HEADER LIGASE 28-FEB-25 9QAL TITLE SOLUTION NMR STRUCTURE OF ARKADIA 2 RING DOMAIN CAVEAT 9QAL LYS A 1 HAS WRONG CHIRALITY AT ATOM CA LYS A 3 HAS WRONG CAVEAT 2 9QAL CHIRALITY AT ATOM CA ASP A 5 HAS WRONG CHIRALITY AT ATOM CA CAVEAT 3 9QAL SER A 10 HAS WRONG CHIRALITY AT ATOM CA COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE ARK2C; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RING FINGER PROTEIN 165,RNF165; COMPND 5 EC: 2.3.2.27; COMPND 6 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: ARK2C, RNF165; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-47-1 KEYWDS ARKADIA 2, ARKADIA, RNF165, E3 UB LIGASE, RING DOMAIN, E2 ENZYME, KEYWDS 2 TGF-B PATHWAY, UBCH5B, LIGASE EXPDTA SOLUTION NMR NUMMDL 31 AUTHOR K.D.MAROUSIS,D.GIANNARI,A.SELIAMI,M.POLITI,M.BIRKOU,D.BENTROP, AUTHOR 2 V.EPISKOPOU,G.A.SPYROULIAS REVDAT 1 11-MAR-26 9QAL 0 JRNL AUTH K.D.MAROUSIS,M.D.POLITI,D.GIANNARI,A.SELIAMI,M.BIRKOU, JRNL AUTH 2 D.BENTROP,V.EPISKOPOU,G.A.SPYROULIAS JRNL TITL MECHANISTIC INSIGHTS INTO THE AUTO-UBIQUITINIATION OF JRNL TITL 2 ARKADIA 2C RING DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 5.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9QAL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1292145549. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-99% 15N] ARKADIA 2 E3 REMARK 210 UB LIGASE, RING DOMAIN, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 2 MM DSS, REMARK 210 90% H2O/10% D2O; 0.7 MM [U-99% REMARK 210 13C; U-99% 15N] ARKADIA 2 E3 UB REMARK 210 LIGASE, RING DOMAIN, 50 MM REMARK 210 POTASSIUM PHOSPHATE, 2 MM DSS, REMARK 210 90% H2O/10% D2O; 0.7 MM ARKADIA REMARK 210 2 E3 UB LIGASE, RING DOMAIN, 50 REMARK 210 MM POTASSIUM PHOSPHATE, 2 MM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC ALIPHATIC; 2D 1H REMARK 210 -13C HSQC AROMATIC; 2D 1H-15N REMARK 210 HSQC; 2D 1H-15N TROSY HSQC; 2D REMARK 210 1H-1H NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; 3D REMARK 210 HCCH-TOCSY; 3D HNCA; 3D HN(CO)CA; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HNHA; 1D 1H REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.8.4, XEASY, DYANA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 31 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 31 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 LYS A 3 108.29 92.99 REMARK 500 1 LYS A 4 128.70 100.38 REMARK 500 1 ASP A 5 -174.31 106.83 REMARK 500 1 GLU A 6 -170.77 31.16 REMARK 500 1 GLU A 9 60.31 -24.20 REMARK 500 1 ASP A 11 83.30 -151.62 REMARK 500 1 THR A 12 73.11 -60.47 REMARK 500 1 ASP A 13 78.35 -152.91 REMARK 500 1 GLU A 14 -34.69 178.51 REMARK 500 1 LYS A 15 18.82 52.64 REMARK 500 1 CYS A 16 74.69 44.03 REMARK 500 1 LEU A 20 52.81 35.89 REMARK 500 1 SER A 21 -103.38 -131.22 REMARK 500 1 ASP A 25 36.44 -152.90 REMARK 500 1 GLU A 27 -68.68 -126.80 REMARK 500 1 ASP A 28 135.47 -177.47 REMARK 500 1 ARG A 31 31.10 -144.12 REMARK 500 1 LEU A 32 -159.23 46.70 REMARK 500 1 MET A 35 -30.84 148.39 REMARK 500 1 LYS A 51 40.83 -143.26 REMARK 500 1 LYS A 52 114.39 -160.68 REMARK 500 1 CYS A 53 115.10 -37.69 REMARK 500 1 ARG A 57 -6.62 61.72 REMARK 500 1 ILE A 60 -97.87 37.69 REMARK 500 1 GLU A 61 -64.41 160.56 REMARK 500 1 THR A 62 22.65 -141.78 REMARK 500 1 GLN A 63 -83.84 50.46 REMARK 500 2 LYS A 3 -70.75 -140.57 REMARK 500 2 GLU A 14 -30.92 -168.79 REMARK 500 2 LYS A 15 -0.56 69.13 REMARK 500 2 CYS A 16 77.65 57.14 REMARK 500 2 LEU A 20 32.63 91.08 REMARK 500 2 MET A 22 100.58 43.14 REMARK 500 2 ASP A 25 30.94 -159.07 REMARK 500 2 GLU A 27 -64.89 -105.74 REMARK 500 2 ASP A 28 136.17 178.91 REMARK 500 2 ARG A 31 29.23 -147.21 REMARK 500 2 LEU A 32 -161.19 48.10 REMARK 500 2 MET A 35 -36.29 151.94 REMARK 500 2 SER A 50 89.54 -154.64 REMARK 500 2 LYS A 52 118.27 -165.83 REMARK 500 2 ILE A 60 -99.63 37.70 REMARK 500 2 GLU A 61 -52.13 169.84 REMARK 500 2 GLN A 63 -81.34 63.24 REMARK 500 3 LYS A 4 -8.16 68.69 REMARK 500 3 ASP A 5 -100.81 -127.93 REMARK 500 3 GLU A 6 28.03 -140.09 REMARK 500 3 SER A 10 158.15 76.72 REMARK 500 3 ASP A 13 32.81 -141.63 REMARK 500 3 GLU A 14 -30.56 -141.63 REMARK 500 REMARK 500 THIS ENTRY HAS 651 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 1 GLY A 2 1 99.07 REMARK 500 GLY A 2 LYS A 3 1 126.18 REMARK 500 LYS A 3 LYS A 4 1 103.54 REMARK 500 ASP A 5 GLU A 6 1 50.25 REMARK 500 GLU A 8 GLU A 9 1 -115.46 REMARK 500 LYS A 1 GLY A 2 10 -148.29 REMARK 500 ASP A 67 SER A 68 24 144.25 REMARK 500 LYS A 1 GLY A 2 31 -145.48 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 1 HIS A 39 0.11 SIDE CHAIN REMARK 500 10 ARG A 31 0.11 SIDE CHAIN REMARK 500 31 ARG A 30 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 A 101 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 16 SG REMARK 620 2 CYS A 19 SG 78.6 REMARK 620 3 HIS A 39 ND1 105.6 122.7 REMARK 620 4 CYS A 42 SG 112.8 122.5 108.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 102 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 34 SG REMARK 620 2 HIS A 36 ND1 113.6 REMARK 620 3 CYS A 53 SG 110.2 118.1 REMARK 620 4 CYS A 56 SG 107.4 95.0 111.1 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34984 RELATED DB: BMRB REMARK 900 SOLUTION NMR STRUCURE OF ARKADIA 2 RING DOMAIN DBREF 9QAL A 1 68 UNP Q6ZSG1 ARK2C_HUMAN 279 346 SEQRES 1 A 68 LYS GLY LYS LYS ASP GLU GLY GLU GLU SER ASP THR ASP SEQRES 2 A 68 GLU LYS CYS THR ILE CYS LEU SER MET LEU GLU ASP GLY SEQRES 3 A 68 GLU ASP VAL ARG ARG LEU PRO CYS MET HIS LEU PHE HIS SEQRES 4 A 68 GLN LEU CYS VAL ASP GLN TRP LEU ALA MET SER LYS LYS SEQRES 5 A 68 CYS PRO ILE CYS ARG VAL ASP ILE GLU THR GLN LEU GLY SEQRES 6 A 68 ALA ASP SER HET ZN A 101 1 HET ZN A 102 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 GLN A 40 SER A 50 1 11 SHEET 1 AA1 2 VAL A 29 ARG A 30 0 SHEET 2 AA1 2 PHE A 38 HIS A 39 -1 O PHE A 38 N ARG A 30 LINK SG CYS A 16 ZN ZN A 101 1555 1555 2.13 LINK SG CYS A 19 ZN ZN A 101 1555 1555 2.13 LINK SG CYS A 34 ZN ZN A 102 1555 1555 2.10 LINK ND1 HIS A 36 ZN ZN A 102 1555 1555 2.15 LINK ND1 HIS A 39 ZN ZN A 101 1555 1555 2.11 LINK SG CYS A 42 ZN ZN A 101 1555 1555 2.02 LINK SG CYS A 53 ZN ZN A 102 1555 1555 2.18 LINK SG CYS A 56 ZN ZN A 102 1555 1555 2.12 CISPEP 1 LYS A 4 ASP A 5 1 -16.98 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MODEL 21 ENDMDL MODEL 22 ENDMDL MODEL 23 ENDMDL MODEL 24 ENDMDL MODEL 25 ENDMDL MODEL 26 ENDMDL MODEL 27 ENDMDL MODEL 28 ENDMDL MODEL 29 ENDMDL MODEL 30 ENDMDL MODEL 31 ENDMDL CONECT 231 1050 CONECT 274 1050 CONECT 508 1051 CONECT 536 1051 CONECT 592 1050 CONECT 644 1050 CONECT 824 1051 CONECT 867 1051 CONECT 1050 231 274 592 644 CONECT 1051 508 536 824 867 MASTER 217 0 2 1 2 0 0 6 535 1 10 6 END