HEADER LIGASE 03-JAN-22 7QPB TITLE CATALYTIC C-LOBE OF THE HECT-TYPE UBIQUITIN LIGASE E6AP IN COMPLEX TITLE 2 WITH A HYBRID FOLDAMER-PEPTIDE MACROCYCLE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ISOFORM I OF UBIQUITIN-PROTEIN LIGASE E3A; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: E6AP UBIQUITIN-PROTEIN LIGASE,HECT-TYPE UBIQUITIN COMPND 5 TRANSFERASE E3A,HUMAN PAPILLOMAVIRUS E6-ASSOCIATED PROTEIN,ONCOGENIC COMPND 6 PROTEIN-ASSOCIATED PROTEIN E6-AP,RENAL CARCINOMA ANTIGEN NY-REN-54; COMPND 7 EC: 2.3.2.26; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: HYBRID FOLDAMER-PEPTIDE MACROCYCLE; COMPND 11 CHAIN: H, I; COMPND 12 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: UBE3A, E6AP, EPVE6AP, HPVE6A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS HECT, E3 LIGASE CATALYTIC DOMAIN, UBIQUITIN PROTEIN LIGASE, KEYWDS 2 TRANSFERASE ACTIVITY, CATALYTIC ACTIVITY, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR S.DENGLER,R.T.HOWARD,V.MOROZOV,C.TSIAMANTAS,C.DOUAT,H.SUGA,I.HUC REVDAT 2 15-NOV-23 7QPB 1 JRNL LINK ATOM REVDAT 1 27-SEP-23 7QPB 0 JRNL AUTH S.DENGLER,R.T.HOWARD,V.MOROZOV,C.TSIAMANTAS,W.E.HUANG,Z.LIU, JRNL AUTH 2 C.DOBRZANSKI,V.POPHRISTIC,S.BRAMEYER,C.DOUAT,H.SUGA,I.HUC JRNL TITL DISPLAY SELECTION OF A HYBRID FOLDAMER-PEPTIDE MACROCYCLE. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 08408 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 37707879 JRNL DOI 10.1002/ANIE.202308408 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.17.1_3660: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 24488 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.5300 - 4.8700 0.96 2611 138 0.1863 0.2199 REMARK 3 2 4.8600 - 3.8600 0.98 2594 136 0.1856 0.2244 REMARK 3 3 3.8600 - 3.3800 0.99 2604 138 0.2037 0.2670 REMARK 3 4 3.3800 - 3.0700 0.98 2555 134 0.2351 0.2764 REMARK 3 5 3.0700 - 2.8500 0.99 2615 138 0.2511 0.3145 REMARK 3 6 2.8500 - 2.6800 0.99 2571 135 0.2693 0.3630 REMARK 3 7 2.6800 - 2.5500 0.99 2595 137 0.2739 0.3295 REMARK 3 8 2.5500 - 2.4400 0.99 2592 136 0.2759 0.3348 REMARK 3 9 2.4400 - 2.3420 0.97 2526 133 0.2814 0.3274 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.500 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.002 3786 REMARK 3 ANGLE : 0.620 5123 REMARK 3 CHIRALITY : 0.035 549 REMARK 3 PLANARITY : 0.003 645 REMARK 3 DIHEDRAL : 18.807 563 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7QPB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1292120007. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9724 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24491 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.342 REMARK 200 RESOLUTION RANGE LOW (A) : 29.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06614 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.9100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.34 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61110 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.910 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1C4Z REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 8000, 0.1 M SODIUM CACODYLATE, REMARK 280 0.1 M CALCIUM ACETATE PH 5.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 74.95500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.52500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 74.95500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.52500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11960 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, H 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 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -6.41534 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.99353 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, H 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -6.41534 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.99353 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, I 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 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -6.41534 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.99353 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, I 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -6.41534 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 66.99353 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 739 REMARK 465 PRO A 740 REMARK 465 LYS A 847 REMARK 465 GLY A 848 REMARK 465 PHE A 849 REMARK 465 GLY A 850 REMARK 465 MET A 851 REMARK 465 LEU A 852 REMARK 465 GLY B 739 REMARK 465 PRO B 740 REMARK 465 LYS B 847 REMARK 465 GLY B 848 REMARK 465 PHE B 849 REMARK 465 GLY B 850 REMARK 465 MET B 851 REMARK 465 LEU B 852 REMARK 465 GLY C 739 REMARK 465 PRO C 740 REMARK 465 LYS C 847 REMARK 465 GLY C 848 REMARK 465 PHE C 849 REMARK 465 GLY C 850 REMARK 465 MET C 851 REMARK 465 LEU C 852 REMARK 465 GLY D 739 REMARK 465 PRO D 740 REMARK 465 ASN D 741 REMARK 465 ALA D 846 REMARK 465 LYS D 847 REMARK 465 GLY D 848 REMARK 465 PHE D 849 REMARK 465 GLY D 850 REMARK 465 MET D 851 REMARK 465 LEU D 852 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 749 CG CD OE1 OE2 REMARK 470 ASN B 741 CG OD1 ND2 REMARK 470 ARG C 791 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 799 CE NZ REMARK 470 GLN D 745 CG CD OE1 NE2 REMARK 470 ARG D 759 NE CZ NH1 NH2 REMARK 470 LYS D 799 CG CD CE NZ REMARK 470 TYR D 845 CG CD1 CD2 CE1 CE2 CZ OH 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 9JC H 2 C ZY9 H 3 N 0.156 REMARK 500 9JV H 4 C GLY H 5 N 0.148 REMARK 500 GLY H 5 C PHE H 6 N 0.142 REMARK 500 PHE H 6 C TRP H 7 N 0.166 REMARK 500 TRP H 7 C ARG H 8 N 0.149 REMARK 500 ARG H 8 NE ARG H 8 CZ 0.144 REMARK 500 ARG H 8 C TYR H 9 N 0.171 REMARK 500 TYR H 9 C VAL H 10 N 0.160 REMARK 500 TYR H 11 C GLN H 12 N 0.156 REMARK 500 GLN H 12 C LYS H 13 N 0.155 REMARK 500 LYS H 13 C CCS H 14 N 0.150 REMARK 500 9JC I 2 C ZY9 I 3 N 0.154 REMARK 500 9JV I 4 C GLY I 5 N 0.146 REMARK 500 GLY I 5 C PHE I 6 N 0.141 REMARK 500 PHE I 6 C TRP I 7 N 0.166 REMARK 500 TRP I 7 C ARG I 8 N 0.147 REMARK 500 ARG I 8 NE ARG I 8 CZ 0.143 REMARK 500 ARG I 8 C TYR I 9 N 0.168 REMARK 500 TYR I 9 C VAL I 10 N 0.158 REMARK 500 TYR I 11 C GLN I 12 N 0.155 REMARK 500 GLN I 12 C LYS I 13 N 0.154 REMARK 500 LYS I 13 C CCS I 14 N 0.151 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 9JC H 2 C - N - CA ANGL. DEV. = 47.6 DEGREES REMARK 500 ZY9 H 3 C - N - CA ANGL. DEV. = 44.1 DEGREES REMARK 500 9JV H 4 C - N - CA ANGL. DEV. = 42.4 DEGREES REMARK 500 9JC I 2 C - N - CA ANGL. DEV. = 48.8 DEGREES REMARK 500 ZY9 I 3 C - N - CA ANGL. DEV. = 43.2 DEGREES REMARK 500 9JV I 4 C - N - CA ANGL. DEV. = 45.4 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 LEU B 742 65.78 -109.55 REMARK 500 ASP B 743 85.92 -65.73 REMARK 500 PRO C 809 -160.16 -79.12 REMARK 500 9JC H 2 24.85 -9.58 REMARK 500 9JV H 4 12.71 -36.56 REMARK 500 9JC I 2 25.87 8.01 REMARK 500 9JV I 4 8.62 -17.99 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 ZY9 H 3 9JV H 4 47.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 7QPB A 741 852 UNP Q05086 UBE3A_HUMAN 741 852 DBREF 7QPB B 741 852 UNP Q05086 UBE3A_HUMAN 741 852 DBREF 7QPB C 741 852 UNP Q05086 UBE3A_HUMAN 741 852 DBREF 7QPB D 741 852 UNP Q05086 UBE3A_HUMAN 741 852 DBREF 7QPB H 1 15 PDB 7QPB 7QPB 1 15 DBREF 7QPB I 1 15 PDB 7QPB 7QPB 1 15 SEQADV 7QPB GLY A 739 UNP Q05086 EXPRESSION TAG SEQADV 7QPB PRO A 740 UNP Q05086 EXPRESSION TAG SEQADV 7QPB GLY B 739 UNP Q05086 EXPRESSION TAG SEQADV 7QPB PRO B 740 UNP Q05086 EXPRESSION TAG SEQADV 7QPB GLY C 739 UNP Q05086 EXPRESSION TAG SEQADV 7QPB PRO C 740 UNP Q05086 EXPRESSION TAG SEQADV 7QPB GLY D 739 UNP Q05086 EXPRESSION TAG SEQADV 7QPB PRO D 740 UNP Q05086 EXPRESSION TAG SEQRES 1 A 114 GLY PRO ASN LEU ASP PHE GLN ALA LEU GLU GLU THR THR SEQRES 2 A 114 GLU TYR ASP GLY GLY TYR THR ARG ASP SER VAL LEU ILE SEQRES 3 A 114 ARG GLU PHE TRP GLU ILE VAL HIS SER PHE THR ASP GLU SEQRES 4 A 114 GLN LYS ARG LEU PHE LEU GLN PHE THR THR GLY THR ASP SEQRES 5 A 114 ARG ALA PRO VAL GLY GLY LEU GLY LYS LEU LYS MET ILE SEQRES 6 A 114 ILE ALA LYS ASN GLY PRO ASP THR GLU ARG LEU PRO THR SEQRES 7 A 114 SER HIS THR CYS PHE ASN VAL LEU LEU LEU PRO GLU TYR SEQRES 8 A 114 SER SER LYS GLU LYS LEU LYS GLU ARG LEU LEU LYS ALA SEQRES 9 A 114 ILE THR TYR ALA LYS GLY PHE GLY MET LEU SEQRES 1 B 114 GLY PRO ASN LEU ASP PHE GLN ALA LEU GLU GLU THR THR SEQRES 2 B 114 GLU TYR ASP GLY GLY TYR THR ARG ASP SER VAL LEU ILE SEQRES 3 B 114 ARG GLU PHE TRP GLU ILE VAL HIS SER PHE THR ASP GLU SEQRES 4 B 114 GLN LYS ARG LEU PHE LEU GLN PHE THR THR GLY THR ASP SEQRES 5 B 114 ARG ALA PRO VAL GLY GLY LEU GLY LYS LEU LYS MET ILE SEQRES 6 B 114 ILE ALA LYS ASN GLY PRO ASP THR GLU ARG LEU PRO THR SEQRES 7 B 114 SER HIS THR CYS PHE ASN VAL LEU LEU LEU PRO GLU TYR SEQRES 8 B 114 SER SER LYS GLU LYS LEU LYS GLU ARG LEU LEU LYS ALA SEQRES 9 B 114 ILE THR TYR ALA LYS GLY PHE GLY MET LEU SEQRES 1 C 114 GLY PRO ASN LEU ASP PHE GLN ALA LEU GLU GLU THR THR SEQRES 2 C 114 GLU TYR ASP GLY GLY TYR THR ARG ASP SER VAL LEU ILE SEQRES 3 C 114 ARG GLU PHE TRP GLU ILE VAL HIS SER PHE THR ASP GLU SEQRES 4 C 114 GLN LYS ARG LEU PHE LEU GLN PHE THR THR GLY THR ASP SEQRES 5 C 114 ARG ALA PRO VAL GLY GLY LEU GLY LYS LEU LYS MET ILE SEQRES 6 C 114 ILE ALA LYS ASN GLY PRO ASP THR GLU ARG LEU PRO THR SEQRES 7 C 114 SER HIS THR CYS PHE ASN VAL LEU LEU LEU PRO GLU TYR SEQRES 8 C 114 SER SER LYS GLU LYS LEU LYS GLU ARG LEU LEU LYS ALA SEQRES 9 C 114 ILE THR TYR ALA LYS GLY PHE GLY MET LEU SEQRES 1 D 114 GLY PRO ASN LEU ASP PHE GLN ALA LEU GLU GLU THR THR SEQRES 2 D 114 GLU TYR ASP GLY GLY TYR THR ARG ASP SER VAL LEU ILE SEQRES 3 D 114 ARG GLU PHE TRP GLU ILE VAL HIS SER PHE THR ASP GLU SEQRES 4 D 114 GLN LYS ARG LEU PHE LEU GLN PHE THR THR GLY THR ASP SEQRES 5 D 114 ARG ALA PRO VAL GLY GLY LEU GLY LYS LEU LYS MET ILE SEQRES 6 D 114 ILE ALA LYS ASN GLY PRO ASP THR GLU ARG LEU PRO THR SEQRES 7 D 114 SER HIS THR CYS PHE ASN VAL LEU LEU LEU PRO GLU TYR SEQRES 8 D 114 SER SER LYS GLU LYS LEU LYS GLU ARG LEU LEU LYS ALA SEQRES 9 D 114 ILE THR TYR ALA LYS GLY PHE GLY MET LEU SEQRES 1 H 15 ZY9 9JC ZY9 9JV GLY PHE TRP ARG TYR VAL TYR GLN LYS SEQRES 2 H 15 CCS GM1 SEQRES 1 I 15 ZY9 9JC ZY9 9JV GLY PHE TRP ARG TYR VAL TYR GLN LYS SEQRES 2 I 15 CCS GM1 HET ZY9 H 1 10 HET 9JC H 2 15 HET ZY9 H 3 10 HET 9JV H 4 15 HET CCS H 14 9 HET GM1 H 15 5 HET ZY9 I 1 10 HET 9JC I 2 15 HET ZY9 I 3 10 HET 9JV I 4 15 HET CCS I 14 9 HET GM1 I 15 5 HETNAM ZY9 6-(AMINOMETHYL)PYRIDINE-2-CARBOXYLIC ACID HETNAM 9JC 4-(AMINOMETHYL)-8-AZANYL-QUINOLINE-2-CARBALDEHYDE HETNAM 9JV 8-AZANYL-4-METHOXY-QUINOLINE-2-CARBOXYLIC ACID HETNAM CCS CARBOXYMETHYLATED CYSTEINE HETNAM GM1 AMINOMETHYLAMIDE HETSYN GM1 GLYCINAMID FORMUL 5 ZY9 4(C7 H8 N2 O2) FORMUL 5 9JC 2(C11 H11 N3 O) FORMUL 5 9JV 2(C11 H10 N2 O3) FORMUL 5 CCS 2(C5 H9 N O4 S) FORMUL 5 GM1 2(C2 H6 N2 O) FORMUL 7 HOH *57(H2 O) HELIX 1 AA1 ASP A 743 THR A 751 1 9 HELIX 2 AA2 SER A 761 SER A 773 1 13 HELIX 3 AA3 THR A 775 GLY A 788 1 14 HELIX 4 AA4 GLY A 796 LYS A 801 5 6 HELIX 5 AA5 SER A 831 TYR A 845 1 15 HELIX 6 AA6 ASP B 743 THR B 751 1 9 HELIX 7 AA7 SER B 761 SER B 773 1 13 HELIX 8 AA8 THR B 775 GLY B 788 1 14 HELIX 9 AA9 GLY B 796 LYS B 801 5 6 HELIX 10 AB1 THR B 819 PHE B 821 5 3 HELIX 11 AB2 SER B 831 ALA B 846 1 16 HELIX 12 AB3 ASP C 743 THR C 751 1 9 HELIX 13 AB4 SER C 761 SER C 773 1 13 HELIX 14 AB5 THR C 775 GLY C 788 1 14 HELIX 15 AB6 GLY C 796 LYS C 801 5 6 HELIX 16 AB7 THR C 819 PHE C 821 5 3 HELIX 17 AB8 SER C 831 THR C 844 1 14 HELIX 18 AB9 ASP D 743 THR D 750 1 8 HELIX 19 AC1 SER D 761 SER D 773 1 13 HELIX 20 AC2 THR D 775 THR D 787 1 13 HELIX 21 AC3 GLY D 796 LYS D 801 5 6 HELIX 22 AC4 THR D 819 PHE D 821 5 3 HELIX 23 AC5 SER D 831 THR D 844 1 14 HELIX 24 AC6 TRP H 7 CCS H 14 1 8 HELIX 25 AC7 TRP I 7 CCS I 14 1 8 SHEET 1 AA1 4 GLU A 752 ASP A 754 0 SHEET 2 AA1 4 ILE A 803 LYS A 806 1 O ILE A 804 N GLU A 752 SHEET 3 AA1 4 VAL A 823 LEU A 826 1 O LEU A 824 N ILE A 803 SHEET 4 AA1 4 THR A 816 HIS A 818 -1 N THR A 816 O LEU A 825 SHEET 1 AA2 4 GLU B 752 ASP B 754 0 SHEET 2 AA2 4 ILE B 803 LYS B 806 1 O ILE B 804 N GLU B 752 SHEET 3 AA2 4 VAL B 823 LEU B 826 1 O LEU B 824 N ILE B 803 SHEET 4 AA2 4 THR B 816 HIS B 818 -1 N HIS B 818 O VAL B 823 SHEET 1 AA3 4 GLU C 752 ASP C 754 0 SHEET 2 AA3 4 ILE C 803 ALA C 805 1 O ILE C 804 N GLU C 752 SHEET 3 AA3 4 VAL C 823 LEU C 825 1 O LEU C 824 N ALA C 805 SHEET 4 AA3 4 THR C 816 HIS C 818 -1 N HIS C 818 O VAL C 823 SHEET 1 AA4 4 GLU D 752 ASP D 754 0 SHEET 2 AA4 4 ILE D 803 ALA D 805 1 O ILE D 804 N GLU D 752 SHEET 3 AA4 4 VAL D 823 LEU D 825 1 O LEU D 824 N ILE D 803 SHEET 4 AA4 4 THR D 816 HIS D 818 -1 N HIS D 818 O VAL D 823 SSBOND 1 CYS A 820 CYS C 820 1555 2556 2.06 SSBOND 2 CYS B 820 CYS D 820 1555 2556 2.13 LINK C ZY9 H 1 N 9JC H 2 1555 1555 1.47 LINK N ZY9 H 1 CE CCS H 14 1555 1555 1.47 LINK C 9JC H 2 N ZY9 H 3 1555 1555 1.49 LINK C ZY9 H 3 N 9JV H 4 1555 1555 1.46 LINK C 9JV H 4 N GLY H 5 1555 1555 1.48 LINK C LYS H 13 N CCS H 14 1555 1555 1.49 LINK C CCS H 14 N2 GM1 H 15 1555 1555 1.46 LINK C ZY9 I 1 N 9JC I 2 1555 1555 1.47 LINK N ZY9 I 1 CE CCS I 14 1555 1555 1.47 LINK C 9JC I 2 N ZY9 I 3 1555 1555 1.49 LINK C ZY9 I 3 N 9JV I 4 1555 1555 1.46 LINK C 9JV I 4 N GLY I 5 1555 1555 1.48 LINK C LYS I 13 N CCS I 14 1555 1555 1.49 LINK C CCS I 14 N2 GM1 I 15 1555 1555 1.46 CRYST1 149.910 59.050 67.300 90.00 95.47 90.00 C 1 2 1 16 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 0.006671 0.000000 0.000638 0.00000 SCALE2 0.000000 0.016935 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014927 0.00000