HEADER LIGASE 28-APR-21 7MLA TITLE SOLUTION NMR STRUCTURE OF HDMX IN COMPLEX WITH ZN AND MCO-52-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN MDM4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DOUBLE MINUTE 4 PROTEIN,MDM2-LIKE P53-BINDING PROTEIN, COMPND 5 PROTEIN MDMX,P53-BINDING PROTEIN MDM4; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: MCO-52-2; COMPND 9 CHAIN: B; COMPND 10 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: MDM4, MDMX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS E3 LIGASE, ZINC-BINDING PROTEIN, CYCLOTIDE, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.S.RAMIREZ,G.THEOPHALL,D.CHAUDHURI,J.C.CAMARERO,A.SHEKHTMAN REVDAT 1 04-MAY-22 7MLA 0 JRNL AUTH D.CHAUDHURI,L.S.RAMIREZ,G.THEOPHALL,A.SHEKHTMAN,J.C.CAMARERO JRNL TITL SOLUTION NMR STRUCTURE OF HDMX IN COMPLEX WITH ZN AND JRNL TITL 2 CYCLOTIDE 52-2 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA 20.4.24 REMARK 3 AUTHORS : KRIEGER ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7MLA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-APR-21. REMARK 100 THE DEPOSITION ID IS D_1000251200. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.100 MM [U-100% 13C; U-100% REMARK 210 15N] HDMX, 0.100 MM MCO-52-2, 90% REMARK 210 H2O/10% D2O; 0.100 MM HDMX, REMARK 210 0.100 MM [U-100% 13C; U-100% 15N] REMARK 210 MCO-52-2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCA; 2D 1H-13C HSQC; 2D 1H REMARK 210 -15N HSQC; 3D 1H-13C NOESY; 3D REMARK 210 1H-15N NOESY; 3D HCCH-TOCSY; 3D REMARK 210 HBHA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 HNCACB; 3D CBCA(CO)NH; 3D H(CCO) REMARK 210 NH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : ASCEND REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, CYANA 3.98.13, CARA REMARK 210 1.9.1.7 REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 421 REMARK 465 SER A 422 REMARK 465 HIS A 423 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 PRO A 436 -166.58 -71.57 REMARK 500 1 GLU A 441 21.53 46.97 REMARK 500 1 ILE A 489 79.27 -109.77 REMARK 500 1 ASN B 6 46.74 -105.15 REMARK 500 1 TYR B 8 58.53 -91.65 REMARK 500 2 TYR A 425 106.65 52.39 REMARK 500 2 PRO A 436 -178.01 -63.68 REMARK 500 2 GLU A 441 16.03 49.84 REMARK 500 2 LYS A 478 15.90 55.69 REMARK 500 2 ASN B 6 38.22 -83.08 REMARK 500 2 SER B 31 60.42 108.94 REMARK 500 3 PRO A 436 -176.83 -69.17 REMARK 500 3 GLU A 441 13.72 51.55 REMARK 500 3 ILE A 489 78.00 -110.05 REMARK 500 4 PRO A 436 -165.56 -65.41 REMARK 500 4 GLU A 441 6.89 50.22 REMARK 500 4 LYS A 478 19.57 53.60 REMARK 500 5 PRO A 436 -174.77 -69.38 REMARK 500 5 GLU A 441 7.57 50.63 REMARK 500 5 LYS A 478 18.99 54.76 REMARK 500 5 ILE A 489 78.87 -111.19 REMARK 500 6 CYS A 430 0.28 -67.71 REMARK 500 6 GLU A 441 6.88 51.00 REMARK 500 6 ILE A 489 79.16 -106.52 REMARK 500 6 SER B 31 70.62 55.32 REMARK 500 7 PRO A 436 -174.35 -64.75 REMARK 500 7 GLU A 441 18.15 47.32 REMARK 500 7 LYS A 478 16.31 53.67 REMARK 500 7 ILE A 489 78.90 -112.85 REMARK 500 8 PRO A 436 -175.71 -64.47 REMARK 500 8 GLU A 441 7.97 50.24 REMARK 500 8 LYS A 478 19.62 52.27 REMARK 500 8 ASN B 6 30.07 -79.14 REMARK 500 9 PRO A 436 -175.74 -63.46 REMARK 500 9 GLU A 441 6.95 50.53 REMARK 500 9 LYS A 478 17.44 52.96 REMARK 500 9 ILE A 489 72.68 -118.16 REMARK 500 9 PRO B 5 49.74 -81.10 REMARK 500 10 PRO A 436 -169.72 -72.40 REMARK 500 10 GLU A 441 7.05 51.44 REMARK 500 10 LYS A 478 16.96 54.58 REMARK 500 10 ASN B 6 35.16 -79.55 REMARK 500 10 HIS B 25 -8.36 -59.99 REMARK 500 11 PRO A 436 -165.62 -69.78 REMARK 500 11 GLU A 441 18.62 51.17 REMARK 500 11 ASP B 26 24.75 -77.08 REMARK 500 11 SER B 31 -83.65 -84.00 REMARK 500 12 PRO A 436 -175.14 -69.24 REMARK 500 12 GLU A 441 6.68 51.91 REMARK 500 12 LYS A 478 14.99 53.35 REMARK 500 REMARK 500 THIS ENTRY HAS 80 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 437 SG REMARK 620 2 CYS A 440 SG 107.7 REMARK 620 3 CYS A 460 SG 112.2 113.0 REMARK 620 4 CYS A 463 SG 113.6 105.9 104.4 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 451 NE2 REMARK 620 2 HIS A 456 ND1 109.4 REMARK 620 3 CYS A 474 SG 125.2 112.9 REMARK 620 4 CYS A 477 SG 99.3 105.7 101.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30899 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCTURE OF HDMX IN COMPLEX WITH ZN AND CYCLOTIDE 52-2 DBREF 7MLA A 428 490 UNP O15151 MDM4_HUMAN 428 490 DBREF 7MLA B 1 34 PDB 7MLA 7MLA 1 34 SEQADV 7MLA GLY A 421 UNP O15151 EXPRESSION TAG SEQADV 7MLA SER A 422 UNP O15151 EXPRESSION TAG SEQADV 7MLA HIS A 423 UNP O15151 EXPRESSION TAG SEQADV 7MLA MET A 424 UNP O15151 EXPRESSION TAG SEQADV 7MLA TYR A 425 UNP O15151 EXPRESSION TAG SEQADV 7MLA SER A 426 UNP O15151 EXPRESSION TAG SEQADV 7MLA GLY A 427 UNP O15151 EXPRESSION TAG SEQRES 1 A 70 GLY SER HIS MET TYR SER GLY GLU ASP CYS GLN ASN LEU SEQRES 2 A 70 LEU LYS PRO CYS SER LEU CYS GLU LYS ARG PRO ARG ASP SEQRES 3 A 70 GLY ASN ILE ILE HIS GLY ARG THR GLY HIS LEU VAL THR SEQRES 4 A 70 CYS PHE HIS CYS ALA ARG ARG LEU LYS LYS ALA GLY ALA SEQRES 5 A 70 SER CYS PRO ILE CYS LYS LYS GLU ILE GLN LEU VAL ILE SEQRES 6 A 70 LYS VAL PHE ILE ALA SEQRES 1 B 34 GLY GLY VAL CYS PRO ASN LEU TYR LEU LEU CYS ARG ARG SEQRES 2 B 34 ASP SER ASP CYS PRO GLY ALA CYS ILE CYS ARG HIS ASP SEQRES 3 B 34 SER TYR CYS GLY SER GLY SER ASP HET ZN A 501 1 HET ZN A 502 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) HELIX 1 AA1 GLY A 427 LEU A 433 5 7 HELIX 2 AA2 CYS A 460 ALA A 470 1 11 HELIX 3 AA3 ARG B 13 CYS B 17 5 5 SHEET 1 AA1 3 THR A 454 THR A 459 0 SHEET 2 AA1 3 GLY A 447 HIS A 451 -1 N HIS A 451 O THR A 454 SHEET 3 AA1 3 LEU A 483 LYS A 486 -1 O LEU A 483 N ILE A 450 SHEET 1 AA2 2 CYS B 23 ARG B 24 0 SHEET 2 AA2 2 TYR B 28 CYS B 29 -1 O TYR B 28 N ARG B 24 SSBOND 1 CYS B 4 CYS B 21 1555 1555 2.03 SSBOND 2 CYS B 11 CYS B 23 1555 1555 2.03 SSBOND 3 CYS B 17 CYS B 29 1555 1555 2.03 LINK N GLY B 1 C ASP B 34 1555 1555 1.33 LINK SG CYS A 437 ZN ZN A 501 1555 1555 2.26 LINK SG CYS A 440 ZN ZN A 501 1555 1555 2.23 LINK NE2 HIS A 451 ZN ZN A 502 1555 1555 2.09 LINK ND1 HIS A 456 ZN ZN A 502 1555 1555 2.10 LINK SG CYS A 460 ZN ZN A 501 1555 1555 2.26 LINK SG CYS A 463 ZN ZN A 501 1555 1555 2.23 LINK SG CYS A 474 ZN ZN A 502 1555 1555 2.41 LINK SG CYS A 477 ZN ZN A 502 1555 1555 2.47 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 MODEL 1