PDB Short entry for 1FXT HEADER LIGASE 26-SEP-00 1FXT TITLE STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN-CONJUGATING ENZYME E2-24 KDA; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.2.19; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: UBIQUITIN; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET3A; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PET3A-HUB KEYWDS MODEL OF THE INTERACTION BETWEEN YEAST UBC1 AND UBIQUITIN AFTER THE KEYWDS 2 FORMATION OF A COVALENT THIOLESTER, LIGASE EXPDTA SOLUTION NMR AUTHOR K.S.HAMILTON,G.S.SHAW,R.S.WILLIAMS,J.T.HUZIL,S.MCKENNA,C.PTAK, AUTHOR 2 M.GLOVER,M.J.ELLISON REVDAT 3 23-FEB-22 1FXT 1 REMARK REVDAT 2 24-FEB-09 1FXT 1 VERSN REVDAT 1 10-OCT-01 1FXT 0 JRNL AUTH K.S.HAMILTON,M.J.ELLISON,K.R.BARBER,R.S.WILLIAMS,J.T.HUZIL, JRNL AUTH 2 S.MCKENNA,C.PTAK,M.GLOVER,G.S.SHAW JRNL TITL STRUCTURE OF A CONJUGATING ENZYME-UBIQUITIN THIOLESTER JRNL TITL 2 INTERMEDIATE REVEALS A NOVEL ROLE FOR THE UBIQUITIN TAIL. JRNL REF STRUCTURE V. 9 897 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11591345 JRNL DOI 10.1016/S0969-2126(01)00657-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRDRAW 1 REMARK 3 AUTHORS : DELAGIO AND GARRETT REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000011993. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 30 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 450MM NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : YEAST UBC1; HUMAN UB REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : ENHANCED 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP 1, STAPP 1 REMARK 210 METHOD USED : DYNAMIC DOCKING BETWEEN UBC1 AND REMARK 210 UB SYSTEM COVALENTLY BOUND AND REMARK 210 MINIMIZED REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SPECTRA OF THIOLESTER FORMATION WERE REMARK 210 ACQUIRED EVERY 10 MINUTES DURING REMARK 210 THE FIRST 60 MINUTES OF REACTION REMARK 210 TIME UNTIL A STABLE LEVEL OF COVALENT REMARK 210 COMPLEX WAS FORMED 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: 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 SER A 81 OD1 ASP A 123 1.54 REMARK 500 HG1 THR A 23 OE1 GLU A 25 1.56 REMARK 500 HG SER A 28 OD2 ASP A 31 1.58 REMARK 500 SG CYS A 88 C GLY B 76 1.79 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 HIS A 21 CG HIS A 21 CD2 0.057 REMARK 500 HIS A 34 CG HIS A 34 CD2 0.055 REMARK 500 SER A 150 C SER A 150 OXT 0.136 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 ARG A 3 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 6 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 HIS A 21 ND1 - CE1 - NE2 ANGL. DEV. = 8.5 DEGREES REMARK 500 HIS A 33 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 HIS A 34 ND1 - CE1 - NE2 ANGL. DEV. = 8.4 DEGREES REMARK 500 HIS A 77 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 HIS A 129 ND1 - CE1 - NE2 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 132 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 134 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 146 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 42 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG B 54 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG B 54 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 HIS B 68 ND1 - CE1 - NE2 ANGL. DEV. = 8.6 DEGREES REMARK 500 ARG B 72 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 74 NE - CZ - NH1 ANGL. DEV. = 4.7 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 LYS A 5 43.61 -84.34 REMARK 500 ARG A 6 -66.92 -142.92 REMARK 500 LEU A 24 79.90 -100.34 REMARK 500 SER A 28 -93.39 -81.13 REMARK 500 GLU A 29 -73.45 -136.82 REMARK 500 ASP A 31 -142.47 -83.89 REMARK 500 HIS A 33 -57.65 -159.20 REMARK 500 THR A 45 149.24 -173.93 REMARK 500 PRO A 46 -10.46 -47.08 REMARK 500 ASN A 94 -63.22 -120.30 REMARK 500 ASN A 119 -59.09 -126.73 REMARK 500 GLN A 122 -89.52 -105.77 REMARK 500 ARG A 134 42.86 -141.90 REMARK 500 GLU A 135 -60.57 -140.85 REMARK 500 LEU A 147 -65.02 -90.82 REMARK 500 LEU B 8 57.85 -96.01 REMARK 500 THR B 9 -33.65 -137.46 REMARK 500 PRO B 19 -18.35 -49.53 REMARK 500 ASP B 32 -85.48 -51.79 REMARK 500 ALA B 46 86.72 51.41 REMARK 500 LEU B 73 -136.12 -90.00 REMARK 500 ARG B 74 60.01 -152.70 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 TYR A 62 PRO A 63 33.01 REMARK 500 ASP A 133 ARG A 134 149.47 REMARK 500 VAL B 17 GLU B 18 147.08 REMARK 500 ILE B 23 GLU B 24 144.49 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 TYR A 47 0.08 SIDE CHAIN REMARK 500 ARG B 42 0.08 SIDE CHAIN REMARK 500 ARG B 72 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1FXT A 2 150 UNP P21734 UBC1_YEAST 2 150 DBREF 1FXT B 1 76 UNP P62988 UBIQ_HUMAN 1 76 SEQRES 1 A 149 SER ARG ALA LYS ARG ILE MET LYS GLU ILE GLN ALA VAL SEQRES 2 A 149 LYS ASP ASP PRO ALA ALA HIS ILE THR LEU GLU PHE VAL SEQRES 3 A 149 SER GLU SER ASP ILE HIS HIS LEU LYS GLY THR PHE LEU SEQRES 4 A 149 GLY PRO PRO GLY THR PRO TYR GLU GLY GLY LYS PHE VAL SEQRES 5 A 149 VAL ASP ILE GLU VAL PRO MET GLU TYR PRO PHE LYS PRO SEQRES 6 A 149 PRO LYS MET GLN PHE ASP THR LYS VAL TYR HIS PRO ASN SEQRES 7 A 149 ILE SER SER VAL THR GLY ALA ILE CYS LEU ASP ILE LEU SEQRES 8 A 149 LYS ASN ALA TRP SER PRO VAL ILE THR LEU LYS SER ALA SEQRES 9 A 149 LEU ILE SER LEU GLN ALA LEU LEU GLN SER PRO GLU PRO SEQRES 10 A 149 ASN ASP PRO GLN ASP ALA GLU VAL ALA GLN HIS TYR LEU SEQRES 11 A 149 ARG ASP ARG GLU SER PHE ASN LYS THR ALA ALA LEU TRP SEQRES 12 A 149 THR ARG LEU TYR ALA SER SEQRES 1 B 76 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 76 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 76 LYS ALA LYS ILE GLN ASP LYS GLU GLY ILE PRO PRO ASP SEQRES 4 B 76 GLN GLN ARG LEU ILE PHE ALA GLY LYS GLN LEU GLU ASP SEQRES 5 B 76 GLY ARG THR LEU SER ASP TYR ASN ILE GLN LYS GLU SER SEQRES 6 B 76 THR LEU HIS LEU VAL LEU ARG LEU ARG GLY GLY HELIX 1 1 ARG A 3 ASP A 17 1 15 HELIX 2 2 PRO A 18 HIS A 21 5 4 HELIX 3 3 LEU A 89 ASN A 94 1 6 HELIX 4 4 THR A 101 SER A 115 1 15 HELIX 5 5 ASP A 123 ASP A 133 1 11 HELIX 6 6 GLU A 135 ALA A 149 1 15 HELIX 7 7 THR B 22 GLU B 34 1 13 HELIX 8 8 LEU B 56 ASN B 60 5 5 SHEET 1 A 4 THR A 23 PHE A 26 0 SHEET 2 A 4 HIS A 34 LEU A 40 -1 N LYS A 36 O GLU A 25 SHEET 3 A 4 LYS A 51 GLU A 57 -1 N PHE A 52 O PHE A 39 SHEET 4 A 4 LYS A 68 PHE A 71 -1 N LYS A 68 O GLU A 57 SHEET 1 B 4 ILE B 13 GLU B 16 0 SHEET 2 B 4 GLN B 2 LYS B 6 -1 O ILE B 3 N LEU B 15 SHEET 3 B 4 THR B 66 LEU B 71 1 O LEU B 67 N LYS B 6 SHEET 4 B 4 GLN B 41 ILE B 44 -1 O ARG B 42 N VAL B 70 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