HEADER TRANSFERASE/INHIBITOR 28-MAY-19 6P4V TITLE 1.65 ANGSTROM TERNARY COMPLEX OF DEOXYHYPUSINE SYNTHASE WITH COFACTOR TITLE 2 NAD AND SPERMIDINE MIMIC INHIBITOR GC7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYHYPUSINE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DHS; COMPND 5 EC: 2.5.1.46; COMPND 6 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: DHPS, DS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEOXYHYPUSINE, NAD COFACTOR, HYPUSINE, SPERMIDINE, GC7, TRANSFERASE, KEYWDS 2 TRANSFERASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.G.KLEIN,G.AMBRUS-AIKELIN REVDAT 3 11-OCT-23 6P4V 1 REMARK REVDAT 2 08-APR-20 6P4V 1 JRNL REVDAT 1 01-APR-20 6P4V 0 JRNL AUTH Y.TANAKA,O.KURASAWA,A.YOKOTA,M.G.KLEIN,K.ONO,B.SAITO, JRNL AUTH 2 S.MATSUMOTO,M.OKANIWA,G.AMBRUS-AIKELIN,D.MORISHITA, JRNL AUTH 3 S.KITAZAWA,N.UCHIYAMA,K.OGAWA,H.KIMURA,S.IMAMURA JRNL TITL DISCOVERY OF NOVEL ALLOSTERIC INHIBITORS OF DEOXYHYPUSINE JRNL TITL 2 SYNTHASE. JRNL REF J.MED.CHEM. V. 63 3215 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32142284 JRNL DOI 10.1021/ACS.JMEDCHEM.9B01979 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0025 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 113578 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) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.175 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6006 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7957 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 444 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5119 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 120 REMARK 3 SOLVENT ATOMS : 326 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.44000 REMARK 3 B22 (A**2) : 1.44000 REMARK 3 B33 (A**2) : -2.16000 REMARK 3 B12 (A**2) : 0.72000 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): 0.067 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.113 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.975 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5409 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5081 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7357 ; 1.269 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11648 ; 0.757 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 673 ; 5.558 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 243 ;36.994 ;24.280 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 885 ;12.089 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;17.704 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 826 ; 0.072 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6145 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1272 ; 0.001 ; 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): 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 28 A 363 REMARK 3 RESIDUE RANGE : A 501 A 502 REMARK 3 RESIDUE RANGE : A 601 A 771 REMARK 3 ORIGIN FOR THE GROUP (A): -41.9467 21.0550 35.9709 REMARK 3 T TENSOR REMARK 3 T11: 0.0998 T22: 0.0266 REMARK 3 T33: 0.0749 T12: 0.0004 REMARK 3 T13: -0.0184 T23: -0.0076 REMARK 3 L TENSOR REMARK 3 L11: 0.3102 L22: 0.7560 REMARK 3 L33: 0.9325 L12: 0.0694 REMARK 3 L13: -0.0421 L23: -0.0645 REMARK 3 S TENSOR REMARK 3 S11: -0.0634 S12: -0.0324 S13: 0.0856 REMARK 3 S21: 0.1020 S22: 0.0874 S23: -0.0220 REMARK 3 S31: -0.2509 S32: 0.0759 S33: -0.0240 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 601 B 755 REMARK 3 RESIDUE RANGE : B 28 B 363 REMARK 3 RESIDUE RANGE : B 501 B 502 REMARK 3 ORIGIN FOR THE GROUP (A): -39.6677 -1.9992 48.8810 REMARK 3 T TENSOR REMARK 3 T11: 0.1052 T22: 0.0605 REMARK 3 T33: 0.0549 T12: 0.0649 REMARK 3 T13: -0.0157 T23: 0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.2346 L22: 0.7340 REMARK 3 L33: 0.9437 L12: 0.0380 REMARK 3 L13: -0.0346 L23: 0.1086 REMARK 3 S TENSOR REMARK 3 S11: -0.0801 S12: -0.0752 S13: -0.0138 REMARK 3 S21: 0.2188 S22: 0.0947 S23: -0.0640 REMARK 3 S31: 0.0429 S32: 0.1252 S33: -0.0145 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 6P4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000241866. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 98 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 120192 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : NULL 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) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 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: 1RLZ.PDB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS (8.0) AND 65% MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 106.32667 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 53.16333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 53.16333 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 106.32667 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 30810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.16333 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 B 744 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 -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 LEU A 5 REMARK 465 GLU A 6 REMARK 465 ARG A 7 REMARK 465 GLU A 8 REMARK 465 ALA A 9 REMARK 465 PRO A 10 REMARK 465 ALA A 11 REMARK 465 GLY A 12 REMARK 465 ALA A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 VAL A 17 REMARK 465 LEU A 18 REMARK 465 LYS A 19 REMARK 465 HIS A 20 REMARK 465 SER A 21 REMARK 465 SER A 22 REMARK 465 THR A 23 REMARK 465 LEU A 24 REMARK 465 PRO A 25 REMARK 465 PRO A 26 REMARK 465 GLU A 27 REMARK 465 HIS A 364 REMARK 465 GLU A 365 REMARK 465 LYS A 366 REMARK 465 ASN A 367 REMARK 465 GLU A 368 REMARK 465 ASP A 369 REMARK 465 GLY B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 GLY B 3 REMARK 465 SER B 4 REMARK 465 LEU B 5 REMARK 465 GLU B 6 REMARK 465 ARG B 7 REMARK 465 GLU B 8 REMARK 465 ALA B 9 REMARK 465 PRO B 10 REMARK 465 ALA B 11 REMARK 465 GLY B 12 REMARK 465 ALA B 13 REMARK 465 LEU B 14 REMARK 465 ALA B 15 REMARK 465 ALA B 16 REMARK 465 VAL B 17 REMARK 465 LEU B 18 REMARK 465 LYS B 19 REMARK 465 HIS B 20 REMARK 465 SER B 21 REMARK 465 SER B 22 REMARK 465 THR B 23 REMARK 465 LEU B 24 REMARK 465 PRO B 25 REMARK 465 PRO B 26 REMARK 465 GLU B 27 REMARK 465 SER B 78 REMARK 465 GLN B 79 REMARK 465 ASP B 80 REMARK 465 GLU B 81 REMARK 465 ASP B 82 REMARK 465 GLN B 83 REMARK 465 HIS B 84 REMARK 465 ALA B 85 REMARK 465 ASP B 86 REMARK 465 LEU B 87 REMARK 465 THR B 88 REMARK 465 GLN B 89 REMARK 465 HIS B 364 REMARK 465 GLU B 365 REMARK 465 LYS B 366 REMARK 465 ASN B 367 REMARK 465 GLU B 368 REMARK 465 ASP B 369 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 174 CG CD OE1 OE2 REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 ARG A 331 NH1 NH2 REMARK 470 ASP A 333 OD1 OD2 REMARK 470 GLN A 335 CD OE1 NE2 REMARK 470 LYS A 358 CE NZ REMARK 470 ASP A 360 CG OD1 OD2 REMARK 470 GLU B 71 OE1 OE2 REMARK 470 ARG B 91 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 92 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 174 CG CD OE1 OE2 REMARK 470 LYS B 178 NZ REMARK 470 LYS B 200 CE NZ REMARK 470 LYS B 212 NZ REMARK 470 LYS B 226 CE NZ REMARK 470 LYS B 274 CG CD CE NZ REMARK 470 GLN B 335 OE1 NE2 REMARK 470 LYS B 358 CD CE NZ 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 PHE A 54 -135.55 51.04 REMARK 500 SER A 233 80.59 -160.68 REMARK 500 ALA A 235 52.70 -106.47 REMARK 500 THR A 354 -91.89 -127.43 REMARK 500 PHE B 54 -136.43 50.52 REMARK 500 SER B 233 79.71 -162.30 REMARK 500 ALA B 235 53.01 -97.96 REMARK 500 ASN B 252 77.17 -154.71 REMARK 500 THR B 354 -92.97 -124.63 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 NAD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GC7 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GC7 B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5V2E RELATED DB: PDB REMARK 900 RELATED ID: 5V4J RELATED DB: PDB DBREF 6P4V A 1 369 UNP P49366 DHYS_HUMAN 1 369 DBREF 6P4V B 1 369 UNP P49366 DHYS_HUMAN 1 369 SEQADV 6P4V GLY A -2 UNP P49366 EXPRESSION TAG SEQADV 6P4V GLY A -1 UNP P49366 EXPRESSION TAG SEQADV 6P4V SER A 0 UNP P49366 EXPRESSION TAG SEQADV 6P4V GLY B -2 UNP P49366 EXPRESSION TAG SEQADV 6P4V GLY B -1 UNP P49366 EXPRESSION TAG SEQADV 6P4V SER B 0 UNP P49366 EXPRESSION TAG SEQRES 1 A 372 GLY GLY SER MET GLU GLY SER LEU GLU ARG GLU ALA PRO SEQRES 2 A 372 ALA GLY ALA LEU ALA ALA VAL LEU LYS HIS SER SER THR SEQRES 3 A 372 LEU PRO PRO GLU SER THR GLN VAL ARG GLY TYR ASP PHE SEQRES 4 A 372 ASN ARG GLY VAL ASN TYR ARG ALA LEU LEU GLU ALA PHE SEQRES 5 A 372 GLY THR THR GLY PHE GLN ALA THR ASN PHE GLY ARG ALA SEQRES 6 A 372 VAL GLN GLN VAL ASN ALA MET ILE GLU LYS LYS LEU GLU SEQRES 7 A 372 PRO LEU SER GLN ASP GLU ASP GLN HIS ALA ASP LEU THR SEQRES 8 A 372 GLN SER ARG ARG PRO LEU THR SER CYS THR ILE PHE LEU SEQRES 9 A 372 GLY TYR THR SER ASN LEU ILE SER SER GLY ILE ARG GLU SEQRES 10 A 372 THR ILE ARG TYR LEU VAL GLN HIS ASN MET VAL ASP VAL SEQRES 11 A 372 LEU VAL THR THR ALA GLY GLY VAL GLU GLU ASP LEU ILE SEQRES 12 A 372 LYS CYS LEU ALA PRO THR TYR LEU GLY GLU PHE SER LEU SEQRES 13 A 372 ARG GLY LYS GLU LEU ARG GLU ASN GLY ILE ASN ARG ILE SEQRES 14 A 372 GLY ASN LEU LEU VAL PRO ASN GLU ASN TYR CYS LYS PHE SEQRES 15 A 372 GLU ASP TRP LEU MET PRO ILE LEU ASP GLN MET VAL MET SEQRES 16 A 372 GLU GLN ASN THR GLU GLY VAL LYS TRP THR PRO SER LYS SEQRES 17 A 372 MET ILE ALA ARG LEU GLY LYS GLU ILE ASN ASN PRO GLU SEQRES 18 A 372 SER VAL TYR TYR TRP ALA GLN LYS ASN HIS ILE PRO VAL SEQRES 19 A 372 PHE SER PRO ALA LEU THR ASP GLY SER LEU GLY ASP MET SEQRES 20 A 372 ILE PHE PHE HIS SER TYR LYS ASN PRO GLY LEU VAL LEU SEQRES 21 A 372 ASP ILE VAL GLU ASP LEU ARG LEU ILE ASN THR GLN ALA SEQRES 22 A 372 ILE PHE ALA LYS CYS THR GLY MET ILE ILE LEU GLY GLY SEQRES 23 A 372 GLY VAL VAL LYS HIS HIS ILE ALA ASN ALA ASN LEU MET SEQRES 24 A 372 ARG ASN GLY ALA ASP TYR ALA VAL TYR ILE ASN THR ALA SEQRES 25 A 372 GLN GLU PHE ASP GLY SER ASP SER GLY ALA ARG PRO ASP SEQRES 26 A 372 GLU ALA VAL SER TRP GLY LYS ILE ARG VAL ASP ALA GLN SEQRES 27 A 372 PRO VAL LYS VAL TYR ALA ASP ALA SER LEU VAL PHE PRO SEQRES 28 A 372 LEU LEU VAL ALA GLU THR PHE ALA GLN LYS MET ASP ALA SEQRES 29 A 372 PHE MET HIS GLU LYS ASN GLU ASP SEQRES 1 B 372 GLY GLY SER MET GLU GLY SER LEU GLU ARG GLU ALA PRO SEQRES 2 B 372 ALA GLY ALA LEU ALA ALA VAL LEU LYS HIS SER SER THR SEQRES 3 B 372 LEU PRO PRO GLU SER THR GLN VAL ARG GLY TYR ASP PHE SEQRES 4 B 372 ASN ARG GLY VAL ASN TYR ARG ALA LEU LEU GLU ALA PHE SEQRES 5 B 372 GLY THR THR GLY PHE GLN ALA THR ASN PHE GLY ARG ALA SEQRES 6 B 372 VAL GLN GLN VAL ASN ALA MET ILE GLU LYS LYS LEU GLU SEQRES 7 B 372 PRO LEU SER GLN ASP GLU ASP GLN HIS ALA ASP LEU THR SEQRES 8 B 372 GLN SER ARG ARG PRO LEU THR SER CYS THR ILE PHE LEU SEQRES 9 B 372 GLY TYR THR SER ASN LEU ILE SER SER GLY ILE ARG GLU SEQRES 10 B 372 THR ILE ARG TYR LEU VAL GLN HIS ASN MET VAL ASP VAL SEQRES 11 B 372 LEU VAL THR THR ALA GLY GLY VAL GLU GLU ASP LEU ILE SEQRES 12 B 372 LYS CYS LEU ALA PRO THR TYR LEU GLY GLU PHE SER LEU SEQRES 13 B 372 ARG GLY LYS GLU LEU ARG GLU ASN GLY ILE ASN ARG ILE SEQRES 14 B 372 GLY ASN LEU LEU VAL PRO ASN GLU ASN TYR CYS LYS PHE SEQRES 15 B 372 GLU ASP TRP LEU MET PRO ILE LEU ASP GLN MET VAL MET SEQRES 16 B 372 GLU GLN ASN THR GLU GLY VAL LYS TRP THR PRO SER LYS SEQRES 17 B 372 MET ILE ALA ARG LEU GLY LYS GLU ILE ASN ASN PRO GLU SEQRES 18 B 372 SER VAL TYR TYR TRP ALA GLN LYS ASN HIS ILE PRO VAL SEQRES 19 B 372 PHE SER PRO ALA LEU THR ASP GLY SER LEU GLY ASP MET SEQRES 20 B 372 ILE PHE PHE HIS SER TYR LYS ASN PRO GLY LEU VAL LEU SEQRES 21 B 372 ASP ILE VAL GLU ASP LEU ARG LEU ILE ASN THR GLN ALA SEQRES 22 B 372 ILE PHE ALA LYS CYS THR GLY MET ILE ILE LEU GLY GLY SEQRES 23 B 372 GLY VAL VAL LYS HIS HIS ILE ALA ASN ALA ASN LEU MET SEQRES 24 B 372 ARG ASN GLY ALA ASP TYR ALA VAL TYR ILE ASN THR ALA SEQRES 25 B 372 GLN GLU PHE ASP GLY SER ASP SER GLY ALA ARG PRO ASP SEQRES 26 B 372 GLU ALA VAL SER TRP GLY LYS ILE ARG VAL ASP ALA GLN SEQRES 27 B 372 PRO VAL LYS VAL TYR ALA ASP ALA SER LEU VAL PHE PRO SEQRES 28 B 372 LEU LEU VAL ALA GLU THR PHE ALA GLN LYS MET ASP ALA SEQRES 29 B 372 PHE MET HIS GLU LYS ASN GLU ASP HET NAD A 501 44 HET GC7 A 502 12 HET MPD A 503 8 HET NAD B 501 44 HET GC7 B 502 12 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM GC7 1-GUANIDINIUM-7-AMINOHEPTANE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 GC7 2(C8 H22 N4) FORMUL 5 MPD C6 H14 O2 FORMUL 8 HOH *326(H2 O) HELIX 1 AA1 ASP A 35 GLY A 39 5 5 HELIX 2 AA2 ASN A 41 ALA A 48 1 8 HELIX 3 AA3 PHE A 49 THR A 52 5 4 HELIX 4 AA4 GLY A 53 GLU A 75 1 23 HELIX 5 AA5 SER A 78 ASP A 86 1 9 HELIX 6 AA6 THR A 104 SER A 110 1 7 HELIX 7 AA7 GLY A 111 HIS A 122 1 12 HELIX 8 AA8 THR A 131 LYS A 141 1 11 HELIX 9 AA9 ARG A 154 ASN A 161 1 8 HELIX 10 AB1 ASN A 173 GLY A 198 1 26 HELIX 11 AB2 THR A 202 ASN A 215 1 14 HELIX 12 AB3 SER A 219 ASN A 227 1 9 HELIX 13 AB4 GLY A 239 ASN A 252 1 14 HELIX 14 AB5 ILE A 259 PHE A 272 1 14 HELIX 15 AB6 GLY A 284 MET A 296 1 13 HELIX 16 AB7 GLN A 310 GLY A 314 5 5 HELIX 17 AB8 ARG A 320 GLY A 328 1 9 HELIX 18 AB9 ASP A 342 THR A 354 1 13 HELIX 19 AC1 PHE A 355 MET A 363 5 9 HELIX 20 AC2 ASP B 35 GLY B 39 5 5 HELIX 21 AC3 ASN B 41 PHE B 49 1 9 HELIX 22 AC4 GLY B 50 THR B 52 5 3 HELIX 23 AC5 GLY B 53 LEU B 74 1 22 HELIX 24 AC6 THR B 104 SER B 110 1 7 HELIX 25 AC7 GLY B 111 HIS B 122 1 12 HELIX 26 AC8 THR B 131 LYS B 141 1 11 HELIX 27 AC9 ARG B 154 ASN B 161 1 8 HELIX 28 AD1 ASN B 173 GLY B 198 1 26 HELIX 29 AD2 THR B 202 ASN B 215 1 14 HELIX 30 AD3 SER B 219 ASN B 227 1 9 HELIX 31 AD4 GLY B 239 ASN B 252 1 14 HELIX 32 AD5 ILE B 259 PHE B 272 1 14 HELIX 33 AD6 GLY B 284 MET B 296 1 13 HELIX 34 AD7 GLN B 310 GLY B 314 5 5 HELIX 35 AD8 ARG B 320 GLY B 328 1 9 HELIX 36 AD9 ASP B 342 THR B 354 1 13 HELIX 37 AE1 PHE B 355 MET B 359 5 5 SHEET 1 AA1 6 VAL A 231 PHE A 232 0 SHEET 2 AA1 6 VAL A 127 THR A 130 1 N LEU A 128 O PHE A 232 SHEET 3 AA1 6 THR A 98 TYR A 103 1 N LEU A 101 O VAL A 127 SHEET 4 AA1 6 THR A 276 LEU A 281 1 O LEU A 281 N GLY A 102 SHEET 5 AA1 6 TYR A 302 ASN A 307 1 O ILE A 306 N ILE A 280 SHEET 6 AA1 6 VAL A 337 TYR A 340 1 O VAL A 339 N TYR A 305 SHEET 1 AA2 3 TYR A 147 LEU A 148 0 SHEET 2 AA2 3 LEU A 169 PRO A 172 -1 O LEU A 170 N TYR A 147 SHEET 3 AA2 3 ILE A 163 ILE A 166 -1 N ASN A 164 O VAL A 171 SHEET 1 AA3 6 VAL B 231 PHE B 232 0 SHEET 2 AA3 6 VAL B 127 THR B 130 1 N LEU B 128 O PHE B 232 SHEET 3 AA3 6 THR B 98 TYR B 103 1 N LEU B 101 O VAL B 127 SHEET 4 AA3 6 THR B 276 LEU B 281 1 O LEU B 281 N GLY B 102 SHEET 5 AA3 6 TYR B 302 ASN B 307 1 O ILE B 306 N ILE B 280 SHEET 6 AA3 6 VAL B 337 TYR B 340 1 O VAL B 339 N TYR B 305 SHEET 1 AA4 3 TYR B 147 LEU B 148 0 SHEET 2 AA4 3 LEU B 169 PRO B 172 -1 O LEU B 170 N TYR B 147 SHEET 3 AA4 3 ILE B 163 ILE B 166 -1 N ASN B 164 O VAL B 171 SITE 1 AC1 32 THR A 104 SER A 105 ASN A 106 LEU A 107 SITE 2 AC1 32 SER A 109 THR A 131 ALA A 132 GLY A 133 SITE 3 AC1 32 GLU A 136 GLU A 137 ASP A 238 GLY A 282 SITE 4 AC1 32 GLY A 283 ASN A 307 THR A 308 ALA A 309 SITE 5 AC1 32 ALA A 341 ASP A 342 ALA A 343 HOH A 611 SITE 6 AC1 32 HOH A 617 HOH A 692 GLY B 284 VAL B 285 SITE 7 AC1 32 HIS B 288 ASP B 313 SER B 315 ASP B 316 SITE 8 AC1 32 SER B 317 NAD B 501 GC7 B 502 HOH B 718 SITE 1 AC2 14 HIS A 288 ASN A 292 LEU A 295 GLY A 314 SITE 2 AC2 14 SER A 315 ASP A 316 GLU A 323 TRP A 327 SITE 3 AC2 14 LYS A 329 HOH A 725 ILE B 166 GLY B 167 SITE 4 AC2 14 ASP B 243 NAD B 501 SITE 1 AC3 6 ARG A 38 GLY A 39 VAL A 40 THR A 268 SITE 2 AC3 6 HOH A 713 TYR B 250 SITE 1 AC4 32 GLY A 284 VAL A 285 HIS A 288 ASP A 313 SITE 2 AC4 32 SER A 315 ASP A 316 SER A 317 NAD A 501 SITE 3 AC4 32 GC7 A 502 THR B 104 SER B 105 ASN B 106 SITE 4 AC4 32 LEU B 107 SER B 109 THR B 131 ALA B 132 SITE 5 AC4 32 GLY B 133 GLU B 136 GLU B 137 ASP B 238 SITE 6 AC4 32 GLY B 282 GLY B 283 ASN B 307 THR B 308 SITE 7 AC4 32 ALA B 309 ALA B 341 ASP B 342 ALA B 343 SITE 8 AC4 32 HOH B 602 HOH B 612 HOH B 668 HOH B 718 SITE 1 AC5 14 ILE A 166 GLY A 167 ASP A 243 NAD A 501 SITE 2 AC5 14 HIS B 288 ASN B 292 LEU B 295 GLY B 314 SITE 3 AC5 14 SER B 315 ASP B 316 GLU B 323 TRP B 327 SITE 4 AC5 14 LYS B 329 HOH B 715 CRYST1 104.466 104.466 159.490 90.00 90.00 120.00 P 32 2 1 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 0.009572 0.005527 0.000000 0.00000 SCALE2 0.000000 0.011053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006270 0.00000