HEADER OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR 31-MAR-14 4P8C TITLE CRYSTAL STRUCTURE OF M. TUBERCULOSIS DPRE1 IN COMPLEX WITH THE NON- TITLE 2 COVALENT INHIBITOR QN127 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE DECAPRENYLPHOSPHORYL-BETA-D-RIBOSE OXIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DPRE1; COMPND 5 EC: 1.-.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: DPRE1, RV3790, MT3898; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS DPRE1, INHIBITOR, COMPLEX, NON-COVALENT, OXIDOREDUCTASE- KEYWDS 2 OXIDOREDUCTASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.NERES,F.POJER,S.T.COLE REVDAT 4 27-SEP-23 4P8C 1 REMARK REVDAT 3 22-NOV-17 4P8C 1 SOURCE REMARK REVDAT 2 01-APR-15 4P8C 1 JRNL REVDAT 1 10-DEC-14 4P8C 0 JRNL AUTH J.NERES,R.C.HARTKOORN,L.R.CHIARELLI,R.GADUPUDI,M.R.PASCA, JRNL AUTH 2 G.MORI,A.VENTURELLI,S.SAVINA,V.MAKAROV,G.S.KOLLY,E.MOLTENI, JRNL AUTH 3 C.BINDA,N.DHAR,S.FERRARI,P.BRODIN,V.DELORME,V.LANDRY, JRNL AUTH 4 A.L.DE JESUS LOPES RIBEIRO,D.FARINA,P.SAXENA,F.POJER, JRNL AUTH 5 A.CARTA,R.LUCIANI,A.PORTA,G.ZANONI,E.DE ROSSI,M.P.COSTI, JRNL AUTH 6 G.RICCARDI,S.T.COLE JRNL TITL 2-CARBOXYQUINOXALINES KILL MYCOBACTERIUM TUBERCULOSIS JRNL TITL 2 THROUGH NONCOVALENT INHIBITION OF DPRE1. JRNL REF ACS CHEM.BIOL. V. 10 705 2015 JRNL REFN ESSN 1554-8937 JRNL PMID 25427196 JRNL DOI 10.1021/CB5007163 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 68581 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3640 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) : 1.95 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.00 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4686 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE SET COUNT : 243 REMARK 3 BIN FREE R VALUE : 0.3620 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 182 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.170 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.153 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.174 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7023 ; 0.007 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9567 ; 1.211 ; 1.985 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 863 ; 5.482 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 297 ;31.844 ;22.626 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1079 ;15.154 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 59 ;15.694 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1049 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5353 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4P8C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000200893. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-13 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 : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : BARTELS MONOCHROMATOR WITH DUAL REMARK 200 CHANNEL CUT CRYSTALS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 135575 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 49.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : 1.982 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.98 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.180 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: 4FDP REMARK 200 REMARK 200 REMARK: RMEAS 0.043 (OVERALL), 0.523 (OUTER SHELL) REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 34% POLYPROPYLENEGLYCOL 400, 100 MM REMARK 280 IMIDAZOLE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 42.07900 REMARK 290 SMTRY3 2 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 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 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 -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 SER A 3 REMARK 465 VAL A 4 REMARK 465 GLY A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 269 REMARK 465 PRO A 270 REMARK 465 GLN A 271 REMARK 465 LEU A 272 REMARK 465 LEU A 273 REMARK 465 ASN A 324 REMARK 465 ARG A 325 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 LEU B 2 REMARK 465 SER B 3 REMARK 465 VAL B 4 REMARK 465 GLY B 5 REMARK 465 ALA B 6 REMARK 465 THR B 7 REMARK 465 GLN B 271 REMARK 465 LEU B 272 REMARK 465 LEU B 273 REMARK 465 THR B 274 REMARK 465 LEU B 275 REMARK 465 PRO B 276 REMARK 465 ASP B 277 REMARK 465 VAL B 278 REMARK 465 PHE B 279 REMARK 465 PRO B 280 REMARK 465 ASN B 281 REMARK 465 GLY B 282 REMARK 465 LEU B 283 REMARK 465 ALA B 284 REMARK 465 ASN B 285 REMARK 465 LYS B 286 REMARK 465 TYR B 287 REMARK 465 THR B 288 REMARK 465 PHE B 289 REMARK 465 GLY B 290 REMARK 465 PRO B 291 REMARK 465 ILE B 292 REMARK 465 GLY B 293 REMARK 465 LEU B 317 REMARK 465 ASP B 318 REMARK 465 MET B 319 REMARK 465 PHE B 320 REMARK 465 GLY B 321 REMARK 465 GLU B 322 REMARK 465 TRP B 323 REMARK 465 ASN B 324 REMARK 465 ARG B 325 REMARK 465 ALA B 326 REMARK 465 TYR B 327 REMARK 465 GLY B 328 REMARK 465 PRO B 329 REMARK 465 ALA B 330 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 ASP A 155 2.25 -67.35 REMARK 500 PRO A 329 -126.64 -74.31 REMARK 500 ARG A 421 -2.20 -140.03 REMARK 500 ALA B 20 72.94 49.91 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 FAD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Y22 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IMD A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2J3 A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Y22 B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4P8H RELATED DB: PDB REMARK 900 RELATED ID: 4P8K RELATED DB: PDB REMARK 900 RELATED ID: 4P8L RELATED DB: PDB REMARK 900 RELATED ID: 4P8M RELATED DB: PDB REMARK 900 RELATED ID: 4P8N RELATED DB: PDB REMARK 900 RELATED ID: 4P8P RELATED DB: PDB REMARK 900 RELATED ID: 4P8T RELATED DB: PDB REMARK 900 RELATED ID: 4P8Y RELATED DB: PDB DBREF 4P8C A 1 461 UNP P72056 DPRE1_MYCTU 1 461 DBREF 4P8C B 1 461 UNP P72056 DPRE1_MYCTU 1 461 SEQRES 1 A 480 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 A 480 VAL PRO ARG GLY SER HIS MET LEU SER VAL GLY ALA THR SEQRES 3 A 480 THR THR ALA THR ARG LEU THR GLY TRP GLY ARG THR ALA SEQRES 4 A 480 PRO SER VAL ALA ASN VAL LEU ARG THR PRO ASP ALA GLU SEQRES 5 A 480 MET ILE VAL LYS ALA VAL ALA ARG VAL ALA GLU SER GLY SEQRES 6 A 480 GLY GLY ARG GLY ALA ILE ALA ARG GLY LEU GLY ARG SER SEQRES 7 A 480 TYR GLY ASP ASN ALA GLN ASN GLY GLY GLY LEU VAL ILE SEQRES 8 A 480 ASP MET THR PRO LEU ASN THR ILE HIS SER ILE ASP ALA SEQRES 9 A 480 ASP THR LYS LEU VAL ASP ILE ASP ALA GLY VAL ASN LEU SEQRES 10 A 480 ASP GLN LEU MET LYS ALA ALA LEU PRO PHE GLY LEU TRP SEQRES 11 A 480 VAL PRO VAL LEU PRO GLY THR ARG GLN VAL THR VAL GLY SEQRES 12 A 480 GLY ALA ILE ALA CYS ASP ILE HIS GLY LYS ASN HIS HIS SEQRES 13 A 480 SER ALA GLY SER PHE GLY ASN HIS VAL ARG SER MET ASP SEQRES 14 A 480 LEU LEU THR ALA ASP GLY GLU ILE ARG HIS LEU THR PRO SEQRES 15 A 480 THR GLY GLU ASP ALA GLU LEU PHE TRP ALA THR VAL GLY SEQRES 16 A 480 GLY ASN GLY LEU THR GLY ILE ILE MET ARG ALA THR ILE SEQRES 17 A 480 GLU MET THR PRO THR SER THR ALA TYR PHE ILE ALA ASP SEQRES 18 A 480 GLY ASP VAL THR ALA SER LEU ASP GLU THR ILE ALA LEU SEQRES 19 A 480 HIS SER ASP GLY SER GLU ALA ARG TYR THR TYR SER SER SEQRES 20 A 480 ALA TRP PHE ASP ALA ILE SER ALA PRO PRO LYS LEU GLY SEQRES 21 A 480 ARG ALA ALA VAL SER ARG GLY ARG LEU ALA THR VAL GLU SEQRES 22 A 480 GLN LEU PRO ALA LYS LEU ARG SER GLU PRO LEU LYS PHE SEQRES 23 A 480 ASP ALA PRO GLN LEU LEU THR LEU PRO ASP VAL PHE PRO SEQRES 24 A 480 ASN GLY LEU ALA ASN LYS TYR THR PHE GLY PRO ILE GLY SEQRES 25 A 480 GLU LEU TRP TYR ARG LYS SER GLY THR TYR ARG GLY LYS SEQRES 26 A 480 VAL GLN ASN LEU THR GLN PHE TYR HIS PRO LEU ASP MET SEQRES 27 A 480 PHE GLY GLU TRP ASN ARG ALA TYR GLY PRO ALA GLY PHE SEQRES 28 A 480 LEU GLN TYR GLN PHE VAL ILE PRO THR GLU ALA VAL ASP SEQRES 29 A 480 GLU PHE LYS LYS ILE ILE GLY VAL ILE GLN ALA SER GLY SEQRES 30 A 480 HIS TYR SER PHE LEU ASN VAL PHE LYS LEU PHE GLY PRO SEQRES 31 A 480 ARG ASN GLN ALA PRO LEU SER PHE PRO ILE PRO GLY TRP SEQRES 32 A 480 ASN ILE CYS VAL ASP PHE PRO ILE LYS ASP GLY LEU GLY SEQRES 33 A 480 LYS PHE VAL SER GLU LEU ASP ARG ARG VAL LEU GLU PHE SEQRES 34 A 480 GLY GLY ARG LEU TYR THR ALA LYS ASP SER ARG THR THR SEQRES 35 A 480 ALA GLU THR PHE HIS ALA MET TYR PRO ARG VAL ASP GLU SEQRES 36 A 480 TRP ILE SER VAL ARG ARG LYS VAL ASP PRO LEU ARG VAL SEQRES 37 A 480 PHE ALA SER ASP MET ALA ARG ARG LEU GLU LEU LEU SEQRES 1 B 480 GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY LEU SEQRES 2 B 480 VAL PRO ARG GLY SER HIS MET LEU SER VAL GLY ALA THR SEQRES 3 B 480 THR THR ALA THR ARG LEU THR GLY TRP GLY ARG THR ALA SEQRES 4 B 480 PRO SER VAL ALA ASN VAL LEU ARG THR PRO ASP ALA GLU SEQRES 5 B 480 MET ILE VAL LYS ALA VAL ALA ARG VAL ALA GLU SER GLY SEQRES 6 B 480 GLY GLY ARG GLY ALA ILE ALA ARG GLY LEU GLY ARG SER SEQRES 7 B 480 TYR GLY ASP ASN ALA GLN ASN GLY GLY GLY LEU VAL ILE SEQRES 8 B 480 ASP MET THR PRO LEU ASN THR ILE HIS SER ILE ASP ALA SEQRES 9 B 480 ASP THR LYS LEU VAL ASP ILE ASP ALA GLY VAL ASN LEU SEQRES 10 B 480 ASP GLN LEU MET LYS ALA ALA LEU PRO PHE GLY LEU TRP SEQRES 11 B 480 VAL PRO VAL LEU PRO GLY THR ARG GLN VAL THR VAL GLY SEQRES 12 B 480 GLY ALA ILE ALA CYS ASP ILE HIS GLY LYS ASN HIS HIS SEQRES 13 B 480 SER ALA GLY SER PHE GLY ASN HIS VAL ARG SER MET ASP SEQRES 14 B 480 LEU LEU THR ALA ASP GLY GLU ILE ARG HIS LEU THR PRO SEQRES 15 B 480 THR GLY GLU ASP ALA GLU LEU PHE TRP ALA THR VAL GLY SEQRES 16 B 480 GLY ASN GLY LEU THR GLY ILE ILE MET ARG ALA THR ILE SEQRES 17 B 480 GLU MET THR PRO THR SER THR ALA TYR PHE ILE ALA ASP SEQRES 18 B 480 GLY ASP VAL THR ALA SER LEU ASP GLU THR ILE ALA LEU SEQRES 19 B 480 HIS SER ASP GLY SER GLU ALA ARG TYR THR TYR SER SER SEQRES 20 B 480 ALA TRP PHE ASP ALA ILE SER ALA PRO PRO LYS LEU GLY SEQRES 21 B 480 ARG ALA ALA VAL SER ARG GLY ARG LEU ALA THR VAL GLU SEQRES 22 B 480 GLN LEU PRO ALA LYS LEU ARG SER GLU PRO LEU LYS PHE SEQRES 23 B 480 ASP ALA PRO GLN LEU LEU THR LEU PRO ASP VAL PHE PRO SEQRES 24 B 480 ASN GLY LEU ALA ASN LYS TYR THR PHE GLY PRO ILE GLY SEQRES 25 B 480 GLU LEU TRP TYR ARG LYS SER GLY THR TYR ARG GLY LYS SEQRES 26 B 480 VAL GLN ASN LEU THR GLN PHE TYR HIS PRO LEU ASP MET SEQRES 27 B 480 PHE GLY GLU TRP ASN ARG ALA TYR GLY PRO ALA GLY PHE SEQRES 28 B 480 LEU GLN TYR GLN PHE VAL ILE PRO THR GLU ALA VAL ASP SEQRES 29 B 480 GLU PHE LYS LYS ILE ILE GLY VAL ILE GLN ALA SER GLY SEQRES 30 B 480 HIS TYR SER PHE LEU ASN VAL PHE LYS LEU PHE GLY PRO SEQRES 31 B 480 ARG ASN GLN ALA PRO LEU SER PHE PRO ILE PRO GLY TRP SEQRES 32 B 480 ASN ILE CYS VAL ASP PHE PRO ILE LYS ASP GLY LEU GLY SEQRES 33 B 480 LYS PHE VAL SER GLU LEU ASP ARG ARG VAL LEU GLU PHE SEQRES 34 B 480 GLY GLY ARG LEU TYR THR ALA LYS ASP SER ARG THR THR SEQRES 35 B 480 ALA GLU THR PHE HIS ALA MET TYR PRO ARG VAL ASP GLU SEQRES 36 B 480 TRP ILE SER VAL ARG ARG LYS VAL ASP PRO LEU ARG VAL SEQRES 37 B 480 PHE ALA SER ASP MET ALA ARG ARG LEU GLU LEU LEU HET FAD A 501 53 HET Y22 A 502 29 HET IMD A 503 5 HET 2J3 A 504 13 HET FAD B 501 53 HET Y22 B 502 29 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM Y22 6-(TRIFLUOROMETHYL)-3-{[4-(TRIFLUOROMETHYL) HETNAM 2 Y22 BENZYL]AMINO}QUINOXALINE-2-CARBOXYLIC ACID HETNAM IMD IMIDAZOLE HETNAM 2J3 (2R)-2-{[(2R)-2-{[(2R)-2- HETNAM 2 2J3 HYDROXYPROPYL]OXY}PROPYL]OXY}PROPAN-1-OL FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 4 Y22 2(C18 H11 F6 N3 O2) FORMUL 5 IMD C3 H5 N2 1+ FORMUL 6 2J3 C9 H20 O4 FORMUL 9 HOH *236(H2 O) HELIX 1 AA1 ASP A 31 GLY A 46 1 16 HELIX 2 AA2 ASN A 97 LEU A 106 1 10 HELIX 3 AA3 THR A 122 CYS A 129 1 8 HELIX 4 AA4 ASN A 135 GLY A 140 1 6 HELIX 5 AA5 SER A 141 ASN A 144 5 4 HELIX 6 AA6 ASP A 167 VAL A 175 1 9 HELIX 7 AA7 SER A 208 ASP A 218 1 11 HELIX 8 AA8 GLY A 219 TYR A 224 5 6 HELIX 9 AA9 THR A 252 LEU A 256 5 5 HELIX 10 AB1 PRO A 257 SER A 262 1 6 HELIX 11 AB2 LEU A 275 PHE A 279 1 5 HELIX 12 AB3 GLY A 290 GLY A 301 1 12 HELIX 13 AB4 ASN A 309 HIS A 315 1 7 HELIX 14 AB5 LEU A 317 GLY A 321 5 5 HELIX 15 AB6 ALA A 343 ALA A 356 1 14 HELIX 16 AB7 GLY A 395 PHE A 410 1 16 HELIX 17 AB8 THR A 416 ASP A 419 5 4 HELIX 18 AB9 THR A 423 TYR A 431 1 9 HELIX 19 AC1 ARG A 433 ASP A 445 1 13 HELIX 20 AC2 SER A 452 LEU A 458 1 7 HELIX 21 AC3 ASP B 31 GLY B 46 1 16 HELIX 22 AC4 ASN B 97 LEU B 106 1 10 HELIX 23 AC5 THR B 122 CYS B 129 1 8 HELIX 24 AC6 ASN B 135 GLY B 140 1 6 HELIX 25 AC7 SER B 141 ASN B 144 5 4 HELIX 26 AC8 ASP B 167 VAL B 175 1 9 HELIX 27 AC9 SER B 208 ASP B 218 1 11 HELIX 28 AD1 GLY B 219 TYR B 224 5 6 HELIX 29 AD2 THR B 252 LEU B 256 5 5 HELIX 30 AD3 PRO B 257 SER B 262 1 6 HELIX 31 AD4 LEU B 295 THR B 302 1 8 HELIX 32 AD5 ASN B 309 HIS B 315 1 7 HELIX 33 AD6 ALA B 343 ALA B 356 1 14 HELIX 34 AD7 GLY B 395 PHE B 410 1 16 HELIX 35 AD8 THR B 416 ASP B 419 5 4 HELIX 36 AD9 THR B 423 TYR B 431 1 9 HELIX 37 AE1 ARG B 433 LYS B 443 1 11 HELIX 38 AE2 SER B 452 LEU B 458 1 7 SHEET 1 AA1 4 THR A 8 LEU A 13 0 SHEET 2 AA1 4 SER A 22 ARG A 28 -1 O ALA A 24 N THR A 11 SHEET 3 AA1 4 LEU A 70 ASP A 73 1 O VAL A 71 N ASN A 25 SHEET 4 AA1 4 ALA A 51 ARG A 54 1 N ILE A 52 O ILE A 72 SHEET 1 AA210 ILE A 158 LEU A 161 0 SHEET 2 AA210 VAL A 146 LEU A 152 -1 N MET A 149 O LEU A 161 SHEET 3 AA210 ILE A 183 GLU A 190 -1 O ILE A 183 N LEU A 152 SHEET 4 AA210 LEU A 89 ASP A 93 -1 N ILE A 92 O ALA A 187 SHEET 5 AA210 ILE A 80 ASP A 84 -1 N SER A 82 O ASP A 91 SHEET 6 AA210 ILE B 80 ASP B 84 -1 O ILE B 83 N ILE A 83 SHEET 7 AA210 LEU B 89 ASP B 93 -1 O ASP B 91 N SER B 82 SHEET 8 AA210 ILE B 183 GLU B 190 -1 O ALA B 187 N ILE B 92 SHEET 9 AA210 VAL B 146 LEU B 152 -1 N LEU B 152 O ILE B 183 SHEET 10 AA210 ILE B 158 LEU B 161 -1 O LEU B 161 N MET B 149 SHEET 1 AA3 2 LEU A 110 TRP A 111 0 SHEET 2 AA3 2 THR A 192 PRO A 193 -1 O THR A 192 N TRP A 111 SHEET 1 AA4 8 TYR A 303 GLN A 308 0 SHEET 2 AA4 8 PHE A 199 VAL A 205 -1 N PHE A 199 O GLN A 308 SHEET 3 AA4 8 ALA A 243 LEU A 250 -1 O ARG A 247 N ASP A 202 SHEET 4 AA4 8 TYR A 226 PHE A 231 -1 N SER A 228 O SER A 246 SHEET 5 AA4 8 VAL A 365 PHE A 369 -1 O PHE A 366 N ALA A 229 SHEET 6 AA4 8 GLY A 383 PRO A 391 -1 O ASN A 385 N LYS A 367 SHEET 7 AA4 8 PHE A 332 PRO A 340 -1 N LEU A 333 O PHE A 390 SHEET 8 AA4 8 ARG A 413 LEU A 414 -1 O ARG A 413 N VAL A 338 SHEET 1 AA5 4 THR B 9 LEU B 13 0 SHEET 2 AA5 4 SER B 22 ARG B 28 -1 O ALA B 24 N THR B 11 SHEET 3 AA5 4 LEU B 70 ASP B 73 1 O VAL B 71 N ASN B 25 SHEET 4 AA5 4 ALA B 51 ARG B 54 1 N ILE B 52 O ILE B 72 SHEET 1 AA6 2 LEU B 110 TRP B 111 0 SHEET 2 AA6 2 THR B 192 PRO B 193 -1 O THR B 192 N TRP B 111 SHEET 1 AA7 4 TYR B 226 PHE B 231 0 SHEET 2 AA7 4 ALA B 243 LEU B 250 -1 O SER B 246 N SER B 228 SHEET 3 AA7 4 PHE B 199 VAL B 205 -1 N ASP B 202 O ARG B 247 SHEET 4 AA7 4 TYR B 303 GLN B 308 -1 O LYS B 306 N ALA B 201 SHEET 1 AA8 4 VAL B 365 PHE B 369 0 SHEET 2 AA8 4 GLY B 383 PRO B 391 -1 O ASN B 385 N LYS B 367 SHEET 3 AA8 4 PHE B 332 PRO B 340 -1 N TYR B 335 O VAL B 388 SHEET 4 AA8 4 ARG B 413 LEU B 414 -1 O ARG B 413 N VAL B 338 CISPEP 1 PRO A 237 PRO A 238 0 7.38 CISPEP 2 PRO B 237 PRO B 238 0 7.06 SITE 1 AC1 33 TRP A 16 ILE A 52 ALA A 53 GLY A 55 SITE 2 AC1 33 LEU A 56 GLY A 57 ARG A 58 SER A 59 SITE 3 AC1 33 TYR A 60 ASN A 63 ALA A 64 MET A 74 SITE 4 AC1 33 ALA A 94 PRO A 116 GLY A 117 THR A 118 SITE 5 AC1 33 VAL A 121 THR A 122 GLY A 124 GLY A 125 SITE 6 AC1 33 ALA A 128 CYS A 129 ILE A 131 HIS A 132 SITE 7 AC1 33 ASN A 178 GLY A 179 GLY A 182 ILE A 184 SITE 8 AC1 33 TYR A 415 ALA A 417 Y22 A 502 HOH A 643 SITE 9 AC1 33 HOH A 675 SITE 1 AC2 15 TYR A 60 HIS A 132 GLY A 133 LYS A 134 SITE 2 AC2 15 TRP A 230 GLN A 334 LEU A 363 ASN A 364 SITE 3 AC2 15 VAL A 365 LYS A 367 ASN A 385 CYS A 387 SITE 4 AC2 15 LYS A 418 FAD A 501 2J3 A 504 SITE 1 AC3 4 SER A 82 ASP A 84 SER B 82 ASP B 84 SITE 1 AC4 4 SER A 228 ALA A 229 ALA A 244 Y22 A 502 SITE 1 AC5 33 TRP B 16 ILE B 52 ALA B 53 GLY B 55 SITE 2 AC5 33 LEU B 56 GLY B 57 ARG B 58 SER B 59 SITE 3 AC5 33 TYR B 60 ASN B 63 ALA B 64 MET B 74 SITE 4 AC5 33 ALA B 94 PRO B 116 GLY B 117 THR B 118 SITE 5 AC5 33 VAL B 121 THR B 122 GLY B 124 GLY B 125 SITE 6 AC5 33 ALA B 128 CYS B 129 ILE B 131 HIS B 132 SITE 7 AC5 33 ASN B 178 GLY B 179 GLY B 182 ILE B 184 SITE 8 AC5 33 TYR B 415 ALA B 417 Y22 B 502 HOH B 643 SITE 9 AC5 33 HOH B 649 SITE 1 AC6 13 TYR B 60 HIS B 132 GLY B 133 LYS B 134 SITE 2 AC6 13 TRP B 230 LEU B 363 ASN B 364 VAL B 365 SITE 3 AC6 13 LYS B 367 ASN B 385 CYS B 387 LYS B 418 SITE 4 AC6 13 FAD B 501 CRYST1 77.678 84.158 80.905 90.00 103.17 90.00 P 1 21 1 4 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 0.012874 0.000000 0.003013 0.00000 SCALE2 0.000000 0.011882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012694 0.00000