HEADER LIGASE/LIGASE INHIBITOR 01-APR-16 5J5A TITLE TRYPANOSOMA BRUCEI METHIONYL-TRNA SYNTHETASE IN COMPLEX WITH INHIBITOR TITLE 2 (CHEM 70786556) COMPND MOL_ID: 1; COMPND 2 MOLECULE: METHIONYL-TRNA SYNTHETASE, PUTATIVE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 6.1.1.10; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TRYPANOSOMA BRUCEI BRUCEI; SOURCE 3 ORGANISM_TAXID: 185431; SOURCE 4 STRAIN: 927/4 GUTAT10.1; SOURCE 5 GENE: TB10.70.6470; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SYNTHETASE, LIGASE, METHIONINE, INHIBITOR, LIGASE-LIGASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.BARROS-ALVAREZ,C.Y.KOH,W.G.J.HOL REVDAT 2 06-MAR-24 5J5A 1 REMARK REVDAT 1 25-JAN-17 5J5A 0 JRNL AUTH W.HUANG,Z.ZHANG,X.BARROS-ALVAREZ,C.Y.KOH,R.M.RANADE, JRNL AUTH 2 J.R.GILLESPIE,S.A.CREASON,S.SHIBATA,C.L.VERLINDE,W.G.HOL, JRNL AUTH 3 F.S.BUCKNER,E.FAN JRNL TITL STRUCTURE-GUIDED DESIGN OF NOVEL TRYPANOSOMA BRUCEI JRNL TITL 2 METHIONYL-TRNA SYNTHETASE INHIBITORS. JRNL REF EUR J MED CHEM V. 124 1081 2016 JRNL REFN ISSN 1768-3254 JRNL PMID 27788467 JRNL DOI 10.1016/J.EJMECH.2016.10.024 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0107 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 50819 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2720 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3641 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3130 REMARK 3 BIN FREE R VALUE SET COUNT : 217 REMARK 3 BIN FREE R VALUE : 0.3640 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8248 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.13000 REMARK 3 B22 (A**2) : -1.46000 REMARK 3 B33 (A**2) : -1.67000 REMARK 3 B12 (A**2) : 0.00000 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): 0.425 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.273 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.891 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8500 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 7989 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11558 ; 1.398 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 18360 ; 3.685 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1035 ; 5.632 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 384 ;35.452 ;23.359 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1371 ;13.922 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 57 ;14.636 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1274 ; 0.087 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9638 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1973 ; 0.005 ; 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): 4161 ; 1.848 ; 3.497 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 4162 ; 1.848 ; 3.496 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5190 ; 3.217 ; 5.224 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 5190 ; 3.217 ; 5.224 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4339 ; 1.687 ; 3.484 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4340 ; 1.687 ; 3.484 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 6369 ; 2.941 ; 5.184 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9637 ; 5.561 ;27.143 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 9635 ; 5.561 ;27.145 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 238 767 B 238 767 58686 0.13 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5J5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000219976. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53600 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 37.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 (%): 68.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.91 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8-2.1 M AMMONIUM SULFATE, 0.2 M REMARK 280 SODIUM CHLORIDE, 0.1 M SODIUM CACODYLATE, PH 6.2-6.8, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 43.79600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 103.62500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.90300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 103.62500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 43.79600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 52.90300 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 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 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 232 REMARK 465 PRO A 233 REMARK 465 GLY A 234 REMARK 465 SER A 235 REMARK 465 MET A 236 REMARK 465 LYS A 237 REMARK 465 ASP A 551 REMARK 465 ARG A 552 REMARK 465 LYS A 553 REMARK 465 LYS A 554 REMARK 465 ILE A 555 REMARK 465 SER A 556 REMARK 465 LYS A 557 REMARK 465 SER A 558 REMARK 465 LEU A 559 REMARK 465 GLY A 560 REMARK 465 GLU A 757 REMARK 465 GLY A 758 REMARK 465 GLU A 768 REMARK 465 ASN A 769 REMARK 465 THR A 770 REMARK 465 LYS A 771 REMARK 465 SER A 772 REMARK 465 THR A 773 REMARK 465 SER B 369 REMARK 465 ILE B 376 REMARK 465 THR B 377 REMARK 465 ASP B 378 REMARK 465 GLY B 379 REMARK 465 VAL B 380 REMARK 465 ASP B 381 REMARK 465 LYS B 382 REMARK 465 ASP B 383 REMARK 465 GLY B 384 REMARK 465 ASN B 385 REMARK 465 PRO B 386 REMARK 465 CYS B 387 REMARK 465 GLU B 768 REMARK 465 ASN B 769 REMARK 465 THR B 770 REMARK 465 LYS B 771 REMARK 465 SER B 772 REMARK 465 THR B 773 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 VAL A 238 CG1 CG2 REMARK 470 LYS A 382 CG CD CE NZ REMARK 470 VAL A 562 CG1 CG2 REMARK 470 GLU A 567 CG CD OE1 OE2 REMARK 470 ASP A 590 CG OD1 OD2 REMARK 470 LYS A 689 CG CD CE NZ REMARK 470 VAL A 756 CG1 CG2 REMARK 470 GLU A 759 CG CD OE1 OE2 REMARK 470 TYR B 363 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ILE B 365 CG1 CG2 CD1 REMARK 470 SER B 366 OG REMARK 470 PHE B 370 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 374 CG CD OE1 NE2 REMARK 470 ASN B 375 CG OD1 ND2 REMARK 470 LYS B 388 CG CD CE NZ REMARK 470 VAL B 389 CG1 CG2 REMARK 470 LEU B 391 CG CD1 CD2 REMARK 470 HIS B 395 CG ND1 CD2 CE1 NE2 REMARK 470 VAL B 396 CG1 CG2 REMARK 470 VAL B 397 CG1 CG2 REMARK 470 GLU B 491 CG CD OE1 OE2 REMARK 470 LYS B 494 CG CD CE NZ REMARK 470 LYS B 553 CG CD CE NZ REMARK 470 LYS B 557 CG CD CE NZ REMARK 470 LYS B 689 CG CD CE NZ REMARK 470 LYS B 736 CG CD CE NZ REMARK 470 GLU B 757 CG CD OE1 OE2 REMARK 470 GLU B 759 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH B 928 O HOH B 1003 1.56 REMARK 500 SG CYS A 470 O HOH A 1003 1.98 REMARK 500 NH2 ARG B 274 O HOH B 901 2.05 REMARK 500 O HOH A 945 O HOH A 981 2.07 REMARK 500 SG CYS B 470 O HOH B 1015 2.11 REMARK 500 O SER B 585 O HOH B 902 2.14 REMARK 500 CD ARG B 434 O HOH B 992 2.18 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 GLU B 288 N - CA - C ANGL. DEV. = 16.5 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 TRP A 459 73.57 -117.45 REMARK 500 ASN A 466 85.19 -159.70 REMARK 500 ALA A 632 -158.25 -86.97 REMARK 500 TRP B 459 75.27 -118.08 REMARK 500 ASN B 466 83.27 -159.50 REMARK 500 ARG B 552 14.28 59.06 REMARK 500 ASN B 561 79.05 -156.46 REMARK 500 ALA B 632 -159.29 -85.39 REMARK 500 GLU B 757 -131.97 48.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MET A 800 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 756 B 801 DBREF 5J5A A 237 773 UNP Q38C91 Q38C91_TRYB2 237 773 DBREF 5J5A B 237 773 UNP Q38C91 Q38C91_TRYB2 237 773 SEQADV 5J5A GLY A 232 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A PRO A 233 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A GLY A 234 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A SER A 235 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A MET A 236 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A THR A 309 UNP Q38C91 ALA 309 ENGINEERED MUTATION SEQADV 5J5A ALA A 452 UNP Q38C91 LYS 452 ENGINEERED MUTATION SEQADV 5J5A ARG A 453 UNP Q38C91 LYS 453 ENGINEERED MUTATION SEQADV 5J5A ALA A 454 UNP Q38C91 GLU 454 ENGINEERED MUTATION SEQADV 5J5A VAL A 499 UNP Q38C91 ALA 499 ENGINEERED MUTATION SEQADV 5J5A ASN A 503 UNP Q38C91 SER 503 ENGINEERED MUTATION SEQADV 5J5A GLY B 232 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A PRO B 233 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A GLY B 234 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A SER B 235 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A MET B 236 UNP Q38C91 EXPRESSION TAG SEQADV 5J5A THR B 309 UNP Q38C91 ALA 309 ENGINEERED MUTATION SEQADV 5J5A ALA B 452 UNP Q38C91 LYS 452 ENGINEERED MUTATION SEQADV 5J5A ARG B 453 UNP Q38C91 LYS 453 ENGINEERED MUTATION SEQADV 5J5A ALA B 454 UNP Q38C91 GLU 454 ENGINEERED MUTATION SEQADV 5J5A VAL B 499 UNP Q38C91 ALA 499 ENGINEERED MUTATION SEQADV 5J5A ASN B 503 UNP Q38C91 SER 503 ENGINEERED MUTATION SEQRES 1 A 542 GLY PRO GLY SER MET LYS VAL GLU LYS VAL PHE PHE VAL SEQRES 2 A 542 THR SER PRO ILE TYR TYR VAL ASN ALA ALA PRO HIS ILE SEQRES 3 A 542 GLY HIS VAL TYR SER THR LEU ILE THR ASP VAL ILE GLY SEQRES 4 A 542 ARG TYR HIS ARG VAL LYS GLY GLU ARG VAL PHE ALA LEU SEQRES 5 A 542 THR GLY THR ASP GLU HIS GLY GLN LYS VAL ALA GLU ALA SEQRES 6 A 542 ALA LYS GLN LYS GLN VAL SER PRO TYR ASP PHE THR THR SEQRES 7 A 542 ALA VAL ALA GLY GLU PHE LYS LYS CYS PHE GLU GLN MET SEQRES 8 A 542 ASP TYR SER ILE ASP TYR PHE ILE ARG THR THR ASN GLU SEQRES 9 A 542 GLN HIS LYS ALA VAL VAL LYS GLU LEU TRP THR LYS LEU SEQRES 10 A 542 GLU GLN LYS GLY ASP ILE TYR LEU GLY ARG TYR GLU GLY SEQRES 11 A 542 TRP TYR SER ILE SER ASP GLU SER PHE LEU THR PRO GLN SEQRES 12 A 542 ASN ILE THR ASP GLY VAL ASP LYS ASP GLY ASN PRO CYS SEQRES 13 A 542 LYS VAL SER LEU GLU SER GLY HIS VAL VAL THR TRP VAL SEQRES 14 A 542 SER GLU GLU ASN TYR MET PHE ARG LEU SER ALA PHE ARG SEQRES 15 A 542 GLU ARG LEU LEU GLU TRP TYR HIS ALA ASN PRO GLY CYS SEQRES 16 A 542 ILE VAL PRO GLU PHE ARG ARG ARG GLU VAL ILE ARG ALA SEQRES 17 A 542 VAL GLU LYS GLY LEU PRO ASP LEU SER VAL SER ARG ALA SEQRES 18 A 542 ARG ALA THR LEU HIS ASN TRP ALA ILE PRO VAL PRO GLY SEQRES 19 A 542 ASN PRO ASP HIS CYS VAL TYR VAL TRP LEU ASP ALA LEU SEQRES 20 A 542 THR ASN TYR LEU THR GLY SER ARG LEU ARG VAL ASP GLU SEQRES 21 A 542 SER GLY LYS GLU VAL SER LEU VAL ASP ASP PHE ASN GLU SEQRES 22 A 542 LEU GLU ARG PHE PRO ALA ASP VAL HIS VAL ILE GLY LYS SEQRES 23 A 542 ASP ILE LEU LYS PHE HIS ALA ILE TYR TRP PRO ALA PHE SEQRES 24 A 542 LEU LEU SER ALA GLY LEU PRO LEU PRO LYS LYS ILE VAL SEQRES 25 A 542 ALA HIS GLY TRP TRP THR LYS ASP ARG LYS LYS ILE SER SEQRES 26 A 542 LYS SER LEU GLY ASN VAL PHE ASP PRO VAL GLU LYS ALA SEQRES 27 A 542 GLU GLU PHE GLY TYR ASP ALA LEU LYS TYR PHE LEU LEU SEQRES 28 A 542 ARG GLU SER GLY PHE SER ASP ASP GLY ASP TYR SER ASP SEQRES 29 A 542 LYS ASN MET ILE ALA ARG LEU ASN GLY GLU LEU ALA ASP SEQRES 30 A 542 THR LEU GLY ASN LEU VAL MET ARG CYS THR SER ALA LYS SEQRES 31 A 542 ILE ASN VAL ASN GLY GLU TRP PRO SER PRO ALA ALA TYR SEQRES 32 A 542 THR GLU GLU ASP GLU SER LEU ILE GLN LEU ILE LYS ASP SEQRES 33 A 542 LEU PRO GLY THR ALA ASP HIS TYR TYR LEU ILE PRO ASP SEQRES 34 A 542 ILE GLN LYS ALA ILE ILE ALA VAL PHE ASP VAL LEU ARG SEQRES 35 A 542 ALA ILE ASN ALA TYR VAL THR ASP MET ALA PRO TRP LYS SEQRES 36 A 542 LEU VAL LYS THR ASP PRO GLU ARG LEU ARG THR VAL LEU SEQRES 37 A 542 TYR ILE THR LEU GLU GLY VAL ARG VAL THR THR LEU LEU SEQRES 38 A 542 LEU SER PRO ILE LEU PRO ARG LYS SER VAL VAL ILE PHE SEQRES 39 A 542 ASP MET LEU GLY VAL PRO GLU VAL HIS ARG LYS GLY ILE SEQRES 40 A 542 GLU ASN PHE GLU PHE GLY ALA VAL PRO PRO GLY THR ARG SEQRES 41 A 542 LEU GLY PRO ALA VAL GLU GLY GLU VAL LEU PHE SER LYS SEQRES 42 A 542 ARG SER THR GLU ASN THR LYS SER THR SEQRES 1 B 542 GLY PRO GLY SER MET LYS VAL GLU LYS VAL PHE PHE VAL SEQRES 2 B 542 THR SER PRO ILE TYR TYR VAL ASN ALA ALA PRO HIS ILE SEQRES 3 B 542 GLY HIS VAL TYR SER THR LEU ILE THR ASP VAL ILE GLY SEQRES 4 B 542 ARG TYR HIS ARG VAL LYS GLY GLU ARG VAL PHE ALA LEU SEQRES 5 B 542 THR GLY THR ASP GLU HIS GLY GLN LYS VAL ALA GLU ALA SEQRES 6 B 542 ALA LYS GLN LYS GLN VAL SER PRO TYR ASP PHE THR THR SEQRES 7 B 542 ALA VAL ALA GLY GLU PHE LYS LYS CYS PHE GLU GLN MET SEQRES 8 B 542 ASP TYR SER ILE ASP TYR PHE ILE ARG THR THR ASN GLU SEQRES 9 B 542 GLN HIS LYS ALA VAL VAL LYS GLU LEU TRP THR LYS LEU SEQRES 10 B 542 GLU GLN LYS GLY ASP ILE TYR LEU GLY ARG TYR GLU GLY SEQRES 11 B 542 TRP TYR SER ILE SER ASP GLU SER PHE LEU THR PRO GLN SEQRES 12 B 542 ASN ILE THR ASP GLY VAL ASP LYS ASP GLY ASN PRO CYS SEQRES 13 B 542 LYS VAL SER LEU GLU SER GLY HIS VAL VAL THR TRP VAL SEQRES 14 B 542 SER GLU GLU ASN TYR MET PHE ARG LEU SER ALA PHE ARG SEQRES 15 B 542 GLU ARG LEU LEU GLU TRP TYR HIS ALA ASN PRO GLY CYS SEQRES 16 B 542 ILE VAL PRO GLU PHE ARG ARG ARG GLU VAL ILE ARG ALA SEQRES 17 B 542 VAL GLU LYS GLY LEU PRO ASP LEU SER VAL SER ARG ALA SEQRES 18 B 542 ARG ALA THR LEU HIS ASN TRP ALA ILE PRO VAL PRO GLY SEQRES 19 B 542 ASN PRO ASP HIS CYS VAL TYR VAL TRP LEU ASP ALA LEU SEQRES 20 B 542 THR ASN TYR LEU THR GLY SER ARG LEU ARG VAL ASP GLU SEQRES 21 B 542 SER GLY LYS GLU VAL SER LEU VAL ASP ASP PHE ASN GLU SEQRES 22 B 542 LEU GLU ARG PHE PRO ALA ASP VAL HIS VAL ILE GLY LYS SEQRES 23 B 542 ASP ILE LEU LYS PHE HIS ALA ILE TYR TRP PRO ALA PHE SEQRES 24 B 542 LEU LEU SER ALA GLY LEU PRO LEU PRO LYS LYS ILE VAL SEQRES 25 B 542 ALA HIS GLY TRP TRP THR LYS ASP ARG LYS LYS ILE SER SEQRES 26 B 542 LYS SER LEU GLY ASN VAL PHE ASP PRO VAL GLU LYS ALA SEQRES 27 B 542 GLU GLU PHE GLY TYR ASP ALA LEU LYS TYR PHE LEU LEU SEQRES 28 B 542 ARG GLU SER GLY PHE SER ASP ASP GLY ASP TYR SER ASP SEQRES 29 B 542 LYS ASN MET ILE ALA ARG LEU ASN GLY GLU LEU ALA ASP SEQRES 30 B 542 THR LEU GLY ASN LEU VAL MET ARG CYS THR SER ALA LYS SEQRES 31 B 542 ILE ASN VAL ASN GLY GLU TRP PRO SER PRO ALA ALA TYR SEQRES 32 B 542 THR GLU GLU ASP GLU SER LEU ILE GLN LEU ILE LYS ASP SEQRES 33 B 542 LEU PRO GLY THR ALA ASP HIS TYR TYR LEU ILE PRO ASP SEQRES 34 B 542 ILE GLN LYS ALA ILE ILE ALA VAL PHE ASP VAL LEU ARG SEQRES 35 B 542 ALA ILE ASN ALA TYR VAL THR ASP MET ALA PRO TRP LYS SEQRES 36 B 542 LEU VAL LYS THR ASP PRO GLU ARG LEU ARG THR VAL LEU SEQRES 37 B 542 TYR ILE THR LEU GLU GLY VAL ARG VAL THR THR LEU LEU SEQRES 38 B 542 LEU SER PRO ILE LEU PRO ARG LYS SER VAL VAL ILE PHE SEQRES 39 B 542 ASP MET LEU GLY VAL PRO GLU VAL HIS ARG LYS GLY ILE SEQRES 40 B 542 GLU ASN PHE GLU PHE GLY ALA VAL PRO PRO GLY THR ARG SEQRES 41 B 542 LEU GLY PRO ALA VAL GLU GLY GLU VAL LEU PHE SER LYS SEQRES 42 B 542 ARG SER THR GLU ASN THR LYS SER THR HET MET A 800 9 HET 756 B 801 27 HETNAM MET METHIONINE HETNAM 756 [(3S)-3-(1H-BENZIMIDAZOL-2-YL)PIPERIDIN-1-YL](2-METHYL- HETNAM 2 756 1-BENZOFURAN-5-YL)METHANONE HETSYN 756 2-[1-(2-METHYL-1-BENZOFURAN-5-CARBONYL)PIPERIDIN-3-YL]- HETSYN 2 756 1H-1,3-BENZODIAZOLE FORMUL 3 MET C5 H11 N O2 S FORMUL 4 756 C22 H21 N3 O2 FORMUL 5 HOH *249(H2 O) HELIX 1 AA1 HIS A 256 LYS A 276 1 21 HELIX 2 AA2 GLY A 290 LYS A 300 1 11 HELIX 3 AA3 SER A 303 MET A 322 1 20 HELIX 4 AA4 ASN A 334 LYS A 351 1 18 HELIX 5 AA5 THR A 372 GLN A 374 5 3 HELIX 6 AA6 LEU A 409 ALA A 411 5 3 HELIX 7 AA7 PHE A 412 ASN A 423 1 12 HELIX 8 AA8 PRO A 429 GLY A 443 1 15 HELIX 9 AA9 TYR A 472 THR A 479 1 8 HELIX 10 AB1 THR A 479 SER A 485 1 7 HELIX 11 AB2 ASP A 501 LEU A 505 5 5 HELIX 12 AB3 ILE A 519 ILE A 525 1 7 HELIX 13 AB4 ILE A 525 GLY A 535 1 11 HELIX 14 AB5 ASP A 564 GLY A 573 1 10 HELIX 15 AB6 GLY A 573 SER A 585 1 13 HELIX 16 AB7 SER A 594 GLU A 605 1 12 HELIX 17 AB8 THR A 609 SER A 619 1 11 HELIX 18 AB9 THR A 635 ILE A 658 1 24 HELIX 19 AC1 ASP A 660 ALA A 683 1 24 HELIX 20 AC2 ALA A 683 ASP A 691 1 9 HELIX 21 AC3 ASP A 691 SER A 714 1 24 HELIX 22 AC4 LEU A 717 GLY A 729 1 13 HELIX 23 AC5 PRO A 731 LYS A 736 5 6 HELIX 24 AC6 GLY A 737 GLU A 742 5 6 HELIX 25 AC7 HIS B 256 LYS B 276 1 21 HELIX 26 AC8 GLY B 290 LYS B 300 1 11 HELIX 27 AC9 SER B 303 MET B 322 1 20 HELIX 28 AD1 ASN B 334 LYS B 351 1 18 HELIX 29 AD2 LEU B 409 ALA B 411 5 3 HELIX 30 AD3 PHE B 412 ASN B 423 1 12 HELIX 31 AD4 PRO B 429 GLY B 443 1 15 HELIX 32 AD5 TYR B 472 LEU B 478 1 7 HELIX 33 AD6 THR B 479 ARG B 486 1 8 HELIX 34 AD7 ASP B 501 LEU B 505 5 5 HELIX 35 AD8 ILE B 519 ILE B 525 1 7 HELIX 36 AD9 ILE B 525 GLY B 535 1 11 HELIX 37 AE1 ASP B 564 GLY B 573 1 10 HELIX 38 AE2 GLY B 573 SER B 585 1 13 HELIX 39 AE3 SER B 594 GLU B 605 1 12 HELIX 40 AE4 THR B 609 SER B 619 1 11 HELIX 41 AE5 THR B 635 ILE B 658 1 24 HELIX 42 AE6 ASP B 660 ALA B 683 1 24 HELIX 43 AE7 ALA B 683 ASP B 691 1 9 HELIX 44 AE8 ASP B 691 SER B 714 1 24 HELIX 45 AE9 LEU B 717 GLY B 729 1 13 HELIX 46 AF1 PRO B 731 LYS B 736 5 6 HELIX 47 AF2 GLY B 737 GLU B 742 5 6 SHEET 1 AA1 6 TYR A 328 ARG A 331 0 SHEET 2 AA1 6 VAL A 280 ASP A 287 1 N THR A 284 O ILE A 330 SHEET 3 AA1 6 PHE A 242 TYR A 250 1 N TYR A 249 O ASP A 287 SHEET 4 AA1 6 VAL A 512 GLY A 516 1 O VAL A 514 N THR A 245 SHEET 5 AA1 6 LYS A 541 HIS A 545 1 O VAL A 543 N HIS A 513 SHEET 6 AA1 6 ILE A 427 VAL A 428 1 N VAL A 428 O ALA A 544 SHEET 1 AA2 4 SER A 369 LEU A 371 0 SHEET 2 AA2 4 ILE A 354 SER A 364 -1 N SER A 364 O SER A 369 SHEET 3 AA2 4 VAL A 397 PHE A 407 -1 O MET A 406 N TYR A 355 SHEET 4 AA2 4 LEU A 447 SER A 448 -1 O LEU A 447 N PHE A 407 SHEET 1 AA3 2 ILE A 376 VAL A 380 0 SHEET 2 AA3 2 PRO A 386 SER A 390 -1 O VAL A 389 N THR A 377 SHEET 1 AA4 3 SER A 450 ALA A 452 0 SHEET 2 AA4 3 ASN A 466 VAL A 471 -1 O CYS A 470 N ARG A 451 SHEET 3 AA4 3 PRO A 462 VAL A 463 -1 N VAL A 463 O HIS A 469 SHEET 1 AA5 2 LEU A 487 VAL A 489 0 SHEET 2 AA5 2 GLU A 495 LEU A 498 -1 O VAL A 496 N ARG A 488 SHEET 1 AA6 6 TYR B 328 ARG B 331 0 SHEET 2 AA6 6 VAL B 280 ASP B 287 1 N THR B 284 O ILE B 330 SHEET 3 AA6 6 PHE B 242 TYR B 250 1 N TYR B 249 O ASP B 287 SHEET 4 AA6 6 VAL B 512 GLY B 516 1 O VAL B 514 N THR B 245 SHEET 5 AA6 6 LYS B 541 HIS B 545 1 O VAL B 543 N HIS B 513 SHEET 6 AA6 6 ILE B 427 VAL B 428 1 N VAL B 428 O ALA B 544 SHEET 1 AA7 3 ILE B 354 SER B 364 0 SHEET 2 AA7 3 VAL B 397 PHE B 407 -1 O ASN B 404 N GLY B 357 SHEET 3 AA7 3 LEU B 447 SER B 448 -1 O LEU B 447 N PHE B 407 SHEET 1 AA8 3 SER B 450 ALA B 452 0 SHEET 2 AA8 3 ASN B 466 VAL B 471 -1 O CYS B 470 N ARG B 451 SHEET 3 AA8 3 PRO B 462 VAL B 463 -1 N VAL B 463 O HIS B 469 SHEET 1 AA9 2 LEU B 487 VAL B 489 0 SHEET 2 AA9 2 GLU B 495 LEU B 498 -1 O VAL B 496 N ARG B 488 SHEET 1 AB1 2 THR B 549 LYS B 550 0 SHEET 2 AB1 2 ASP B 592 TYR B 593 1 O TYR B 593 N THR B 549 CISPEP 1 VAL A 428 PRO A 429 0 -2.59 CISPEP 2 PHE A 508 PRO A 509 0 -3.59 CISPEP 3 ILE A 658 PRO A 659 0 -3.26 CISPEP 4 VAL B 428 PRO B 429 0 -4.49 CISPEP 5 PHE B 508 PRO B 509 0 -1.36 CISPEP 6 ILE B 658 PRO B 659 0 -4.11 SITE 1 AC1 11 ILE A 248 TYR A 250 ASP A 287 TRP A 474 SITE 2 AC1 11 ALA A 477 LEU A 478 TYR A 481 ILE A 519 SITE 3 AC1 11 HIS A 523 LYS A 550 HOH A 910 SITE 1 AC2 11 ILE B 248 TYR B 250 ASP B 287 HIS B 289 SITE 2 AC2 11 GLY B 290 VAL B 473 ASP B 476 LEU B 478 SITE 3 AC2 11 TYR B 481 PHE B 522 HIS B 523 CRYST1 87.592 105.806 207.250 90.00 90.00 90.00 P 21 21 21 8 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 0.011417 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009451 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004825 0.00000