HEADER LIGASE 29-JUL-04 1W4U TITLE NMR SOLUTION STRUCTURE OF THE UBIQUITIN CONJUGATING ENZYME UBCH5B COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: UBCH5B, UBIQUITIN-PROTEIN LIGASE, UBIQUITIN CARRIER PROTEIN; COMPND 5 EC: 6.3.2.19; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS UBIQUITINATION, E2 ENZYME, LIGASE, BL CONJUGATION PATHWAY EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR K.HOUBEN,C.DOMINGUEZ,F.M.A.VAN SCHAIK,H.T.M.TIMMERS,A.M.J.J.BONVIN, AUTHOR 2 R.BOELENS REVDAT 3 19-APR-17 1W4U 1 REMARK ATOM REVDAT 2 24-FEB-09 1W4U 1 VERSN REVDAT 1 10-NOV-04 1W4U 0 JRNL AUTH K.HOUBEN,C.DOMINGUEZ,F.M.A.VAN SCHAIK,H.T.M.TIMMERS, JRNL AUTH 2 A.M.J.J.BONVIN,R.BOELENS JRNL TITL SOLUTION STRUCTURE OF THE UBIQUITIN-CONJUGATING ENZYME JRNL TITL 2 UBCH5B JRNL REF J.MOL.BIOL. V. 344 513 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15522302 JRNL DOI 10.1016/J.JMB.2004.09.054 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: NULL REMARK 4 REMARK 4 1W4U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-JUL-04. REMARK 100 THE PDBE ID CODE IS EBI-20615. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 20MM KPI, 150MM KCL, 0.01MM REMARK 210 ZNCL2, 10%D2O, UBCH5B 0.3MM REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 750 MHZ; 900 MHZ; 500 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS REMARK 210 METHOD USED : ARIA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY 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 CATALYZES THE COVALENT ATTACHMENT OF UBIQUITIN TO OTHER REMARK 400 PROTEINS REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HG CYS A 85 OD1 ASP A 117 1.56 REMARK 500 O ASP A 87 H SER A 91 1.56 REMARK 500 HG SER A 43 O LEU A 110 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 8 TYR A 45 CE1 TYR A 45 CZ 0.102 REMARK 500 8 TYR A 45 CZ TYR A 45 CE2 -0.107 REMARK 500 9 TYR A 74 CE1 TYR A 74 CZ -0.078 REMARK 500 9 TYR A 74 CZ TYR A 74 CE2 0.081 REMARK 500 9 TYR A 127 CE1 TYR A 127 CZ 0.079 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 PRO A 18 -80.16 -84.60 REMARK 500 1 GLN A 20 11.87 49.77 REMARK 500 1 CYS A 21 115.94 -162.19 REMARK 500 1 ASP A 28 -4.45 72.55 REMARK 500 1 PRO A 40 94.10 -24.22 REMARK 500 1 ASN A 41 -86.73 171.27 REMARK 500 1 ASP A 42 89.44 -152.47 REMARK 500 1 TYR A 45 40.51 -106.38 REMARK 500 1 THR A 58 68.63 24.46 REMARK 500 1 TYR A 60 142.33 -39.96 REMARK 500 1 HIS A 75 141.03 -179.99 REMARK 500 1 SER A 80 14.62 -62.05 REMARK 500 1 ILE A 88 -1.04 -58.76 REMARK 500 1 PRO A 95 22.76 -66.36 REMARK 500 1 PRO A 113 103.89 0.36 REMARK 500 1 PRO A 115 45.61 -101.71 REMARK 500 1 ASP A 116 -74.94 -119.95 REMARK 500 1 THR A 129 -63.62 -151.61 REMARK 500 1 ARG A 131 -29.60 -39.10 REMARK 500 1 ALA A 146 -97.68 -99.41 REMARK 500 2 PRO A 18 -70.33 -72.17 REMARK 500 2 GLN A 20 -30.04 57.74 REMARK 500 2 VAL A 26 -62.32 -105.49 REMARK 500 2 ASP A 28 -14.92 74.16 REMARK 500 2 ASN A 41 -78.97 60.03 REMARK 500 2 THR A 58 67.49 32.19 REMARK 500 2 PHE A 62 -86.06 -88.52 REMARK 500 2 LYS A 63 77.40 87.82 REMARK 500 2 HIS A 75 92.62 -53.97 REMARK 500 2 ASN A 81 -95.34 -82.41 REMARK 500 2 PRO A 95 67.19 -63.20 REMARK 500 2 ALA A 96 -19.83 -164.41 REMARK 500 2 PRO A 113 108.28 1.01 REMARK 500 2 ASP A 116 -73.55 -78.58 REMARK 500 2 THR A 129 -73.52 -152.56 REMARK 500 2 TYR A 145 -16.27 -145.22 REMARK 500 2 ALA A 146 -74.36 -125.94 REMARK 500 3 PRO A 18 -70.81 -85.42 REMARK 500 3 GLN A 20 1.36 52.51 REMARK 500 3 SER A 22 126.11 -171.45 REMARK 500 3 ASP A 28 -10.60 76.33 REMARK 500 3 ASN A 41 115.25 -37.41 REMARK 500 3 THR A 58 62.51 27.22 REMARK 500 3 HIS A 75 121.67 167.20 REMARK 500 3 SER A 80 -44.33 -28.53 REMARK 500 3 ASN A 81 -94.50 -82.58 REMARK 500 3 ILE A 88 -5.70 -57.36 REMARK 500 3 PRO A 95 79.55 -64.98 REMARK 500 3 ALA A 96 -36.72 -177.12 REMARK 500 3 CYS A 111 -71.71 -94.34 REMARK 500 REMARK 500 THIS ENTRY HAS 220 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 5 TYR A 134 0.09 SIDE CHAIN REMARK 500 9 TYR A 127 0.06 SIDE CHAIN REMARK 500 10 PHE A 50 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UR6 RELATED DB: PDB REMARK 900 NMR BASED STRUCTURAL MODEL OF THE UBCH5B- CNOT4 COMPLEX DBREF 1W4U A 1 147 UNP P51669 UB5B_HUMAN 1 147 SEQRES 1 A 147 MET ALA LEU LYS ARG ILE HIS LYS GLU LEU ASN ASP LEU SEQRES 2 A 147 ALA ARG ASP PRO PRO ALA GLN CYS SER ALA GLY PRO VAL SEQRES 3 A 147 GLY ASP ASP MET PHE HIS TRP GLN ALA THR ILE MET GLY SEQRES 4 A 147 PRO ASN ASP SER PRO TYR GLN GLY GLY VAL PHE PHE LEU SEQRES 5 A 147 THR ILE HIS PHE PRO THR ASP TYR PRO PHE LYS PRO PRO SEQRES 6 A 147 LYS VAL ALA PHE THR THR ARG ILE TYR HIS PRO ASN ILE SEQRES 7 A 147 ASN SER ASN GLY SER ILE CYS LEU ASP ILE LEU ARG SER SEQRES 8 A 147 GLN TRP SER PRO ALA LEU THR ILE SER LYS VAL LEU LEU SEQRES 9 A 147 SER ILE CYS SER LEU LEU CYS ASP PRO ASN PRO ASP ASP SEQRES 10 A 147 PRO LEU VAL PRO GLU ILE ALA ARG ILE TYR LYS THR ASP SEQRES 11 A 147 ARG GLU LYS TYR ASN ARG ILE ALA ARG GLU TRP THR GLN SEQRES 12 A 147 LYS TYR ALA MET HELIX 1 1 ALA A 2 LEU A 10 1 9 HELIX 2 2 ASN A 11 ASP A 16 1 6 HELIX 3 3 LEU A 86 SER A 91 1 6 HELIX 4 4 THR A 98 ASP A 112 1 15 HELIX 5 5 GLU A 122 THR A 129 1 8 HELIX 6 6 ASP A 130 TYR A 145 1 16 SHEET 1 AA 3 TRP A 33 MET A 38 0 SHEET 2 AA 3 VAL A 49 HIS A 55 -1 O PHE A 50 N ILE A 37 SHEET 3 AA 3 LYS A 66 PHE A 69 -1 O LYS A 66 N HIS A 55 CISPEP 1 TYR A 60 PRO A 61 1 0.43 CISPEP 2 TYR A 60 PRO A 61 2 0.46 CISPEP 3 TYR A 60 PRO A 61 3 0.24 CISPEP 4 TYR A 60 PRO A 61 4 0.50 CISPEP 5 TYR A 60 PRO A 61 5 -0.76 CISPEP 6 TYR A 60 PRO A 61 6 0.41 CISPEP 7 TYR A 60 PRO A 61 7 0.25 CISPEP 8 TYR A 60 PRO A 61 8 -0.30 CISPEP 9 TYR A 60 PRO A 61 9 0.49 CISPEP 10 TYR A 60 PRO A 61 10 0.61 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