HEADER OXIDOREDUCTASE 02-DEC-22 8FD8 TITLE HUMAN 15-PGDH WITH NADH BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: 15-HYDROXYPROSTAGLANDIN DEHYDROGENASE [NAD(+)]; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 15-PGDH,EICOSANOID/DOCOSANOID DEHYDROGENASE [NAD(+)], COMPND 5 PROSTAGLANDIN DEHYDROGENASE 1,SHORT CHAIN DEHYDROGENASE/REDUCTASE COMPND 6 FAMILY 36C MEMBER 1; COMPND 7 EC: 1.1.1.141,1.1.1.-,1.1.1.232; COMPND 8 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: HPGD, PGDH1, SDR36C1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS DEHYDROGENASE, INHIBITOR, OXIDOREDUCTASE, OXIDOREDUCTASE-INHIBITOR KEYWDS 2 COMPLEX EXPDTA ELECTRON MICROSCOPY AUTHOR W.HUANG,D.TAYLOR REVDAT 2 19-JUN-24 8FD8 1 REMARK REVDAT 1 08-MAR-23 8FD8 0 JRNL AUTH W.HUANG,H.LI,J.KISELAR,S.P.FINK,S.REGMI,A.DAY,Y.YUAN, JRNL AUTH 2 M.CHANCE,J.M.READY,S.D.MARKOWITZ,D.J.TAYLOR JRNL TITL SMALL MOLECULE INHIBITORS OF 15-PGDH EXPLOIT A PHYSIOLOGIC JRNL TITL 2 INDUCED-FIT CLOSING SYSTEM. JRNL REF NAT COMMUN V. 14 784 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 36774348 JRNL DOI 10.1038/S41467-023-36463-7 REMARK 2 REMARK 2 RESOLUTION. 3.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : NULL REMARK 3 RECONSTRUCTION SCHEMA : NULL REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : NULL REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 3.300 REMARK 3 NUMBER OF PARTICLES : 267049 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 8FD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1000270428. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT; POINT; POINT; POINT REMARK 245 NAME OF SAMPLE : HUMAN 15-PGDH IN COMPLEX WITH REMARK 245 INHIBITOR REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : NULL REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOQUANTUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 250.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 108.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. 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 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 ASN A 187 REMARK 465 THR A 188 REMARK 465 ALA A 189 REMARK 465 ILE A 190 REMARK 465 LEU A 191 REMARK 465 GLU A 192 REMARK 465 SER A 193 REMARK 465 ILE A 194 REMARK 465 GLU A 195 REMARK 465 LYS A 196 REMARK 465 GLU A 197 REMARK 465 GLU A 198 REMARK 465 ASN A 199 REMARK 465 MET A 200 REMARK 465 GLY A 201 REMARK 465 GLN A 202 REMARK 465 TYR A 203 REMARK 465 ILE A 204 REMARK 465 GLU A 205 REMARK 465 TYR A 206 REMARK 465 LYS A 207 REMARK 465 ASP A 208 REMARK 465 HIS A 209 REMARK 465 ILE A 210 REMARK 465 LYS A 211 REMARK 465 ASP A 212 REMARK 465 MET A 213 REMARK 465 ILE A 214 REMARK 465 LYS A 215 REMARK 465 TYR A 216 REMARK 465 TYR A 217 REMARK 465 GLY A 218 REMARK 465 ILE A 219 REMARK 465 PHE B 185 REMARK 465 VAL B 186 REMARK 465 ASN B 187 REMARK 465 THR B 188 REMARK 465 ALA B 189 REMARK 465 ILE B 190 REMARK 465 LEU B 191 REMARK 465 GLU B 192 REMARK 465 SER B 193 REMARK 465 ILE B 194 REMARK 465 GLU B 195 REMARK 465 LYS B 196 REMARK 465 GLU B 197 REMARK 465 GLU B 198 REMARK 465 ASN B 199 REMARK 465 MET B 200 REMARK 465 GLY B 201 REMARK 465 GLN B 202 REMARK 465 TYR B 203 REMARK 465 ILE B 204 REMARK 465 GLU B 205 REMARK 465 TYR B 206 REMARK 465 LYS B 207 REMARK 465 ASP B 208 REMARK 465 HIS B 209 REMARK 465 ILE B 210 REMARK 465 LYS B 211 REMARK 465 ASP B 212 REMARK 465 MET B 213 REMARK 465 ILE B 214 REMARK 465 LYS B 215 REMARK 465 TYR B 216 REMARK 465 TYR B 217 REMARK 465 GLY B 218 REMARK 465 ILE B 219 REMARK 465 LEU B 220 REMARK 465 ASP B 221 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 GLU A 40 NE2 GLN A 44 2.04 REMARK 500 NE2 GLN A 125 O ASN A 173 2.10 REMARK 500 O GLU B 40 NE2 GLN B 44 2.12 REMARK 500 OG SER B 123 OG SER B 174 2.16 REMARK 500 O VAL B 65 OG SER B 110 2.19 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 LEU A 85 133.75 -170.17 REMARK 500 SER A 137 -166.93 -126.67 REMARK 500 ASN A 173 61.28 61.76 REMARK 500 THR A 247 49.34 -91.02 REMARK 500 CYS B 63 118.65 -162.31 REMARK 500 ALA B 66 -15.56 -140.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-29005 RELATED DB: EMDB REMARK 900 HUMAN 15-PGDH WITH NADH BOUND DBREF 8FD8 A 1 256 UNP P15428 PGDH_HUMAN 1 256 DBREF 8FD8 B 1 256 UNP P15428 PGDH_HUMAN 1 256 SEQRES 1 A 256 MET HIS VAL ASN GLY LYS VAL ALA LEU VAL THR GLY ALA SEQRES 2 A 256 ALA GLN GLY ILE GLY ARG ALA PHE ALA GLU ALA LEU LEU SEQRES 3 A 256 LEU LYS GLY ALA LYS VAL ALA LEU VAL ASP TRP ASN LEU SEQRES 4 A 256 GLU ALA GLY VAL GLN CYS LYS ALA ALA LEU ASP GLU GLN SEQRES 5 A 256 PHE GLU PRO GLN LYS THR LEU PHE ILE GLN CYS ASP VAL SEQRES 6 A 256 ALA ASP GLN GLN GLN LEU ARG ASP THR PHE ARG LYS VAL SEQRES 7 A 256 VAL ASP HIS PHE GLY ARG LEU ASP ILE LEU VAL ASN ASN SEQRES 8 A 256 ALA GLY VAL ASN ASN GLU LYS ASN TRP GLU LYS THR LEU SEQRES 9 A 256 GLN ILE ASN LEU VAL SER VAL ILE SER GLY THR TYR LEU SEQRES 10 A 256 GLY LEU ASP TYR MET SER LYS GLN ASN GLY GLY GLU GLY SEQRES 11 A 256 GLY ILE ILE ILE ASN MET SER SER LEU ALA GLY LEU MET SEQRES 12 A 256 PRO VAL ALA GLN GLN PRO VAL TYR CYS ALA SER LYS HIS SEQRES 13 A 256 GLY ILE VAL GLY PHE THR ARG SER ALA ALA LEU ALA ALA SEQRES 14 A 256 ASN LEU MET ASN SER GLY VAL ARG LEU ASN ALA ILE CYS SEQRES 15 A 256 PRO GLY PHE VAL ASN THR ALA ILE LEU GLU SER ILE GLU SEQRES 16 A 256 LYS GLU GLU ASN MET GLY GLN TYR ILE GLU TYR LYS ASP SEQRES 17 A 256 HIS ILE LYS ASP MET ILE LYS TYR TYR GLY ILE LEU ASP SEQRES 18 A 256 PRO PRO LEU ILE ALA ASN GLY LEU ILE THR LEU ILE GLU SEQRES 19 A 256 ASP ASP ALA LEU ASN GLY ALA ILE MET LYS ILE THR THR SEQRES 20 A 256 SER LYS GLY ILE HIS PHE GLN ASP TYR SEQRES 1 B 256 MET HIS VAL ASN GLY LYS VAL ALA LEU VAL THR GLY ALA SEQRES 2 B 256 ALA GLN GLY ILE GLY ARG ALA PHE ALA GLU ALA LEU LEU SEQRES 3 B 256 LEU LYS GLY ALA LYS VAL ALA LEU VAL ASP TRP ASN LEU SEQRES 4 B 256 GLU ALA GLY VAL GLN CYS LYS ALA ALA LEU ASP GLU GLN SEQRES 5 B 256 PHE GLU PRO GLN LYS THR LEU PHE ILE GLN CYS ASP VAL SEQRES 6 B 256 ALA ASP GLN GLN GLN LEU ARG ASP THR PHE ARG LYS VAL SEQRES 7 B 256 VAL ASP HIS PHE GLY ARG LEU ASP ILE LEU VAL ASN ASN SEQRES 8 B 256 ALA GLY VAL ASN ASN GLU LYS ASN TRP GLU LYS THR LEU SEQRES 9 B 256 GLN ILE ASN LEU VAL SER VAL ILE SER GLY THR TYR LEU SEQRES 10 B 256 GLY LEU ASP TYR MET SER LYS GLN ASN GLY GLY GLU GLY SEQRES 11 B 256 GLY ILE ILE ILE ASN MET SER SER LEU ALA GLY LEU MET SEQRES 12 B 256 PRO VAL ALA GLN GLN PRO VAL TYR CYS ALA SER LYS HIS SEQRES 13 B 256 GLY ILE VAL GLY PHE THR ARG SER ALA ALA LEU ALA ALA SEQRES 14 B 256 ASN LEU MET ASN SER GLY VAL ARG LEU ASN ALA ILE CYS SEQRES 15 B 256 PRO GLY PHE VAL ASN THR ALA ILE LEU GLU SER ILE GLU SEQRES 16 B 256 LYS GLU GLU ASN MET GLY GLN TYR ILE GLU TYR LYS ASP SEQRES 17 B 256 HIS ILE LYS ASP MET ILE LYS TYR TYR GLY ILE LEU ASP SEQRES 18 B 256 PRO PRO LEU ILE ALA ASN GLY LEU ILE THR LEU ILE GLU SEQRES 19 B 256 ASP ASP ALA LEU ASN GLY ALA ILE MET LYS ILE THR THR SEQRES 20 B 256 SER LYS GLY ILE HIS PHE GLN ASP TYR HET NAI A 300 44 HET NAI B 300 44 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETSYN NAI NADH FORMUL 3 NAI 2(C21 H29 N7 O14 P2) HELIX 1 AA1 GLN A 15 LYS A 28 1 14 HELIX 2 AA2 ASN A 38 GLU A 51 1 14 HELIX 3 AA3 GLU A 54 GLN A 56 5 3 HELIX 4 AA4 ASP A 67 GLY A 83 1 17 HELIX 5 AA5 ASN A 99 LEU A 108 1 10 HELIX 6 AA6 LEU A 108 SER A 123 1 16 HELIX 7 AA7 LYS A 124 GLY A 127 5 4 HELIX 8 AA8 SER A 138 LEU A 142 5 5 HELIX 9 AA9 GLN A 148 MET A 172 1 25 HELIX 10 AB1 PRO A 222 ASP A 235 1 14 HELIX 11 AB2 GLY B 16 LYS B 28 1 13 HELIX 12 AB3 ASN B 38 GLU B 51 1 14 HELIX 13 AB4 GLN B 52 PHE B 53 5 2 HELIX 14 AB5 GLU B 54 GLN B 56 5 3 HELIX 15 AB6 ASP B 67 GLY B 83 1 17 HELIX 16 AB7 ASN B 99 LEU B 108 1 10 HELIX 17 AB8 LEU B 108 SER B 123 1 16 HELIX 18 AB9 LYS B 124 GLY B 127 5 4 HELIX 19 AC1 SER B 138 LEU B 142 5 5 HELIX 20 AC2 GLN B 148 ASN B 173 1 26 HELIX 21 AC3 PRO B 223 GLU B 234 1 12 SHEET 1 AA1 8 THR A 58 GLN A 62 0 SHEET 2 AA1 8 LYS A 31 ASP A 36 1 N LEU A 34 O LEU A 59 SHEET 3 AA1 8 VAL A 7 THR A 11 1 N ALA A 8 O LYS A 31 SHEET 4 AA1 8 ILE A 87 ASN A 90 1 O VAL A 89 N THR A 11 SHEET 5 AA1 8 ILE A 132 MET A 136 1 O ILE A 134 N ASN A 90 SHEET 6 AA1 8 ARG A 177 CYS A 182 1 O ILE A 181 N ASN A 135 SHEET 7 AA1 8 ILE A 242 THR A 246 1 O MET A 243 N CYS A 182 SHEET 8 AA1 8 GLY A 250 PHE A 253 -1 O HIS A 252 N LYS A 244 SHEET 1 AA2 8 THR B 58 ILE B 61 0 SHEET 2 AA2 8 LYS B 31 VAL B 35 1 N VAL B 32 O LEU B 59 SHEET 3 AA2 8 VAL B 7 THR B 11 1 N VAL B 10 O VAL B 35 SHEET 4 AA2 8 ILE B 87 ASN B 90 1 O VAL B 89 N LEU B 9 SHEET 5 AA2 8 ILE B 132 MET B 136 1 O MET B 136 N ASN B 90 SHEET 6 AA2 8 LEU B 178 ILE B 181 1 O ILE B 181 N ASN B 135 SHEET 7 AA2 8 ILE B 242 THR B 246 1 O MET B 243 N ALA B 180 SHEET 8 AA2 8 GLY B 250 PHE B 253 -1 O HIS B 252 N LYS B 244 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000