HEADER OXIDOREDUCTASE 12-JAN-20 6LPP TITLE CRYSTAL STRUCTURE OF HUMAN D-2-HYDROXYGLUTARATE DEHYDROGENASE IN TITLE 2 COMPLEX WITH D-2-HYDROXYGLUTARATE (D-2-HG) COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 EC: 1.1.99.-; 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 GENE: D2HGDH, D2HGD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEHYDROGENASE, FLAVOPROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.YANG,H.ZHU,J.DING REVDAT 3 29-NOV-23 6LPP 1 REMARK REVDAT 2 28-JUL-21 6LPP 1 JRNL REVDAT 1 13-JAN-21 6LPP 0 JRNL AUTH J.YANG,H.ZHU,T.ZHANG,J.DING JRNL TITL STRUCTURE, SUBSTRATE SPECIFICITY, AND CATALYTIC MECHANISM OF JRNL TITL 2 HUMAN D-2-HGDH AND INSIGHTS INTO PATHOGENICITY OF JRNL TITL 3 DISEASE-ASSOCIATED MUTATIONS. JRNL REF CELL DISCOV V. 7 3 2021 JRNL REFN ESSN 2056-5968 JRNL PMID 33431826 JRNL DOI 10.1038/S41421-020-00227-0 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 26610 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 1267 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 40.7800 - 5.4852 0.98 2846 165 0.2142 0.2436 REMARK 3 2 5.4852 - 4.3554 0.99 2863 138 0.1725 0.1942 REMARK 3 3 4.3554 - 3.8053 1.00 2854 133 0.1693 0.1952 REMARK 3 4 3.8053 - 3.4576 0.99 2814 157 0.1914 0.2556 REMARK 3 5 3.4576 - 3.2099 0.99 2877 99 0.2084 0.2862 REMARK 3 6 3.2099 - 3.0207 1.00 2840 145 0.2286 0.2469 REMARK 3 7 3.0207 - 2.8695 1.00 2845 161 0.2329 0.3243 REMARK 3 8 2.8695 - 2.7446 0.98 2790 139 0.2452 0.3282 REMARK 3 9 2.7446 - 2.6500 0.92 2614 130 0.2596 0.2924 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.68 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 6LPP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1300015251. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-MAR-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26662 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.639 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.10400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.37500 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: PHENIX REMARK 200 STARTING MODEL: 6LPN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS, PH 6.5, 25% (W/V) PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 47.29650 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9080 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31370 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 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 47 REMARK 465 PRO A 48 REMARK 465 GLY A 49 REMARK 465 SER A 50 REMARK 465 ARG A 51 REMARK 465 TYR A 52 REMARK 465 PRO A 53 REMARK 465 GLN A 520 REMARK 465 ALA A 521 REMARK 465 HIS A 522 REMARK 465 HIS A 523 REMARK 465 HIS A 524 REMARK 465 HIS A 525 REMARK 465 HIS A 526 REMARK 465 HIS A 527 REMARK 465 GLY B 47 REMARK 465 PRO B 48 REMARK 465 GLY B 49 REMARK 465 SER B 50 REMARK 465 ARG B 51 REMARK 465 TYR B 52 REMARK 465 GLN B 520 REMARK 465 ALA B 521 REMARK 465 HIS B 522 REMARK 465 HIS B 523 REMARK 465 HIS B 524 REMARK 465 HIS B 525 REMARK 465 HIS B 526 REMARK 465 HIS B 527 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 ARG A 55 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 64 CG CD CE NZ REMARK 470 ARG A 72 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 86 CG CD OE1 NE2 REMARK 470 ARG A 94 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 107 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 117 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 155 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 160 CG ND1 CD2 CE1 NE2 REMARK 470 SER A 161 OG REMARK 470 ARG A 179 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 183 CG CD OE1 OE2 REMARK 470 ASP A 185 CG OD1 OD2 REMARK 470 GLN A 294 CG CD OE1 NE2 REMARK 470 ARG A 323 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 332 CG CD OE1 NE2 REMARK 470 GLU A 333 CG CD OE1 OE2 REMARK 470 GLU A 359 CG CD OE1 OE2 REMARK 470 MET A 372 CG SD CE REMARK 470 ASP A 375 CG OD1 OD2 REMARK 470 GLN A 376 CG CD OE1 NE2 REMARK 470 ARG A 377 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 378 CG CD CE NZ REMARK 470 LYS A 380 CG CD CE NZ REMARK 470 MET A 381 CG SD CE REMARK 470 ARG A 395 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 447 CG CD OE1 OE2 REMARK 470 SER A 519 OG REMARK 470 PRO B 53 CG CD REMARK 470 ARG B 55 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 64 CG CD CE NZ REMARK 470 GLN B 65 CG CD OE1 NE2 REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 86 CG CD OE1 NE2 REMARK 470 ARG B 97 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 101 CG CD CE NZ REMARK 470 GLU B 121 CG CD OE1 OE2 REMARK 470 ARG B 179 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 183 CG CD OE1 OE2 REMARK 470 ARG B 323 CG CD NE CZ NH1 NH2 REMARK 470 GLN B 332 CG CD OE1 NE2 REMARK 470 GLN B 376 CG CD OE1 NE2 REMARK 470 ARG B 377 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 380 CG CD CE NZ REMARK 470 GLU B 391 CG CD OE1 OE2 REMARK 470 ARG B 395 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 481 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 490 CG 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 143 -111.22 -123.70 REMARK 500 LEU A 239 57.59 -91.55 REMARK 500 ASN A 246 51.29 -99.42 REMARK 500 THR A 247 67.99 -102.59 REMARK 500 GLU A 475 -51.30 -129.22 REMARK 500 SER B 60 -176.92 -69.90 REMARK 500 PHE B 143 -110.93 -113.10 REMARK 500 MET B 153 71.36 -100.42 REMARK 500 ASP B 245 97.68 -168.56 REMARK 500 ASN B 246 55.25 -104.80 REMARK 500 THR B 247 71.90 -104.93 REMARK 500 GLU B 475 -36.48 -133.69 REMARK 500 VAL B 478 -66.52 -104.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS B 515 THR B 516 -30.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 754 DISTANCE = 6.05 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 434 NE2 REMARK 620 2 HIS A 441 NE2 93.6 REMARK 620 3 GLU A 475 OE1 97.0 81.9 REMARK 620 4 2HG A 603 O1 99.6 92.1 162.7 REMARK 620 5 2HG A 603 O3 173.3 84.7 89.2 74.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 602 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 434 NE2 REMARK 620 2 HIS B 441 NE2 96.1 REMARK 620 3 GLU B 475 OE1 102.7 101.9 REMARK 620 4 2HG B 603 O1 93.4 90.7 158.2 REMARK 620 5 2HG B 603 O3 168.7 88.3 86.5 76.0 REMARK 620 N 1 2 3 4 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 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2HG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2HG B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 608 DBREF 6LPP A 51 521 UNP Q8N465 D2HDH_HUMAN 51 521 DBREF 6LPP B 51 521 UNP Q8N465 D2HDH_HUMAN 51 521 SEQADV 6LPP GLY A 47 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP PRO A 48 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP GLY A 49 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP SER A 50 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS A 522 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS A 523 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS A 524 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS A 525 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS A 526 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS A 527 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP GLY B 47 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP PRO B 48 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP GLY B 49 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP SER B 50 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS B 522 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS B 523 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS B 524 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS B 525 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS B 526 UNP Q8N465 EXPRESSION TAG SEQADV 6LPP HIS B 527 UNP Q8N465 EXPRESSION TAG SEQRES 1 A 481 GLY PRO GLY SER ARG TYR PRO VAL ARG ARG LEU PRO PHE SEQRES 2 A 481 SER THR VAL SER LYS GLN ASP LEU ALA ALA PHE GLU ARG SEQRES 3 A 481 ILE VAL PRO GLY GLY VAL VAL THR ASP PRO GLU ALA LEU SEQRES 4 A 481 GLN ALA PRO ASN VAL ASP TRP LEU ARG THR LEU ARG GLY SEQRES 5 A 481 CYS SER LYS VAL LEU LEU ARG PRO ARG THR SER GLU GLU SEQRES 6 A 481 VAL SER HIS ILE LEU ARG HIS CYS HIS GLU ARG ASN LEU SEQRES 7 A 481 ALA VAL ASN PRO GLN GLY GLY ASN THR GLY MET VAL GLY SEQRES 8 A 481 GLY SER VAL PRO VAL PHE ASP GLU ILE ILE LEU SER THR SEQRES 9 A 481 ALA ARG MET ASN ARG VAL LEU SER PHE HIS SER VAL SER SEQRES 10 A 481 GLY ILE LEU VAL CYS GLN ALA GLY CYS VAL LEU GLU GLU SEQRES 11 A 481 LEU SER ARG TYR VAL GLU GLU ARG ASP PHE ILE MET PRO SEQRES 12 A 481 LEU ASP LEU GLY ALA LYS GLY SER CYS HIS ILE GLY GLY SEQRES 13 A 481 ASN VAL ALA THR ASN ALA GLY GLY LEU ARG PHE LEU ARG SEQRES 14 A 481 TYR GLY SER LEU HIS GLY THR VAL LEU GLY LEU GLU VAL SEQRES 15 A 481 VAL LEU ALA ASP GLY THR VAL LEU ASP CYS LEU THR SER SEQRES 16 A 481 LEU ARG LYS ASP ASN THR GLY TYR ASP LEU LYS GLN LEU SEQRES 17 A 481 PHE ILE GLY SER GLU GLY THR LEU GLY ILE ILE THR THR SEQRES 18 A 481 VAL SER ILE LEU CYS PRO PRO LYS PRO ARG ALA VAL ASN SEQRES 19 A 481 VAL ALA PHE LEU GLY CYS PRO GLY PHE ALA GLU VAL LEU SEQRES 20 A 481 GLN THR PHE SER THR CYS LYS GLY MET LEU GLY GLU ILE SEQRES 21 A 481 LEU SER ALA PHE GLU PHE MET ASP ALA VAL CYS MET GLN SEQRES 22 A 481 LEU VAL GLY ARG HIS LEU HIS LEU ALA SER PRO VAL GLN SEQRES 23 A 481 GLU SER PRO PHE TYR VAL LEU ILE GLU THR SER GLY SER SEQRES 24 A 481 ASN ALA GLY HIS ASP ALA GLU LYS LEU GLY HIS PHE LEU SEQRES 25 A 481 GLU HIS ALA LEU GLY SER GLY LEU VAL THR ASP GLY THR SEQRES 26 A 481 MET ALA THR ASP GLN ARG LYS VAL LYS MET LEU TRP ALA SEQRES 27 A 481 LEU ARG GLU ARG ILE THR GLU ALA LEU SER ARG ASP GLY SEQRES 28 A 481 TYR VAL TYR LYS TYR ASP LEU SER LEU PRO VAL GLU ARG SEQRES 29 A 481 LEU TYR ASP ILE VAL THR ASP LEU ARG ALA ARG LEU GLY SEQRES 30 A 481 PRO HIS ALA LYS HIS VAL VAL GLY TYR GLY HIS LEU GLY SEQRES 31 A 481 ASP GLY ASN LEU HIS LEU ASN VAL THR ALA GLU ALA PHE SEQRES 32 A 481 SER PRO SER LEU LEU ALA ALA LEU GLU PRO HIS VAL TYR SEQRES 33 A 481 GLU TRP THR ALA GLY GLN GLN GLY SER VAL SER ALA GLU SEQRES 34 A 481 HIS GLY VAL GLY PHE ARG LYS ARG ASP VAL LEU GLY TYR SEQRES 35 A 481 SER LYS PRO PRO GLY ALA LEU GLN LEU MET GLN GLN LEU SEQRES 36 A 481 LYS ALA LEU LEU ASP PRO LYS GLY ILE LEU ASN PRO TYR SEQRES 37 A 481 LYS THR LEU PRO SER GLN ALA HIS HIS HIS HIS HIS HIS SEQRES 1 B 481 GLY PRO GLY SER ARG TYR PRO VAL ARG ARG LEU PRO PHE SEQRES 2 B 481 SER THR VAL SER LYS GLN ASP LEU ALA ALA PHE GLU ARG SEQRES 3 B 481 ILE VAL PRO GLY GLY VAL VAL THR ASP PRO GLU ALA LEU SEQRES 4 B 481 GLN ALA PRO ASN VAL ASP TRP LEU ARG THR LEU ARG GLY SEQRES 5 B 481 CYS SER LYS VAL LEU LEU ARG PRO ARG THR SER GLU GLU SEQRES 6 B 481 VAL SER HIS ILE LEU ARG HIS CYS HIS GLU ARG ASN LEU SEQRES 7 B 481 ALA VAL ASN PRO GLN GLY GLY ASN THR GLY MET VAL GLY SEQRES 8 B 481 GLY SER VAL PRO VAL PHE ASP GLU ILE ILE LEU SER THR SEQRES 9 B 481 ALA ARG MET ASN ARG VAL LEU SER PHE HIS SER VAL SER SEQRES 10 B 481 GLY ILE LEU VAL CYS GLN ALA GLY CYS VAL LEU GLU GLU SEQRES 11 B 481 LEU SER ARG TYR VAL GLU GLU ARG ASP PHE ILE MET PRO SEQRES 12 B 481 LEU ASP LEU GLY ALA LYS GLY SER CYS HIS ILE GLY GLY SEQRES 13 B 481 ASN VAL ALA THR ASN ALA GLY GLY LEU ARG PHE LEU ARG SEQRES 14 B 481 TYR GLY SER LEU HIS GLY THR VAL LEU GLY LEU GLU VAL SEQRES 15 B 481 VAL LEU ALA ASP GLY THR VAL LEU ASP CYS LEU THR SER SEQRES 16 B 481 LEU ARG LYS ASP ASN THR GLY TYR ASP LEU LYS GLN LEU SEQRES 17 B 481 PHE ILE GLY SER GLU GLY THR LEU GLY ILE ILE THR THR SEQRES 18 B 481 VAL SER ILE LEU CYS PRO PRO LYS PRO ARG ALA VAL ASN SEQRES 19 B 481 VAL ALA PHE LEU GLY CYS PRO GLY PHE ALA GLU VAL LEU SEQRES 20 B 481 GLN THR PHE SER THR CYS LYS GLY MET LEU GLY GLU ILE SEQRES 21 B 481 LEU SER ALA PHE GLU PHE MET ASP ALA VAL CYS MET GLN SEQRES 22 B 481 LEU VAL GLY ARG HIS LEU HIS LEU ALA SER PRO VAL GLN SEQRES 23 B 481 GLU SER PRO PHE TYR VAL LEU ILE GLU THR SER GLY SER SEQRES 24 B 481 ASN ALA GLY HIS ASP ALA GLU LYS LEU GLY HIS PHE LEU SEQRES 25 B 481 GLU HIS ALA LEU GLY SER GLY LEU VAL THR ASP GLY THR SEQRES 26 B 481 MET ALA THR ASP GLN ARG LYS VAL LYS MET LEU TRP ALA SEQRES 27 B 481 LEU ARG GLU ARG ILE THR GLU ALA LEU SER ARG ASP GLY SEQRES 28 B 481 TYR VAL TYR LYS TYR ASP LEU SER LEU PRO VAL GLU ARG SEQRES 29 B 481 LEU TYR ASP ILE VAL THR ASP LEU ARG ALA ARG LEU GLY SEQRES 30 B 481 PRO HIS ALA LYS HIS VAL VAL GLY TYR GLY HIS LEU GLY SEQRES 31 B 481 ASP GLY ASN LEU HIS LEU ASN VAL THR ALA GLU ALA PHE SEQRES 32 B 481 SER PRO SER LEU LEU ALA ALA LEU GLU PRO HIS VAL TYR SEQRES 33 B 481 GLU TRP THR ALA GLY GLN GLN GLY SER VAL SER ALA GLU SEQRES 34 B 481 HIS GLY VAL GLY PHE ARG LYS ARG ASP VAL LEU GLY TYR SEQRES 35 B 481 SER LYS PRO PRO GLY ALA LEU GLN LEU MET GLN GLN LEU SEQRES 36 B 481 LYS ALA LEU LEU ASP PRO LYS GLY ILE LEU ASN PRO TYR SEQRES 37 B 481 LYS THR LEU PRO SER GLN ALA HIS HIS HIS HIS HIS HIS HET FAD A 601 53 HET ZN A 602 1 HET 2HG A 603 10 HET GOL A 604 6 HET GOL A 605 6 HET FAD B 601 53 HET ZN B 602 1 HET 2HG B 603 10 HET GOL B 604 6 HET GOL B 605 6 HET GOL B 606 6 HET GOL B 607 6 HET GOL B 608 6 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM ZN ZINC ION HETNAM 2HG (2R)-2-HYDROXYPENTANEDIOIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 4 ZN 2(ZN 2+) FORMUL 5 2HG 2(C5 H8 O5) FORMUL 6 GOL 7(C3 H8 O3) FORMUL 16 HOH *103(H2 O) HELIX 1 AA1 SER A 63 VAL A 74 1 12 HELIX 2 AA2 LEU A 85 VAL A 90 1 6 HELIX 3 AA3 THR A 108 ASN A 123 1 16 HELIX 4 AA4 VAL A 173 ARG A 184 1 12 HELIX 5 AA5 HIS A 199 ASN A 207 1 9 HELIX 6 AA6 ARG A 212 GLY A 217 1 6 HELIX 7 AA7 SER A 218 THR A 222 1 5 HELIX 8 AA8 LEU A 251 ILE A 256 1 6 HELIX 9 AA9 GLY A 288 LEU A 303 1 16 HELIX 10 AB1 ALA A 315 HIS A 326 1 12 HELIX 11 AB2 ASN A 346 SER A 364 1 19 HELIX 12 AB3 ASP A 375 ARG A 388 1 14 HELIX 13 AB4 ARG A 388 ARG A 395 1 8 HELIX 14 AB5 PRO A 407 LEU A 411 5 5 HELIX 15 AB6 TYR A 412 GLY A 423 1 12 HELIX 16 AB7 PRO A 424 ALA A 426 5 3 HELIX 17 AB8 HIS A 434 ASP A 437 5 4 HELIX 18 AB9 SER A 450 GLU A 458 1 9 HELIX 19 AC1 PRO A 459 GLN A 468 1 10 HELIX 20 AC2 VAL A 485 SER A 489 5 5 HELIX 21 AC3 PRO A 491 ASP A 506 1 16 HELIX 22 AC4 SER B 63 VAL B 74 1 12 HELIX 23 AC5 ASP B 81 VAL B 90 1 10 HELIX 24 AC6 THR B 108 ASN B 123 1 16 HELIX 25 AC7 VAL B 173 ARG B 184 1 12 HELIX 26 AC8 LEU B 192 SER B 197 5 6 HELIX 27 AC9 HIS B 199 ASN B 207 1 9 HELIX 28 AD1 ARG B 212 GLY B 217 1 6 HELIX 29 AD2 SER B 218 THR B 222 1 5 HELIX 30 AD3 LEU B 251 ILE B 256 1 6 HELIX 31 AD4 GLY B 288 GLY B 304 1 17 HELIX 32 AD5 ALA B 315 HIS B 326 1 12 HELIX 33 AD6 ASN B 346 SER B 364 1 19 HELIX 34 AD7 ASP B 375 ARG B 388 1 14 HELIX 35 AD8 ARG B 388 GLY B 397 1 10 HELIX 36 AD9 PRO B 407 LEU B 411 5 5 HELIX 37 AE1 TYR B 412 LEU B 422 1 11 HELIX 38 AE2 HIS B 434 ASP B 437 5 4 HELIX 39 AE3 SER B 450 GLU B 458 1 9 HELIX 40 AE4 PRO B 459 GLN B 468 1 10 HELIX 41 AE5 VAL B 485 SER B 489 5 5 HELIX 42 AE6 PRO B 491 ASP B 506 1 16 SHEET 1 AA1 4 VAL A 78 VAL A 79 0 SHEET 2 AA1 4 LEU A 103 LEU A 104 -1 O LEU A 103 N VAL A 79 SHEET 3 AA1 4 ILE A 146 SER A 149 1 O ILE A 147 N LEU A 104 SHEET 4 AA1 4 VAL A 126 GLN A 129 1 N ASN A 127 O ILE A 146 SHEET 1 AA2 5 VAL A 156 PHE A 159 0 SHEET 2 AA2 5 ILE A 165 GLN A 169 -1 O VAL A 167 N SER A 158 SHEET 3 AA2 5 ILE A 264 LEU A 271 -1 O VAL A 268 N CYS A 168 SHEET 4 AA2 5 VAL A 223 VAL A 229 -1 N GLU A 227 O THR A 266 SHEET 5 AA2 5 VAL A 235 CYS A 238 -1 O LEU A 236 N VAL A 228 SHEET 1 AA3 7 ASP A 369 ALA A 373 0 SHEET 2 AA3 7 ALA A 278 CYS A 286 -1 N PHE A 283 O THR A 371 SHEET 3 AA3 7 PHE A 336 GLY A 344 -1 O VAL A 338 N LEU A 284 SHEET 4 AA3 7 LEU A 307 ASP A 314 -1 N SER A 308 O GLU A 341 SHEET 5 AA3 7 HIS A 428 GLY A 433 -1 O GLY A 433 N PHE A 312 SHEET 6 AA3 7 ASN A 439 ALA A 446 -1 O HIS A 441 N TYR A 432 SHEET 7 AA3 7 TYR A 398 SER A 405 -1 N TYR A 400 O VAL A 444 SHEET 1 AA4 4 VAL B 78 VAL B 79 0 SHEET 2 AA4 4 LEU B 103 LEU B 104 -1 O LEU B 103 N VAL B 79 SHEET 3 AA4 4 ILE B 146 SER B 149 1 O SER B 149 N LEU B 104 SHEET 4 AA4 4 VAL B 126 GLN B 129 1 N ASN B 127 O ILE B 146 SHEET 1 AA5 5 VAL B 156 PHE B 159 0 SHEET 2 AA5 5 ILE B 165 GLN B 169 -1 O VAL B 167 N SER B 158 SHEET 3 AA5 5 ILE B 264 LEU B 271 -1 O VAL B 268 N CYS B 168 SHEET 4 AA5 5 VAL B 223 VAL B 229 -1 N VAL B 229 O ILE B 264 SHEET 5 AA5 5 VAL B 235 CYS B 238 -1 O LEU B 236 N VAL B 228 SHEET 1 AA6 7 ASP B 369 ALA B 373 0 SHEET 2 AA6 7 ALA B 278 CYS B 286 -1 N GLY B 285 O ASP B 369 SHEET 3 AA6 7 PHE B 336 GLY B 344 -1 O ILE B 340 N ALA B 282 SHEET 4 AA6 7 LEU B 307 ASP B 314 -1 N SER B 308 O GLU B 341 SHEET 5 AA6 7 HIS B 428 GLY B 433 -1 O GLY B 433 N PHE B 312 SHEET 6 AA6 7 ASN B 439 ALA B 446 -1 O HIS B 441 N TYR B 432 SHEET 7 AA6 7 TYR B 398 SER B 405 -1 N TYR B 400 O VAL B 444 LINK NE2 HIS A 434 ZN ZN A 602 1555 1555 2.17 LINK NE2 HIS A 441 ZN ZN A 602 1555 1555 2.22 LINK OE1 GLU A 475 ZN ZN A 602 1555 1555 1.92 LINK ZN ZN A 602 O1 2HG A 603 1555 1555 2.26 LINK ZN ZN A 602 O3 2HG A 603 1555 1555 2.10 LINK NE2 HIS B 434 ZN ZN B 602 1555 1555 2.24 LINK NE2 HIS B 441 ZN ZN B 602 1555 1555 2.10 LINK OE1 GLU B 475 ZN ZN B 602 1555 1555 1.94 LINK ZN ZN B 602 O1 2HG B 603 1555 1555 2.01 LINK ZN ZN B 602 O3 2HG B 603 1555 1555 2.26 CISPEP 1 GLU A 458 PRO A 459 0 8.31 CISPEP 2 LYS A 515 THR A 516 0 -20.76 CISPEP 3 GLU B 458 PRO B 459 0 5.76 SITE 1 AC1 31 TRP A 92 PRO A 128 GLY A 130 GLY A 131 SITE 2 AC1 31 ASN A 132 THR A 133 GLY A 134 MET A 135 SITE 3 AC1 31 GLY A 138 SER A 139 LEU A 192 ALA A 194 SITE 4 AC1 31 CYS A 198 HIS A 199 GLY A 202 ASN A 203 SITE 5 AC1 31 ALA A 205 THR A 206 ALA A 208 GLY A 209 SITE 6 AC1 31 GLY A 210 GLU A 259 GLY A 260 ILE A 265 SITE 7 AC1 31 GLU A 475 HIS A 476 ASN A 512 ZN A 602 SITE 8 AC1 31 2HG A 603 HOH A 714 HOH A 736 SITE 1 AC2 5 HIS A 434 HIS A 441 GLU A 475 FAD A 601 SITE 2 AC2 5 2HG A 603 SITE 1 AC3 13 ARG A 386 THR A 390 LYS A 401 TYR A 432 SITE 2 AC3 13 HIS A 434 HIS A 441 ASN A 443 GLU A 475 SITE 3 AC3 13 HIS A 476 FAD A 601 ZN A 602 HOH A 706 SITE 4 AC3 13 HOH A 712 SITE 1 AC4 2 LYS A 427 HIS A 428 SITE 1 AC5 1 HIS A 118 SITE 1 AC6 33 TRP B 92 PRO B 128 GLY B 130 GLY B 131 SITE 2 AC6 33 ASN B 132 THR B 133 GLY B 134 MET B 135 SITE 3 AC6 33 GLY B 138 SER B 139 LEU B 192 ALA B 194 SITE 4 AC6 33 CYS B 198 HIS B 199 GLY B 202 ASN B 203 SITE 5 AC6 33 ALA B 205 THR B 206 ALA B 208 GLY B 209 SITE 6 AC6 33 GLY B 210 GLU B 259 GLY B 260 GLY B 263 SITE 7 AC6 33 ILE B 265 GLU B 475 HIS B 476 ASN B 512 SITE 8 AC6 33 ZN B 602 2HG B 603 HOH B 708 HOH B 716 SITE 9 AC6 33 HOH B 725 SITE 1 AC7 5 HIS B 434 HIS B 441 GLU B 475 FAD B 601 SITE 2 AC7 5 2HG B 603 SITE 1 AC8 12 ARG B 386 THR B 390 LYS B 401 TYR B 432 SITE 2 AC8 12 HIS B 434 HIS B 441 ASN B 443 GLU B 475 SITE 3 AC8 12 HIS B 476 FAD B 601 ZN B 602 HOH B 709 SITE 1 AC9 1 HIS B 120 SITE 1 AD1 7 ASP B 191 LYS B 195 ARG B 212 GLU B 341 SITE 2 AD1 7 TRP B 383 GLU B 387 GOL B 606 SITE 1 AD2 7 ILE B 187 ARG B 212 TYR B 216 PRO B 276 SITE 2 AD2 7 GLU B 341 SER B 343 GOL B 605 SITE 1 AD3 4 HIS B 425 SER B 450 SER B 452 LEU B 453 SITE 1 AD4 2 LYS B 427 HIS B 428 CRYST1 72.275 94.593 73.399 90.00 111.90 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 0.013836 0.000000 0.005561 0.00000 SCALE2 0.000000 0.010572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014684 0.00000