PDB Short entry for 1JAS HEADER LIGASE 31-MAY-01 1JAS TITLE HSUBC2B COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-17 KDA; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.2.19; COMPND 5 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 UBIQUITIN CONJUGATION, UBIQUITIN CONJUGATING ENZYME, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.MIURA,W.KLAUS,A.ROSS,P.GUENTERT,H.SENN REVDAT 3 23-FEB-22 1JAS 1 REMARK REVDAT 2 24-FEB-09 1JAS 1 VERSN REVDAT 1 09-SEP-03 1JAS 0 JRNL AUTH T.MIURA,W.KLAUS,A.ROSS,P.GUENTERT,H.SENN JRNL TITL THE NMR STRUCTURE OF THE CLASS I HUMAN UBIQUITIN-CONJUGATING JRNL TITL 2 ENZYME 2B JRNL REF J.BIOMOL.NMR V. 22 89 2002 JRNL REFN ISSN 0925-2738 JRNL PMID 11885984 JRNL DOI 10.1023/A:1013807519703 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, DYANA 1.65 REMARK 3 AUTHORS : VARIOUS (XWINNMR), P. GUENTERT ET AL (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CANDID: AUTOMATED NOE CROSS REMARK 3 PEAK ASSIGNMENT REMARK 4 REMARK 4 1JAS COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000013564. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.7 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : UL-13C, UL-15N; 75 MM AMMONIUM REMARK 210 ACETATE (DEUT.), 100 MM AMMONIUM REMARK 210 SULPHATE, PH 6.7; UL-13C, 75 MM REMARK 210 AMMONIUM ACETATE (DEUT.), 100 MM REMARK 210 AMMONIUM SULPHATE, PH 6.7 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; 3D_13C- REMARK 210 SEPARATED_NOESY; 4D_13C- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 1.7, DYANA 1.65 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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: 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 OD1 ASP A 101 HG SER A 103 1.54 REMARK 500 REMARK 500 REMARK: NULL 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 6 VAL A 56 CG1 - CB - CG2 ANGL. DEV. = -9.6 DEGREES REMARK 500 6 ARG A 135 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 9 TYR A 63 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 11 TYR A 63 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 14 TYR A 63 CB - CG - CD2 ANGL. DEV. = 3.8 DEGREES REMARK 500 14 TYR A 63 CB - CG - CD1 ANGL. DEV. = -5.9 DEGREES REMARK 500 19 ARG A 7 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 20 ARG A 11 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 20 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.1 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 SER A 29 170.59 -55.36 REMARK 500 1 GLN A 93 -145.30 -122.55 REMARK 500 1 GLU A 132 -90.09 -81.79 REMARK 500 1 ASN A 133 68.33 -101.60 REMARK 500 2 SER A 2 -68.81 -152.63 REMARK 500 2 GLU A 62 39.37 -74.13 REMARK 500 2 GLN A 93 -103.04 -123.68 REMARK 500 2 THR A 99 -40.07 -145.85 REMARK 500 2 GLU A 132 -89.94 -82.58 REMARK 500 2 ASN A 133 68.84 -107.22 REMARK 500 3 PRO A 79 1.38 -68.76 REMARK 500 3 GLN A 93 -148.98 -103.09 REMARK 500 3 PRO A 98 38.85 -71.71 REMARK 500 3 PRO A 121 48.27 -89.55 REMARK 500 3 GLU A 132 -74.04 -77.23 REMARK 500 3 ASN A 133 72.65 -111.38 REMARK 500 4 GLN A 93 -154.80 -96.13 REMARK 500 4 THR A 99 -27.09 -143.33 REMARK 500 4 GLU A 132 -89.27 -96.53 REMARK 500 5 SER A 2 29.85 -151.87 REMARK 500 5 GLU A 62 31.72 -80.77 REMARK 500 5 GLN A 93 -156.09 -111.78 REMARK 500 5 GLU A 132 -72.66 -78.39 REMARK 500 5 ASN A 133 68.94 -111.28 REMARK 500 6 GLN A 93 -120.23 -114.32 REMARK 500 6 THR A 99 -34.29 -136.94 REMARK 500 6 GLU A 132 -83.72 -96.49 REMARK 500 6 ASN A 133 77.03 -110.05 REMARK 500 7 GLU A 62 62.10 -106.70 REMARK 500 7 PRO A 64 22.48 -78.35 REMARK 500 7 GLN A 93 -106.85 -117.97 REMARK 500 7 PRO A 98 78.56 -69.94 REMARK 500 7 THR A 99 -45.89 -152.30 REMARK 500 7 GLU A 132 -73.57 -71.01 REMARK 500 7 ASN A 133 68.02 -109.76 REMARK 500 8 GLN A 93 -137.37 -107.02 REMARK 500 8 GLU A 132 -84.80 -88.48 REMARK 500 9 GLN A 93 -143.55 -113.17 REMARK 500 9 THR A 99 -30.86 -138.08 REMARK 500 9 GLU A 132 -79.61 -77.53 REMARK 500 9 ASN A 133 68.78 -110.55 REMARK 500 9 TRP A 149 23.13 -73.88 REMARK 500 10 GLN A 93 -146.93 -102.59 REMARK 500 10 GLU A 132 -96.46 -82.84 REMARK 500 11 GLN A 93 -150.54 -114.95 REMARK 500 11 THR A 99 -59.92 -128.39 REMARK 500 11 GLU A 132 -77.31 -81.63 REMARK 500 11 ASN A 133 78.40 -109.62 REMARK 500 12 GLN A 93 -137.85 -109.21 REMARK 500 12 THR A 99 -44.25 -139.06 REMARK 500 REMARK 500 THIS ENTRY HAS 86 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 ILE A 87 CYS A 88 6 149.52 REMARK 500 PRO A 68 THR A 69 17 146.79 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 ARG A 8 0.09 SIDE CHAIN REMARK 500 1 TYR A 63 0.07 SIDE CHAIN REMARK 500 1 ARG A 140 0.08 SIDE CHAIN REMARK 500 2 ARG A 7 0.09 SIDE CHAIN REMARK 500 3 ARG A 71 0.10 SIDE CHAIN REMARK 500 5 ARG A 6 0.09 SIDE CHAIN REMARK 500 5 ARG A 71 0.11 SIDE CHAIN REMARK 500 6 TYR A 130 0.07 SIDE CHAIN REMARK 500 7 TYR A 100 0.08 SIDE CHAIN REMARK 500 7 ARG A 140 0.08 SIDE CHAIN REMARK 500 8 ARG A 135 0.11 SIDE CHAIN REMARK 500 9 ARG A 6 0.09 SIDE CHAIN REMARK 500 9 ARG A 8 0.08 SIDE CHAIN REMARK 500 11 ARG A 140 0.09 SIDE CHAIN REMARK 500 12 ARG A 71 0.09 SIDE CHAIN REMARK 500 12 ARG A 135 0.09 SIDE CHAIN REMARK 500 15 ARG A 15 0.08 SIDE CHAIN REMARK 500 15 TYR A 63 0.08 SIDE CHAIN REMARK 500 15 TYR A 82 0.07 SIDE CHAIN REMARK 500 16 ARG A 11 0.09 SIDE CHAIN REMARK 500 16 TYR A 137 0.08 SIDE CHAIN REMARK 500 17 ARG A 140 0.12 SIDE CHAIN REMARK 500 18 TYR A 82 0.07 SIDE CHAIN REMARK 500 18 ARG A 140 0.08 SIDE CHAIN REMARK 500 19 ARG A 7 0.08 SIDE CHAIN REMARK 500 20 TYR A 130 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1JAS A 1 152 UNP P63146 UBE2B_HUMAN 1 152 SEQRES 1 A 152 MET SER THR PRO ALA ARG ARG ARG LEU MET ARG ASP PHE SEQRES 2 A 152 LYS ARG LEU GLN GLU ASP PRO PRO VAL GLY VAL SER GLY SEQRES 3 A 152 ALA PRO SER GLU ASN ASN ILE MET GLN TRP ASN ALA VAL SEQRES 4 A 152 ILE PHE GLY PRO GLU GLY THR PRO PHE GLU ASP GLY THR SEQRES 5 A 152 PHE LYS LEU VAL ILE GLU PHE SER GLU GLU TYR PRO ASN SEQRES 6 A 152 LYS PRO PRO THR VAL ARG PHE LEU SER LYS MET PHE HIS SEQRES 7 A 152 PRO ASN VAL TYR ALA ASP GLY SER ILE CYS LEU ASP ILE SEQRES 8 A 152 LEU GLN ASN ARG TRP SER PRO THR TYR ASP VAL SER SER SEQRES 9 A 152 ILE LEU THR SER ILE GLN SER LEU LEU ASP GLU PRO ASN SEQRES 10 A 152 PRO ASN SER PRO ALA ASN SER GLN ALA ALA GLN LEU TYR SEQRES 11 A 152 GLN GLU ASN LYS ARG GLU TYR GLU LYS ARG VAL SER ALA SEQRES 12 A 152 ILE VAL GLU GLN SER TRP ASN ASP SER HELIX 1 1 THR A 3 ASP A 19 1 17 HELIX 2 2 LEU A 89 GLN A 93 5 5 HELIX 3 3 ASP A 101 GLU A 115 1 15 HELIX 4 4 ASN A 123 GLU A 132 1 10 HELIX 5 5 ASN A 133 GLN A 147 1 15 HELIX 6 6 SER A 148 ASP A 151 5 4 SHEET 1 A 4 VAL A 24 PRO A 28 0 SHEET 2 A 4 GLN A 35 PHE A 41 -1 N ASN A 37 O ALA A 27 SHEET 3 A 4 THR A 52 GLU A 58 -1 N PHE A 53 O ILE A 40 SHEET 4 A 4 THR A 69 PHE A 72 -1 O THR A 69 N GLU A 58 CISPEP 1 TYR A 63 PRO A 64 1 -12.57 CISPEP 2 TYR A 63 PRO A 64 2 -14.18 CISPEP 3 TYR A 63 PRO A 64 3 2.62 CISPEP 4 TYR A 63 PRO A 64 4 -3.75 CISPEP 5 TYR A 63 PRO A 64 5 -11.75 CISPEP 6 TYR A 63 PRO A 64 6 -12.59 CISPEP 7 TYR A 63 PRO A 64 7 -7.17 CISPEP 8 TYR A 63 PRO A 64 8 0.06 CISPEP 9 TYR A 63 PRO A 64 9 1.87 CISPEP 10 TYR A 63 PRO A 64 10 -10.55 CISPEP 11 TYR A 63 PRO A 64 11 -6.39 CISPEP 12 TYR A 63 PRO A 64 12 1.32 CISPEP 13 TYR A 63 PRO A 64 13 -13.91 CISPEP 14 TYR A 63 PRO A 64 14 -3.61 CISPEP 15 TYR A 63 PRO A 64 15 -7.36 CISPEP 16 TYR A 63 PRO A 64 16 -5.47 CISPEP 17 TYR A 63 PRO A 64 17 -2.02 CISPEP 18 TYR A 63 PRO A 64 18 -4.55 CISPEP 19 TYR A 63 PRO A 64 19 1.16 CISPEP 20 TYR A 63 PRO A 64 20 -8.01 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