HEADER TRANSFERASE 11-JUN-23 8PD6 TITLE CRYSTAL STRUCTURE OF THE TRIM58 PRY-SPRY DOMAIN IN COMPLEX WITH TRIM- TITLE 2 473 COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE TRIM58; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN BIA2,RING-TYPE E3 UBIQUITIN TRANSFERASE TRIM58, COMPND 5 TRIPARTITE MOTIF-CONTAINING PROTEIN 58; COMPND 6 EC: 2.3.2.27; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: TRIM58; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS E3 LIGASE, TRIM58, PRY-SPRY, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.RENATUS,K.HOEGENAUER,M.SCHROEDER REVDAT 2 07-FEB-24 8PD6 1 JRNL REVDAT 1 31-JAN-24 8PD6 0 JRNL AUTH K.HOEGENAUER,S.AN,J.AXFORD,C.BENANDER,C.BERGSDORF,J.BOTSCH, JRNL AUTH 2 S.CHAU,C.FERNANDEZ,S.GLEIM,U.HASSIEPEN,J.HUNZIKER,E.JOLY, JRNL AUTH 3 A.KELLER,S.LOPEZ ROMERO,R.MAHER,A.S.MANGOLD,C.MICKANIN, JRNL AUTH 4 M.MIHALIC,P.NEUNER,A.W.PATTERSON,F.PERRUCCIO,S.ROGGO, JRNL AUTH 5 J.SCESA,M.SCHRODER,D.SHKOZA,B.THAI,A.VULPETTI,M.RENATUS, JRNL AUTH 6 J.S.REECE-HOYES JRNL TITL DISCOVERY OF LIGANDS FOR TRIM58, A NOVEL TISSUE-SELECTIVE E3 JRNL TITL 2 LIGASE. JRNL REF ACS MED.CHEM.LETT. V. 14 1631 2023 JRNL REFN ISSN 1948-5875 JRNL PMID 38116426 JRNL DOI 10.1021/ACSMEDCHEMLETT.3C00259 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 44022 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.141 REMARK 3 R VALUE (WORKING SET) : 0.139 REMARK 3 FREE R VALUE : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2323 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3176 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2070 REMARK 3 BIN FREE R VALUE SET COUNT : 186 REMARK 3 BIN FREE R VALUE : 0.2410 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1428 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.15000 REMARK 3 B22 (A**2) : -0.15000 REMARK 3 B33 (A**2) : 0.48000 REMARK 3 B12 (A**2) : -0.07000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.045 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.046 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.649 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.961 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1601 ; 0.015 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 1446 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2201 ; 1.913 ; 1.670 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3351 ; 1.492 ; 1.569 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 201 ; 7.253 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 78 ;29.023 ;21.923 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 242 ;11.489 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;19.187 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 197 ; 0.377 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1839 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 365 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 777 ; 2.634 ; 1.506 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 776 ; 2.512 ; 1.503 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 987 ; 2.855 ; 2.260 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 988 ; 2.882 ; 2.263 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 824 ; 3.143 ; 1.769 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 825 ; 3.142 ; 1.771 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1215 ; 3.996 ; 2.570 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 1775 ; 3.895 ;18.583 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 1750 ; 3.732 ;18.252 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3046 ; 3.721 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8PD6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131094. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46465 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 20.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 18.60 REMARK 200 R MERGE (I) : 0.11200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 18.60 REMARK 200 R MERGE FOR SHELL (I) : 0.95900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG 3550, 0.2 M MGCL2, 0.1 M REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.58767 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 135.17533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 101.38150 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 168.96917 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.79383 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 67.58767 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 135.17533 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 168.96917 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 101.38150 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 33.79383 REMARK 290 REMARK 290 REMARK: NULL 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 TOTAL BURIED SURFACE AREA: 460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 722 LIES ON A SPECIAL POSITION. 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 249 REMARK 465 PRO A 250 REMARK 465 VAL A 251 REMARK 465 ARG A 252 REMARK 465 GLY A 253 REMARK 465 VAL A 254 REMARK 465 LEU A 255 REMARK 465 SER A 256 REMARK 465 ARG A 257 REMARK 465 SER A 258 REMARK 465 LYS A 259 REMARK 465 ALA A 260 REMARK 465 VAL A 261 REMARK 465 THR A 262 REMARK 465 ARG A 263 REMARK 465 LEU A 264 REMARK 465 GLU A 265 REMARK 465 ALA A 266 REMARK 465 GLU A 267 REMARK 465 ASN A 268 REMARK 465 ILE A 269 REMARK 465 PRO A 270 REMARK 465 MET A 271 REMARK 465 GLU A 272 REMARK 465 LEU A 273 REMARK 465 LYS A 274 REMARK 465 THR A 275 REMARK 465 ALA A 276 REMARK 465 SER A 277 REMARK 465 PRO A 318 REMARK 465 TRP A 319 REMARK 465 ARG A 320 REMARK 465 THR A 462 REMARK 465 ILE A 463 REMARK 465 ALA A 464 REMARK 465 GLY A 465 REMARK 465 SER A 466 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 ASP A 321 CG OD1 OD2 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 THR A 331 -51.93 -133.72 REMARK 500 LEU A 395 48.13 -97.61 REMARK 500 ALA A 396 -178.92 -179.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 750 DISTANCE = 6.34 ANGSTROMS REMARK 525 HOH A 751 DISTANCE = 6.76 ANGSTROMS 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 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 354 OE2 REMARK 620 2 HOH A 602 O 89.0 REMARK 620 3 HOH A 639 O 90.2 87.6 REMARK 620 4 HOH A 686 O 87.1 175.4 89.9 REMARK 620 5 HOH A 724 O 178.5 92.0 88.8 91.8 REMARK 620 6 HOH A 732 O 91.9 91.6 177.7 91.1 89.1 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8PD4 RELATED DB: PDB DBREF 8PD6 A 251 466 UNP Q8NG06 TRI58_HUMAN 251 466 SEQADV 8PD6 GLY A 249 UNP Q8NG06 EXPRESSION TAG SEQADV 8PD6 PRO A 250 UNP Q8NG06 EXPRESSION TAG SEQADV 8PD6 SER A 277 UNP Q8NG06 CYS 277 ENGINEERED MUTATION SEQADV 8PD6 SER A 278 UNP Q8NG06 CYS 278 ENGINEERED MUTATION SEQRES 1 A 218 GLY PRO VAL ARG GLY VAL LEU SER ARG SER LYS ALA VAL SEQRES 2 A 218 THR ARG LEU GLU ALA GLU ASN ILE PRO MET GLU LEU LYS SEQRES 3 A 218 THR ALA SER SER ILE PRO GLY ARG ARG GLU LEU LEU ARG SEQRES 4 A 218 LYS PHE GLN VAL ASP VAL LYS LEU ASP PRO ALA THR ALA SEQRES 5 A 218 HIS PRO SER LEU LEU LEU THR ALA ASP LEU ARG SER VAL SEQRES 6 A 218 GLN ASP GLY GLU PRO TRP ARG ASP VAL PRO ASN ASN PRO SEQRES 7 A 218 GLU ARG PHE ASP THR TRP PRO CYS ILE LEU GLY LEU GLN SEQRES 8 A 218 SER PHE SER SER GLY ARG HIS TYR TRP GLU VAL LEU VAL SEQRES 9 A 218 GLY GLU GLY ALA GLU TRP GLY LEU GLY VAL CYS GLN ASP SEQRES 10 A 218 THR LEU PRO ARG LYS GLY GLU THR THR PRO SER PRO GLU SEQRES 11 A 218 ASN GLY VAL TRP ALA LEU TRP LEU LEU LYS GLY ASN GLU SEQRES 12 A 218 TYR MET VAL LEU ALA SER PRO SER VAL PRO LEU LEU GLN SEQRES 13 A 218 LEU GLU SER PRO ARG CYS ILE GLY ILE PHE LEU ASP TYR SEQRES 14 A 218 GLU ALA GLY GLU ILE SER PHE TYR ASN VAL THR ASP GLY SEQRES 15 A 218 SER TYR ILE TYR THR PHE ASN GLN LEU PHE SER GLY LEU SEQRES 16 A 218 LEU ARG PRO TYR PHE PHE ILE CYS ASP ALA THR PRO LEU SEQRES 17 A 218 ILE LEU PRO PRO THR THR ILE ALA GLY SER HET YCB A 501 31 HET MG A 502 1 HET MG A 503 1 HET CL A 504 1 HET EDO A 505 4 HETNAM YCB ~{N}2-[3-(DIMETHYLAMINO)PROPYL]-6-PHENYL-~{N}4- HETNAM 2 YCB (PIPERIDIN-4-YLMETHYL)QUINAZOLINE-2,4-DIAMINE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 YCB C25 H34 N6 FORMUL 3 MG 2(MG 2+) FORMUL 5 CL CL 1- FORMUL 6 EDO C2 H6 O2 FORMUL 7 HOH *151(H2 O) HELIX 1 AA1 GLY A 281 LYS A 288 1 8 HELIX 2 AA2 ASP A 296 ALA A 300 5 5 HELIX 3 AA3 SER A 376 ASN A 379 5 4 HELIX 4 AA4 SER A 399 GLN A 404 5 6 SHEET 1 AA1 3 LEU A 305 LEU A 306 0 SHEET 2 AA1 3 SER A 312 GLN A 314 -1 O GLN A 314 N LEU A 305 SHEET 3 AA1 3 LEU A 456 ILE A 457 -1 O LEU A 456 N VAL A 313 SHEET 1 AA2 5 CYS A 334 LEU A 336 0 SHEET 2 AA2 5 LEU A 444 ILE A 450 -1 O PHE A 448 N ILE A 335 SHEET 3 AA2 5 TRP A 358 GLN A 364 -1 N GLY A 359 O PHE A 449 SHEET 4 AA2 5 VAL A 381 LEU A 387 -1 O TRP A 382 N VAL A 362 SHEET 5 AA2 5 GLU A 391 MET A 393 -1 O GLU A 391 N LEU A 387 SHEET 1 AA3 4 ARG A 345 LEU A 351 0 SHEET 2 AA3 4 CYS A 410 ASP A 416 -1 O ILE A 413 N TRP A 348 SHEET 3 AA3 4 GLU A 421 ASN A 426 -1 O SER A 423 N PHE A 414 SHEET 4 AA3 4 SER A 431 ASN A 437 -1 O ILE A 433 N PHE A 424 LINK OE2 GLU A 354 MG MG A 502 1555 1555 2.08 LINK OE1 GLN A 364 MG MG A 503 1555 1555 2.84 LINK MG MG A 502 O HOH A 602 1555 6555 1.99 LINK MG MG A 502 O HOH A 639 1555 1555 2.13 LINK MG MG A 502 O HOH A 686 1555 1555 2.07 LINK MG MG A 502 O HOH A 724 1555 6555 1.97 LINK MG MG A 502 O HOH A 732 1555 6555 2.02 CRYST1 55.284 55.284 202.763 90.00 90.00 120.00 P 61 2 2 12 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 0.018088 0.010443 0.000000 0.00000 SCALE2 0.000000 0.020887 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004932 0.00000