HEADER OXIDOREDUCTASE 13-MAR-00 1EL3 TITLE HUMAN ALDOSE REDUCTASE COMPLEXED WITH IDD384 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDOSE REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.21; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: PLACENTA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS ALDOSE REDUCTASE, INHIBITION, DIABETES, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.PODJARNY REVDAT 5 03-APR-24 1EL3 1 REMARK REVDAT 4 07-FEB-24 1EL3 1 REMARK REVDAT 3 24-FEB-09 1EL3 1 VERSN REVDAT 2 01-APR-03 1EL3 1 JRNL REVDAT 1 10-MAY-00 1EL3 0 JRNL AUTH V.CALDERONE,B.CHEVRIER,M.VAN ZANDT,V.LAMOUR,E.HOWARD, JRNL AUTH 2 A.POTERSZMAN,P.BARTH,A.MITSCHLER,J.LU,D.M.DVORNIK,G.KLEBE, JRNL AUTH 3 O.KRAEMER,A.R.MOORMAN,D.MORAS,A.PODJARNY JRNL TITL THE STRUCTURE OF HUMAN ALDOSE REDUCTASE BOUND TO THE JRNL TITL 2 INHIBITOR IDD384. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 536 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 10771421 JRNL DOI 10.1107/S0907444900002341 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10466377.080 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 32736 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 SET) : 0.165 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3271 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3559 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE : 0.2250 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 371 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2525 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 239 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.80 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.290 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.040 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.490 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.760 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP_PARAM REMARK 3 PARAMETER FILE 2 : NADP.PARAM REMARK 3 PARAMETER FILE 3 : I0384.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX_PLUS.PRO REMARK 3 TOPOLOGY FILE 2 : NADP.TOPOL REMARK 3 TOPOLOGY FILE 3 : I0384.TOPOL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EL3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010695. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 5.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33072 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 14.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 1.500 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : 0.04700 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) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.0 REMARK 200 DATA REDUNDANCY IN SHELL : 1.40 REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : 0.17000 REMARK 200 FOR SHELL : 5.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: ALDOSE REDUCTASE NATIVE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15 MG/ML AR, 5% PEG 6000, 50 MM REMARK 280 AMMONIUM CITRATE PH 5.0 (DROP), 20% PEG 6000, 120 MM AMMONIUM REMARK 280 CITRATE PH 5.0 (RESERVOIR), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277.0K 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 33.60500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 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 GLU A 126 -11.89 -47.21 REMARK 500 ASP A 134 31.32 -86.15 REMARK 500 PRO A 222 -29.90 -26.78 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 209 0.08 SIDE CHAIN 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 NAP A 318 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE I84 A 320 DBREF 1EL3 A 1A 315 UNP P15121 ALDR_HUMAN 1 316 SEQRES 1 A 316 MET ALA SER ARG LEU LEU LEU ASN ASN GLY ALA LYS MET SEQRES 2 A 316 PRO ILE LEU GLY LEU GLY THR TRP LYS SER PRO PRO GLY SEQRES 3 A 316 GLN VAL THR GLU ALA VAL LYS VAL ALA ILE ASP VAL GLY SEQRES 4 A 316 TYR ARG HIS ILE ASP CYS ALA HIS VAL TYR GLN ASN GLU SEQRES 5 A 316 ASN GLU VAL GLY VAL ALA ILE GLN GLU LYS LEU ARG GLU SEQRES 6 A 316 GLN VAL VAL LYS ARG GLU GLU LEU PHE ILE VAL SER LYS SEQRES 7 A 316 LEU TRP CYS THR TYR HIS GLU LYS GLY LEU VAL LYS GLY SEQRES 8 A 316 ALA CYS GLN LYS THR LEU SER ASP LEU LYS LEU ASP TYR SEQRES 9 A 316 LEU ASP LEU TYR LEU ILE HIS TRP PRO THR GLY PHE LYS SEQRES 10 A 316 PRO GLY LYS GLU PHE PHE PRO LEU ASP GLU SER GLY ASN SEQRES 11 A 316 VAL VAL PRO SER ASP THR ASN ILE LEU ASP THR TRP ALA SEQRES 12 A 316 ALA MET GLU GLU LEU VAL ASP GLU GLY LEU VAL LYS ALA SEQRES 13 A 316 ILE GLY ILE SER ASN PHE ASN HIS LEU GLN VAL GLU MET SEQRES 14 A 316 ILE LEU ASN LYS PRO GLY LEU LYS TYR LYS PRO ALA VAL SEQRES 15 A 316 ASN GLN ILE GLU CYS HIS PRO TYR LEU THR GLN GLU LYS SEQRES 16 A 316 LEU ILE GLN TYR CYS GLN SER LYS GLY ILE VAL VAL THR SEQRES 17 A 316 ALA TYR SER PRO LEU GLY SER PRO ASP ARG PRO TRP ALA SEQRES 18 A 316 LYS PRO GLU ASP PRO SER LEU LEU GLU ASP PRO ARG ILE SEQRES 19 A 316 LYS ALA ILE ALA ALA LYS HIS ASN LYS THR THR ALA GLN SEQRES 20 A 316 VAL LEU ILE ARG PHE PRO MET GLN ARG ASN LEU VAL VAL SEQRES 21 A 316 ILE PRO LYS SER VAL THR PRO GLU ARG ILE ALA GLU ASN SEQRES 22 A 316 PHE LYS VAL PHE ASP PHE GLU LEU SER SER GLN ASP MET SEQRES 23 A 316 THR THR LEU LEU SER TYR ASN ARG ASN TRP ARG VAL CYS SEQRES 24 A 316 ALA LEU LEU SER CYS THR SER HIS LYS ASP TYR PRO PHE SEQRES 25 A 316 HIS GLU GLU PHE HET NAP A 318 48 HET I84 A 320 27 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM I84 [2,6-DIMETHYL-4-(2-O-TOLYL-ACETYLAMINO)- HETNAM 2 I84 BENZENESULFONYL]-GLYCINE HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN I84 INHIBITOR IDD 384 FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 I84 C19 H22 N2 O5 S FORMUL 4 HOH *239(H2 O) HELIX 1 1 PRO A 23 GLY A 38 1 16 HELIX 2 2 ALA A 45 GLN A 49 5 5 HELIX 3 3 ASN A 50 GLU A 64 1 15 HELIX 4 4 LYS A 68 LEU A 72 5 5 HELIX 5 5 TRP A 79 HIS A 83 5 5 HELIX 6 6 LEU A 87 LYS A 100 1 14 HELIX 7 7 ASN A 136 GLU A 150 1 15 HELIX 8 8 ASN A 162 ASN A 171 1 10 HELIX 9 9 GLN A 192 LYS A 202 1 11 HELIX 10 10 SER A 226 GLU A 229 5 4 HELIX 11 11 ASP A 230 HIS A 240 1 11 HELIX 12 12 THR A 243 GLN A 254 1 12 HELIX 13 13 THR A 265 LYS A 274 1 10 HELIX 14 14 SER A 281 SER A 290 1 10 HELIX 15 15 LEU A 300 THR A 304 5 5 SHEET 1 A 2 ARG A 3 LEU A 5 0 SHEET 2 A 2 LYS A 11 PRO A 13 -1 O MET A 12 N LEU A 4 SHEET 1 B 8 LEU A 17 GLY A 18 0 SHEET 2 B 8 HIS A 41 ASP A 43 1 O HIS A 41 N LEU A 17 SHEET 3 B 8 PHE A 73 LEU A 78 1 O PHE A 73 N ILE A 42 SHEET 4 B 8 LEU A 106 ILE A 109 1 O LEU A 106 N SER A 76 SHEET 5 B 8 ILE A 156 SER A 159 1 N GLY A 157 O TYR A 107 SHEET 6 B 8 VAL A 181 GLU A 185 1 O VAL A 181 N ILE A 158 SHEET 7 B 8 VAL A 205 TYR A 209 1 O VAL A 205 N ASN A 182 SHEET 8 B 8 VAL A 258 VAL A 259 1 O VAL A 258 N ALA A 208 SITE 1 AC1 34 GLY A 18 THR A 19 TRP A 20 LYS A 21 SITE 2 AC1 34 ASP A 43 TYR A 48 HIS A 110 SER A 159 SITE 3 AC1 34 ASN A 160 GLN A 183 TYR A 209 SER A 210 SITE 4 AC1 34 PRO A 211 LEU A 212 GLY A 213 SER A 214 SITE 5 AC1 34 PRO A 215 ASP A 216 ALA A 245 ILE A 260 SITE 6 AC1 34 PRO A 261 LYS A 262 SER A 263 VAL A 264 SITE 7 AC1 34 THR A 265 ARG A 268 GLU A 271 ASN A 272 SITE 8 AC1 34 CYS A 298 I84 A 320 HOH A 646 HOH A 724 SITE 9 AC1 34 HOH A 726 HOH A 727 SITE 1 AC2 10 TRP A 20 VAL A 47 TYR A 48 TRP A 79 SITE 2 AC2 10 HIS A 110 TRP A 111 PRO A 218 TRP A 219 SITE 3 AC2 10 NAP A 318 HOH A 535 CRYST1 49.930 67.210 47.650 90.00 92.50 90.00 P 1 21 1 2 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 0.020028 0.000000 0.000874 0.00000 SCALE2 0.000000 0.014879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021006 0.00000