HEADER OXIDOREDUCTASE 11-NOV-19 6TE5 TITLE CRYSTAL STRUCTURE OF HUMAN ALDEHYDE DEHYDROGENASE 1A3 IN COMPLEX WITH TITLE 2 LQ43 INHIBITOR COMPOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDEHYDE DEHYDROGENASE FAMILY 1 MEMBER A3; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALDEHYDE DEHYDROGENASE 6,RETINALDEHYDE DEHYDROGENASE 3, COMPND 5 RALDH3; COMPND 6 EC: 1.2.1.36; COMPND 7 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: ALDH1A3, ALDH6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS DEHYDROGENASE ISOENZYME ALDH1A3 SELECTIVE INHIBITOR HIGH GRADE KEYWDS 2 GLIOMA, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR E.L.M.GELARDI,S.GARAVAGLIA REVDAT 3 24-JAN-24 6TE5 1 REMARK REVDAT 2 17-FEB-21 6TE5 1 AUTHOR JRNL REVDAT 1 18-NOV-20 6TE5 0 JRNL AUTH L.QUATTRINI,E.L.M.GELARDI,V.COVIELLO,S.SARTINI,D.M.FERRARIS, JRNL AUTH 2 M.MORI,I.NAKANO,S.GARAVAGLIA,C.LA MOTTA JRNL TITL IMIDAZO[1,2- A ]PYRIDINE DERIVATIVES AS ALDEHYDE JRNL TITL 2 DEHYDROGENASE INHIBITORS: NOVEL CHEMOTYPES TO TARGET JRNL TITL 3 GLIOBLASTOMA STEM CELLS. JRNL REF J.MED.CHEM. V. 63 4603 2020 JRNL REFN ISSN 0022-2623 JRNL PMID 32223240 JRNL DOI 10.1021/ACS.JMEDCHEM.9B01910 REMARK 2 REMARK 2 RESOLUTION. 3.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260-000 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.96 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18829 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105326. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.967 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.22 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18856 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.250 REMARK 200 RESOLUTION RANGE LOW (A) : 47.956 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) : 0.16800 REMARK 200 FOR THE DATA SET : 8.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.43 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.77200 REMARK 200 R SYM FOR SHELL (I) : 0.77200 REMARK 200 FOR SHELL : 1.000 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: 5FHZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE 2.4M PH 7.0, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,-Y,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 40.59200 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 79.60400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 40.59200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 79.60400 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 34100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 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 MET A 1 REMARK 465 ALA A 2 REMARK 465 THR A 3 REMARK 465 ALA A 4 REMARK 465 ASN A 5 REMARK 465 GLY A 6 REMARK 465 ALA A 7 REMARK 465 VAL A 8 REMARK 465 GLU A 9 REMARK 465 ASN A 10 REMARK 465 GLY A 11 REMARK 465 GLN A 12 REMARK 465 PRO A 13 REMARK 465 ASP A 14 REMARK 465 ARG A 15 REMARK 465 LYS A 16 REMARK 465 PRO A 17 REMARK 465 PRO A 18 REMARK 465 ALA A 19 REMARK 465 LEU A 20 REMARK 465 PRO A 21 REMARK 465 ARG A 22 REMARK 465 PRO A 23 REMARK 465 ASP A 509 REMARK 465 LYS A 510 REMARK 465 ASN A 511 REMARK 465 PRO A 512 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 THR B 3 REMARK 465 ALA B 4 REMARK 465 ASN B 5 REMARK 465 GLY B 6 REMARK 465 ALA B 7 REMARK 465 VAL B 8 REMARK 465 GLU B 9 REMARK 465 ASN B 10 REMARK 465 GLY B 11 REMARK 465 GLN B 12 REMARK 465 PRO B 13 REMARK 465 ASP B 14 REMARK 465 ARG B 15 REMARK 465 LYS B 16 REMARK 465 PRO B 17 REMARK 465 PRO B 18 REMARK 465 ALA B 19 REMARK 465 LEU B 20 REMARK 465 PRO B 21 REMARK 465 ARG B 22 REMARK 465 PRO B 23 REMARK 465 ILE B 24 REMARK 465 GLU B 387 REMARK 465 ASP B 388 REMARK 465 LYS B 389 REMARK 465 GLY B 390 REMARK 465 LEU B 391 REMARK 465 ASP B 509 REMARK 465 LYS B 510 REMARK 465 ASN B 511 REMARK 465 PRO B 512 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 ALA A 473 O LEU A 489 1.39 REMARK 500 O VAL A 500 NH2 ARG B 487 1.67 REMARK 500 O ALA B 473 O LEU B 489 1.92 REMARK 500 O ASN A 53 O THR A 56 1.96 REMARK 500 O PRO B 248 ND2 ASN B 273 1.97 REMARK 500 OE2 GLU B 324 NZ LYS B 421 1.98 REMARK 500 O HOH B 812 O HOH B 813 2.05 REMARK 500 N THR B 212 O HOH B 801 2.06 REMARK 500 N LEU A 185 O HOH A 701 2.15 REMARK 500 OD2 ASP A 110 OH TYR A 215 2.16 REMARK 500 N LEU B 211 O HOH B 801 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP B 363 N7N NAD A 601 3555 0.92 REMARK 500 OD1 ASP B 363 O7N NAD A 601 3555 2.00 REMARK 500 OG SER A 328 OE1 GLU B 324 1565 2.01 REMARK 500 OD2 ASP B 363 N7N NAD A 601 3555 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 PRO A 179 CD PRO A 179 N -0.195 REMARK 500 ARG A 341 C PRO A 342 N 0.158 REMARK 500 PRO B 157 N PRO B 157 CA 0.212 REMARK 500 PRO B 179 N PRO B 179 CA 0.186 REMARK 500 PRO B 179 CD PRO B 179 N -0.096 REMARK 500 LYS B 204 C PRO B 205 N 0.132 REMARK 500 PRO B 205 CD PRO B 205 N 0.395 REMARK 500 ASN B 285 C PRO B 286 N 0.156 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 PRO A 179 C - N - CD ANGL. DEV. = -16.0 DEGREES REMARK 500 PRO A 179 CA - N - CD ANGL. DEV. = 10.5 DEGREES REMARK 500 PRO A 179 N - CA - CB ANGL. DEV. = -8.8 DEGREES REMARK 500 LYS A 275 CB - CA - C ANGL. DEV. = -12.1 DEGREES REMARK 500 ASP A 294 N - CA - C ANGL. DEV. = -19.1 DEGREES REMARK 500 SER A 318 CB - CA - C ANGL. DEV. = -13.4 DEGREES REMARK 500 PRO A 342 C - N - CA ANGL. DEV. = 17.1 DEGREES REMARK 500 PRO A 342 C - N - CD ANGL. DEV. = -17.4 DEGREES REMARK 500 ASN A 404 N - CA - C ANGL. DEV. = -22.1 DEGREES REMARK 500 MET A 405 N - CA - CB ANGL. DEV. = 22.6 DEGREES REMARK 500 MET A 405 N - CA - C ANGL. DEV. = -22.4 DEGREES REMARK 500 LEU B 94 CA - CB - CG ANGL. DEV. = 14.9 DEGREES REMARK 500 PRO B 157 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 PRO B 157 CA - N - CD ANGL. DEV. = -10.4 DEGREES REMARK 500 ASP B 159 N - CA - CB ANGL. DEV. = 19.8 DEGREES REMARK 500 ASP B 159 N - CA - C ANGL. DEV. = -18.2 DEGREES REMARK 500 PRO B 179 C - N - CA ANGL. DEV. = 20.5 DEGREES REMARK 500 PRO B 179 C - N - CD ANGL. DEV. = -15.1 DEGREES REMARK 500 PRO B 205 C - N - CA ANGL. DEV. = 26.1 DEGREES REMARK 500 PRO B 205 CA - N - CD ANGL. DEV. = -19.8 DEGREES REMARK 500 PRO B 205 N - CA - CB ANGL. DEV. = 15.3 DEGREES REMARK 500 PRO B 286 C - N - CA ANGL. DEV. = 14.9 DEGREES REMARK 500 PRO B 286 C - N - CD ANGL. DEV. = -14.6 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 ARG A 25 -74.24 -112.68 REMARK 500 ASN A 26 59.34 -91.62 REMARK 500 ASP A 110 35.53 -85.01 REMARK 500 ILE A 132 -80.06 -111.33 REMARK 500 THR A 158 -59.66 -137.42 REMARK 500 HIS A 168 72.56 -109.04 REMARK 500 ASN A 273 -4.04 83.47 REMARK 500 LEU A 281 67.70 -151.33 REMARK 500 LYS A 284 58.60 -96.71 REMARK 500 THR A 315 37.66 -98.33 REMARK 500 LEU A 391 45.68 -95.46 REMARK 500 GLU A 400 28.89 41.13 REMARK 500 LYS A 423 -75.45 -108.67 REMARK 500 ALA A 470 77.20 -104.22 REMARK 500 LYS A 481 -130.58 54.37 REMARK 500 THR B 32 13.75 -146.84 REMARK 500 CYS B 52 -169.05 -118.99 REMARK 500 ASP B 110 35.75 -85.11 REMARK 500 ILE B 132 -71.10 -106.67 REMARK 500 THR B 158 -71.43 -130.76 REMARK 500 THR B 239 -71.23 -92.43 REMARK 500 ASN B 273 -10.76 80.39 REMARK 500 LEU B 281 -164.48 -126.60 REMARK 500 ILE B 357 -63.88 -95.07 REMARK 500 GLN B 359 -9.21 -58.42 REMARK 500 CYS B 381 142.92 -172.17 REMARK 500 SER B 384 -178.88 -173.30 REMARK 500 GLU B 400 16.02 49.04 REMARK 500 PHE B 413 58.17 -92.25 REMARK 500 LEU B 420 -168.86 -105.84 REMARK 500 ASN B 466 42.32 37.24 REMARK 500 LYS B 481 -122.57 51.60 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 N4Q A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N4Q B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide NAD A 601 and ASP B REMARK 800 363 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide NAD A 601 and ASP B REMARK 800 363 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6S6W RELATED DB: PDB DBREF 6TE5 A 1 512 UNP P47895 AL1A3_HUMAN 1 512 DBREF 6TE5 B 1 512 UNP P47895 AL1A3_HUMAN 1 512 SEQRES 1 A 512 MET ALA THR ALA ASN GLY ALA VAL GLU ASN GLY GLN PRO SEQRES 2 A 512 ASP ARG LYS PRO PRO ALA LEU PRO ARG PRO ILE ARG ASN SEQRES 3 A 512 LEU GLU VAL LYS PHE THR LYS ILE PHE ILE ASN ASN GLU SEQRES 4 A 512 TRP HIS GLU SER LYS SER GLY LYS LYS PHE ALA THR CYS SEQRES 5 A 512 ASN PRO SER THR ARG GLU GLN ILE CYS GLU VAL GLU GLU SEQRES 6 A 512 GLY ASP LYS PRO ASP VAL ASP LYS ALA VAL GLU ALA ALA SEQRES 7 A 512 GLN VAL ALA PHE GLN ARG GLY SER PRO TRP ARG ARG LEU SEQRES 8 A 512 ASP ALA LEU SER ARG GLY ARG LEU LEU HIS GLN LEU ALA SEQRES 9 A 512 ASP LEU VAL GLU ARG ASP ARG ALA THR LEU ALA ALA LEU SEQRES 10 A 512 GLU THR MET ASP THR GLY LYS PRO PHE LEU HIS ALA PHE SEQRES 11 A 512 PHE ILE ASP LEU GLU GLY CYS ILE ARG THR LEU ARG TYR SEQRES 12 A 512 PHE ALA GLY TRP ALA ASP LYS ILE GLN GLY LYS THR ILE SEQRES 13 A 512 PRO THR ASP ASP ASN VAL VAL CYS PHE THR ARG HIS GLU SEQRES 14 A 512 PRO ILE GLY VAL CYS GLY ALA ILE THR PRO TRP ASN PHE SEQRES 15 A 512 PRO LEU LEU MET LEU VAL TRP LYS LEU ALA PRO ALA LEU SEQRES 16 A 512 CYS CYS GLY ASN THR MET VAL LEU LYS PRO ALA GLU GLN SEQRES 17 A 512 THR PRO LEU THR ALA LEU TYR LEU GLY SER LEU ILE LYS SEQRES 18 A 512 GLU ALA GLY PHE PRO PRO GLY VAL VAL ASN ILE VAL PRO SEQRES 19 A 512 GLY PHE GLY PRO THR VAL GLY ALA ALA ILE SER SER HIS SEQRES 20 A 512 PRO GLN ILE ASN LYS ILE ALA PHE THR GLY SER THR GLU SEQRES 21 A 512 VAL GLY LYS LEU VAL LYS GLU ALA ALA SER ARG SER ASN SEQRES 22 A 512 LEU LYS ARG VAL THR LEU GLU LEU GLY GLY LYS ASN PRO SEQRES 23 A 512 CYS ILE VAL CYS ALA ASP ALA ASP LEU ASP LEU ALA VAL SEQRES 24 A 512 GLU CYS ALA HIS GLN GLY VAL PHE PHE ASN GLN GLY GLN SEQRES 25 A 512 CYS CYS THR ALA ALA SER ARG VAL PHE VAL GLU GLU GLN SEQRES 26 A 512 VAL TYR SER GLU PHE VAL ARG ARG SER VAL GLU TYR ALA SEQRES 27 A 512 LYS LYS ARG PRO VAL GLY ASP PRO PHE ASP VAL LYS THR SEQRES 28 A 512 GLU GLN GLY PRO GLN ILE ASP GLN LYS GLN PHE ASP LYS SEQRES 29 A 512 ILE LEU GLU LEU ILE GLU SER GLY LYS LYS GLU GLY ALA SEQRES 30 A 512 LYS LEU GLU CYS GLY GLY SER ALA MET GLU ASP LYS GLY SEQRES 31 A 512 LEU PHE ILE LYS PRO THR VAL PHE SER GLU VAL THR ASP SEQRES 32 A 512 ASN MET ARG ILE ALA LYS GLU GLU ILE PHE GLY PRO VAL SEQRES 33 A 512 GLN PRO ILE LEU LYS PHE LYS SER ILE GLU GLU VAL ILE SEQRES 34 A 512 LYS ARG ALA ASN SER THR ASP TYR GLY LEU THR ALA ALA SEQRES 35 A 512 VAL PHE THR LYS ASN LEU ASP LYS ALA LEU LYS LEU ALA SEQRES 36 A 512 SER ALA LEU GLU SER GLY THR VAL TRP ILE ASN CYS TYR SEQRES 37 A 512 ASN ALA LEU TYR ALA GLN ALA PRO PHE GLY GLY PHE LYS SEQRES 38 A 512 MET SER GLY ASN GLY ARG GLU LEU GLY GLU TYR ALA LEU SEQRES 39 A 512 ALA GLU TYR THR GLU VAL LYS THR VAL THR ILE LYS LEU SEQRES 40 A 512 GLY ASP LYS ASN PRO SEQRES 1 B 512 MET ALA THR ALA ASN GLY ALA VAL GLU ASN GLY GLN PRO SEQRES 2 B 512 ASP ARG LYS PRO PRO ALA LEU PRO ARG PRO ILE ARG ASN SEQRES 3 B 512 LEU GLU VAL LYS PHE THR LYS ILE PHE ILE ASN ASN GLU SEQRES 4 B 512 TRP HIS GLU SER LYS SER GLY LYS LYS PHE ALA THR CYS SEQRES 5 B 512 ASN PRO SER THR ARG GLU GLN ILE CYS GLU VAL GLU GLU SEQRES 6 B 512 GLY ASP LYS PRO ASP VAL ASP LYS ALA VAL GLU ALA ALA SEQRES 7 B 512 GLN VAL ALA PHE GLN ARG GLY SER PRO TRP ARG ARG LEU SEQRES 8 B 512 ASP ALA LEU SER ARG GLY ARG LEU LEU HIS GLN LEU ALA SEQRES 9 B 512 ASP LEU VAL GLU ARG ASP ARG ALA THR LEU ALA ALA LEU SEQRES 10 B 512 GLU THR MET ASP THR GLY LYS PRO PHE LEU HIS ALA PHE SEQRES 11 B 512 PHE ILE ASP LEU GLU GLY CYS ILE ARG THR LEU ARG TYR SEQRES 12 B 512 PHE ALA GLY TRP ALA ASP LYS ILE GLN GLY LYS THR ILE SEQRES 13 B 512 PRO THR ASP ASP ASN VAL VAL CYS PHE THR ARG HIS GLU SEQRES 14 B 512 PRO ILE GLY VAL CYS GLY ALA ILE THR PRO TRP ASN PHE SEQRES 15 B 512 PRO LEU LEU MET LEU VAL TRP LYS LEU ALA PRO ALA LEU SEQRES 16 B 512 CYS CYS GLY ASN THR MET VAL LEU LYS PRO ALA GLU GLN SEQRES 17 B 512 THR PRO LEU THR ALA LEU TYR LEU GLY SER LEU ILE LYS SEQRES 18 B 512 GLU ALA GLY PHE PRO PRO GLY VAL VAL ASN ILE VAL PRO SEQRES 19 B 512 GLY PHE GLY PRO THR VAL GLY ALA ALA ILE SER SER HIS SEQRES 20 B 512 PRO GLN ILE ASN LYS ILE ALA PHE THR GLY SER THR GLU SEQRES 21 B 512 VAL GLY LYS LEU VAL LYS GLU ALA ALA SER ARG SER ASN SEQRES 22 B 512 LEU LYS ARG VAL THR LEU GLU LEU GLY GLY LYS ASN PRO SEQRES 23 B 512 CYS ILE VAL CYS ALA ASP ALA ASP LEU ASP LEU ALA VAL SEQRES 24 B 512 GLU CYS ALA HIS GLN GLY VAL PHE PHE ASN GLN GLY GLN SEQRES 25 B 512 CYS CYS THR ALA ALA SER ARG VAL PHE VAL GLU GLU GLN SEQRES 26 B 512 VAL TYR SER GLU PHE VAL ARG ARG SER VAL GLU TYR ALA SEQRES 27 B 512 LYS LYS ARG PRO VAL GLY ASP PRO PHE ASP VAL LYS THR SEQRES 28 B 512 GLU GLN GLY PRO GLN ILE ASP GLN LYS GLN PHE ASP LYS SEQRES 29 B 512 ILE LEU GLU LEU ILE GLU SER GLY LYS LYS GLU GLY ALA SEQRES 30 B 512 LYS LEU GLU CYS GLY GLY SER ALA MET GLU ASP LYS GLY SEQRES 31 B 512 LEU PHE ILE LYS PRO THR VAL PHE SER GLU VAL THR ASP SEQRES 32 B 512 ASN MET ARG ILE ALA LYS GLU GLU ILE PHE GLY PRO VAL SEQRES 33 B 512 GLN PRO ILE LEU LYS PHE LYS SER ILE GLU GLU VAL ILE SEQRES 34 B 512 LYS ARG ALA ASN SER THR ASP TYR GLY LEU THR ALA ALA SEQRES 35 B 512 VAL PHE THR LYS ASN LEU ASP LYS ALA LEU LYS LEU ALA SEQRES 36 B 512 SER ALA LEU GLU SER GLY THR VAL TRP ILE ASN CYS TYR SEQRES 37 B 512 ASN ALA LEU TYR ALA GLN ALA PRO PHE GLY GLY PHE LYS SEQRES 38 B 512 MET SER GLY ASN GLY ARG GLU LEU GLY GLU TYR ALA LEU SEQRES 39 B 512 ALA GLU TYR THR GLU VAL LYS THR VAL THR ILE LYS LEU SEQRES 40 B 512 GLY ASP LYS ASN PRO HET NAD A 601 44 HET N4Q A 602 27 HET GOL A 603 6 HET NAD B 701 44 HET N4Q B 702 27 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM N4Q 6-(3,5-DIMETHOXYPHENYL)-2-(4-METHOXYPHENYL)IMIDAZO[1,2- HETNAM 2 N4Q A]PYRIDINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 N4Q 2(C22 H20 N2 O3) FORMUL 5 GOL C3 H8 O3 FORMUL 8 HOH *20(H2 O) HELIX 1 AA1 ASP A 67 PHE A 82 1 16 HELIX 2 AA2 ASP A 92 ASP A 110 1 19 HELIX 3 AA3 ASP A 110 GLY A 123 1 14 HELIX 4 AA4 PRO A 125 ILE A 132 1 8 HELIX 5 AA5 ILE A 132 ALA A 148 1 17 HELIX 6 AA6 ASP A 149 ILE A 151 5 3 HELIX 7 AA7 PHE A 182 CYS A 197 1 16 HELIX 8 AA8 PRO A 210 ALA A 223 1 14 HELIX 9 AA9 THR A 239 HIS A 247 1 9 HELIX 10 AB1 SER A 258 SER A 272 1 15 HELIX 11 AB2 ASP A 294 PHE A 308 1 15 HELIX 12 AB3 ASN A 309 GLN A 312 5 4 HELIX 13 AB4 GLU A 324 ARG A 341 1 18 HELIX 14 AB5 ASP A 358 GLU A 375 1 18 HELIX 15 AB6 SER A 424 ASN A 433 1 10 HELIX 16 AB7 ASN A 447 LEU A 458 1 12 HELIX 17 AB8 PHE A 480 MET A 482 5 3 HELIX 18 AB9 TYR A 492 TYR A 497 1 6 HELIX 19 AC1 ASP B 67 GLN B 83 1 17 HELIX 20 AC2 SER B 86 LEU B 91 1 6 HELIX 21 AC3 ASP B 92 ASP B 110 1 19 HELIX 22 AC4 ASP B 110 GLY B 123 1 14 HELIX 23 AC5 PRO B 125 ILE B 132 1 8 HELIX 24 AC6 ILE B 132 ALA B 148 1 17 HELIX 25 AC7 PHE B 182 CYS B 197 1 16 HELIX 26 AC8 PRO B 210 GLY B 224 1 15 HELIX 27 AC9 THR B 239 SER B 246 1 8 HELIX 28 AD1 SER B 258 SER B 272 1 15 HELIX 29 AD2 ASP B 294 GLY B 305 1 12 HELIX 30 AD3 PHE B 307 GLN B 312 5 6 HELIX 31 AD4 VAL B 326 LYS B 340 1 15 HELIX 32 AD5 ASP B 358 GLU B 375 1 18 HELIX 33 AD6 MET B 405 GLU B 410 1 6 HELIX 34 AD7 SER B 424 SER B 434 1 11 HELIX 35 AD8 ASN B 447 LEU B 458 1 12 HELIX 36 AD9 PHE B 480 MET B 482 5 3 HELIX 37 AE1 TYR B 492 THR B 498 5 7 SHEET 1 AA1 2 ILE A 34 ILE A 36 0 SHEET 2 AA1 2 GLU A 39 HIS A 41 -1 O GLU A 39 N ILE A 36 SHEET 1 AA2 2 LYS A 48 ASN A 53 0 SHEET 2 AA2 2 GLU A 58 GLU A 64 -1 O VAL A 63 N PHE A 49 SHEET 1 AA3 9 VAL A 162 PRO A 170 0 SHEET 2 AA3 9 THR A 498 LYS A 506 -1 O VAL A 503 N PHE A 165 SHEET 3 AA3 9 THR B 462 ILE B 465 1 O VAL B 463 N THR A 502 SHEET 4 AA3 9 THR B 440 PHE B 444 1 N ALA B 441 O TRP B 464 SHEET 5 AA3 9 CYS B 287 VAL B 289 1 N ILE B 288 O ALA B 442 SHEET 6 AA3 9 VAL B 320 GLU B 323 1 O PHE B 321 N VAL B 289 SHEET 7 AA3 9 VAL B 416 PHE B 422 1 O LEU B 420 N VAL B 320 SHEET 8 AA3 9 THR B 396 PHE B 398 1 N PHE B 398 O ILE B 419 SHEET 9 AA3 9 LEU B 379 CYS B 381 -1 N GLU B 380 O VAL B 397 SHEET 1 AA4 6 VAL A 230 ILE A 232 0 SHEET 2 AA4 6 THR A 200 LYS A 204 1 N LEU A 203 O ASN A 231 SHEET 3 AA4 6 VAL A 173 ILE A 177 1 N CYS A 174 O THR A 200 SHEET 4 AA4 6 LYS A 252 THR A 256 1 O LYS A 252 N GLY A 175 SHEET 5 AA4 6 ARG A 276 GLU A 280 1 O ARG A 276 N ILE A 253 SHEET 6 AA4 6 GLY A 484 ASN A 485 -1 O ASN A 485 N LEU A 279 SHEET 1 AA5 9 THR A 396 PHE A 398 0 SHEET 2 AA5 9 VAL A 416 PHE A 422 1 O GLN A 417 N PHE A 398 SHEET 3 AA5 9 ARG A 319 GLU A 323 1 N VAL A 320 O LEU A 420 SHEET 4 AA5 9 PRO A 286 VAL A 289 1 N VAL A 289 O PHE A 321 SHEET 5 AA5 9 THR A 440 PHE A 444 1 O ALA A 442 N ILE A 288 SHEET 6 AA5 9 THR A 462 ILE A 465 1 O TRP A 464 N ALA A 441 SHEET 7 AA5 9 GLU B 499 LYS B 506 1 O THR B 502 N VAL A 463 SHEET 8 AA5 9 VAL B 162 GLU B 169 -1 N VAL B 163 O ILE B 505 SHEET 9 AA5 9 THR B 155 ILE B 156 -1 N ILE B 156 O CYS B 164 SHEET 1 AA6 2 ILE B 34 ILE B 36 0 SHEET 2 AA6 2 GLU B 39 HIS B 41 -1 O HIS B 41 N ILE B 34 SHEET 1 AA7 2 LYS B 48 PHE B 49 0 SHEET 2 AA7 2 VAL B 63 GLU B 64 -1 O VAL B 63 N PHE B 49 SHEET 1 AA8 6 VAL B 230 ILE B 232 0 SHEET 2 AA8 6 THR B 200 LYS B 204 1 N LEU B 203 O ASN B 231 SHEET 3 AA8 6 VAL B 173 ILE B 177 1 N CYS B 174 O THR B 200 SHEET 4 AA8 6 LYS B 252 THR B 256 1 O LYS B 252 N GLY B 175 SHEET 5 AA8 6 ARG B 276 GLU B 280 1 O ARG B 276 N ILE B 253 SHEET 6 AA8 6 GLY B 484 ASN B 485 -1 O ASN B 485 N LEU B 279 LINK NZ LYS A 204 O2B NAD A 601 1555 1555 1.38 LINK N7N NAD A 601 CG ASP B 363 3555 1555 1.41 LINK C7N NAD A 601 OD1 ASP B 363 3555 1555 1.37 SITE 1 AC1 3 GLY A 136 THR A 140 TRP A 189 SITE 1 AC2 4 LYS A 266 VAL A 277 LYS B 266 VAL B 277 SITE 1 AC3 19 LYS A 47 LYS A 48 GLU A 65 ILE B 177 SITE 2 AC3 19 THR B 178 PRO B 179 TRP B 180 LYS B 204 SITE 3 AC3 19 GLU B 207 GLY B 237 GLY B 241 ALA B 242 SITE 4 AC3 19 PHE B 255 SER B 258 VAL B 261 LEU B 264 SITE 5 AC3 19 GLN B 361 LYS B 364 HOH B 806 SITE 1 AC4 7 GLU B 135 GLY B 136 THR B 140 TRP B 189 SITE 2 AC4 7 ASN B 469 LEU B 471 ALA B 473 SITE 1 AC5 34 ILE A 177 THR A 178 TRP A 180 LYS A 204 SITE 2 AC5 34 ALA A 206 GLU A 207 GLN A 208 PHE A 236 SITE 3 AC5 34 GLY A 237 GLY A 241 ALA A 242 PHE A 255 SITE 4 AC5 34 GLY A 257 SER A 258 VAL A 261 VAL A 265 SITE 5 AC5 34 ASP A 358 GLN A 359 GLN A 361 PHE A 362 SITE 6 AC5 34 LYS A 364 ILE A 365 LEU A 366 GLU A 367 SITE 7 AC5 34 ARG B 57 GLN B 359 LYS B 360 GLN B 361 SITE 8 AC5 34 PHE B 362 LYS B 364 ILE B 365 LEU B 366 SITE 9 AC5 34 GLU B 367 SER B 384 SITE 1 AC6 34 ILE A 177 THR A 178 TRP A 180 LYS A 204 SITE 2 AC6 34 ALA A 206 GLU A 207 GLN A 208 PHE A 236 SITE 3 AC6 34 GLY A 237 GLY A 241 ALA A 242 PHE A 255 SITE 4 AC6 34 GLY A 257 SER A 258 VAL A 261 VAL A 265 SITE 5 AC6 34 ASP A 358 GLN A 359 GLN A 361 PHE A 362 SITE 6 AC6 34 LYS A 364 ILE A 365 LEU A 366 GLU A 367 SITE 7 AC6 34 ARG B 57 GLN B 359 LYS B 360 GLN B 361 SITE 8 AC6 34 PHE B 362 LYS B 364 ILE B 365 LEU B 366 SITE 9 AC6 34 GLU B 367 SER B 384 CRYST1 81.184 89.338 159.208 90.00 90.00 90.00 P 21 2 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 0.012318 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011193 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006281 0.00000