63 GLN GLY ARG PRO LYS ASN GLY CYS ILE VAL HIS GLY LYS SEQRES 3 B 63 THR GLY HIS LEU MET ALA CYS PHE THR CYS ALA LYS LYS SEQRES 4 B 63 LEU LYS LYS ARG ASN LYS PRO CYS PRO VAL CYS ARG GLN SEQRES 5 B 63 PRO ILE GLN MET ILE VAL LEU THR TYR PHE PRO HET ZN A 493 1 HET ZN A 492 1 HET ZN B 492 1 HET ZN B 493 1 HETNAM ZN ZINC ION FORMUL 3 ZN 4(ZN 2+) HELIX 1 1 CYS A 461 ARG A 471 1 11 HELIX 2 2 CYS B 461 ARG B 471 1 11 SHEET 1 A 7 CYS A 449 HIS A 452 0 SHEET 2 A 7 THR A 455 HIS A 457 -1 O THR A 455 N HIS A 452 SHEET 3 A 7 MET B 484 TYR B 489 1 O LEU B 487 N GLY A 456 SHEET 4 A 7 CYS B 449 HIS B 452 -1 N VAL B 451 O MET B 484 SHEET 5 A 7 THR B 455 HIS B 457 -1 O THR B 455 N HIS B 452 SHEET 6 A 7 MET A 484 TYR A 489 1 N LEU A 487 O GLY B 456 SHEET 7 A 7 CYS A 449 HIS A 452 -1 N VAL A 451 O MET A 484 LINK SG CYS A 438 ZN ZN B 492 1555 1555 2.27 LINK SG CYS A 441 ZN ZN B 492 1555 1555 2.27 LINK NE2 HIS A 452 ZN ZN A 493 1555 1555 2.07 LINK ND1 HIS A 457 ZN ZN A 493 1555 1555 2.08 LINK SG CYS A 461 ZN ZN B 492 1555 1555 2.27 LINK SG CYS A 464 ZN ZN B 492 1555 1555 2.25 LINK SG CYS A 475 ZN ZN A 493 1555 1555 2.28 LINK SG CYS A 478 ZN ZN A 493 1555 1555 2.29 LINK ZN ZN A 492 SG CYS B 438 1555 1555 2.26 LINK ZN ZN A 492 SG CYS B 441 1555 1555 2.27 LINK ZN ZN A 492 SG CYS B 461 1555 1555 2.26 LINK ZN ZN A 492 SG CYS B 464 1555 1555 2.26 LINK NE2 HIS B 452 ZN ZN B 493 1555 1555 2.07 LINK ND1 HIS B 457 ZN ZN B 493 1555 1555 2.07 LINK SG CYS B 475 ZN ZN B 493 1555 1555 2.28 LINK SG CYS B 478 ZN ZN B 493 1555 1555 2.29 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 4 CYS B 438 CYS B 441 CYS B 461 CYS B 464 SITE 1 AC4 4 HIS B 452 HIS B 457 CYS B 475 CYS B 478 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