HEADER OXIDOREDUCTASE 15-MAY-23 8JDQ TITLE CRYSTAL STRUCTURE OF H405A MLDHD IN COMPLEX WITH D-2-HYDROXYISOCAPROIC TITLE 2 ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE D-LACTATE DEHYDROGENASE, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DLD,LACTATE DEHYDROGENASE D; COMPND 5 EC: 1.1.2.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: LDHD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS D-LACTATE DEHYDROGENASE, LDHD, 2-HYDROXYACID, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.JIN,X.CHEN,J.YANG,J.DING REVDAT 2 21-FEB-24 8JDQ 1 JRNL REVDAT 1 18-OCT-23 8JDQ 0 JRNL AUTH S.JIN,X.CHEN,J.YANG,J.DING JRNL TITL LACTATE DEHYDROGENASE D IS A GENERAL DEHYDROGENASE FOR JRNL TITL 2 D-2-HYDROXYACIDS AND IS ASSOCIATED WITH D-LACTIC ACIDOSIS. JRNL REF NAT COMMUN V. 14 6638 2023 JRNL REFN ESSN 2041-1723 JRNL PMID 37863926 JRNL DOI 10.1038/S41467-023-42456-3 REMARK 2 REMARK 2 RESOLUTION. 1.39 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.39 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 97877 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 4911 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 30.6200 - 4.3200 1.00 3451 205 0.1605 0.1638 REMARK 3 2 4.3200 - 3.4300 1.00 3329 188 0.1488 0.1763 REMARK 3 3 3.4300 - 2.9900 1.00 3351 147 0.1633 0.1702 REMARK 3 4 2.9900 - 2.7200 1.00 3297 172 0.1832 0.1976 REMARK 3 5 2.7200 - 2.5300 1.00 3301 187 0.1817 0.2091 REMARK 3 6 2.5300 - 2.3800 1.00 3288 157 0.1752 0.1869 REMARK 3 7 2.3800 - 2.2600 1.00 3281 163 0.1662 0.1844 REMARK 3 8 2.2600 - 2.1600 1.00 3279 176 0.1655 0.1635 REMARK 3 9 2.1600 - 2.0800 1.00 3249 190 0.1619 0.1864 REMARK 3 10 2.0800 - 2.0000 1.00 3240 194 0.1643 0.2138 REMARK 3 11 2.0000 - 1.9400 1.00 3267 167 0.1825 0.2068 REMARK 3 12 1.9400 - 1.8900 1.00 3265 156 0.1796 0.1997 REMARK 3 13 1.8900 - 1.8400 1.00 3252 181 0.1848 0.2188 REMARK 3 14 1.8400 - 1.7900 1.00 3245 181 0.1839 0.2082 REMARK 3 15 1.7900 - 1.7500 1.00 3280 154 0.1857 0.1970 REMARK 3 16 1.7500 - 1.7100 1.00 3241 179 0.1798 0.1912 REMARK 3 17 1.7100 - 1.6800 1.00 3240 177 0.1838 0.2055 REMARK 3 18 1.6800 - 1.6500 1.00 3281 153 0.1845 0.2079 REMARK 3 19 1.6500 - 1.6200 1.00 3216 183 0.1807 0.1841 REMARK 3 20 1.6200 - 1.5900 1.00 3250 170 0.1802 0.2056 REMARK 3 21 1.5900 - 1.5700 1.00 3235 160 0.1847 0.2170 REMARK 3 22 1.5700 - 1.5400 1.00 3234 175 0.1965 0.2094 REMARK 3 23 1.5400 - 1.5200 0.97 3139 178 0.1977 0.2252 REMARK 3 24 1.5200 - 1.5000 0.91 2980 122 0.2107 0.2013 REMARK 3 25 1.5000 - 1.4800 0.87 2817 143 0.2087 0.2514 REMARK 3 26 1.4800 - 1.4600 0.82 2642 150 0.2219 0.2456 REMARK 3 27 1.4600 - 1.4400 0.78 2555 140 0.2315 0.2284 REMARK 3 28 1.4400 - 1.4200 0.74 2382 126 0.2429 0.2636 REMARK 3 29 1.4200 - 1.4100 0.71 2286 122 0.2538 0.2789 REMARK 3 30 1.4100 - 1.3900 0.65 2093 115 0.2659 0.3115 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.005 3562 REMARK 3 ANGLE : 1.032 4855 REMARK 3 CHIRALITY : 0.085 556 REMARK 3 PLANARITY : 0.006 634 REMARK 3 DIHEDRAL : 11.071 493 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 8JDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAY-23. REMARK 100 THE DEPOSITION ID IS D_1300037690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JAN-23 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 : 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) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 97883 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.390 REMARK 200 RESOLUTION RANGE LOW (A) : 31.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 11.60 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.39 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.43 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.82400 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4.0 M SODIUM FORMATE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 40.66000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.50500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.23500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.66000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.50500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 61.23500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.66000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.50500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 61.23500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.66000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.50500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 61.23500 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 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 A 961 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1022 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1023 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1041 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1056 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 TRP A 14 REMARK 465 SER A 15 REMARK 465 HIS A 16 REMARK 465 PRO A 17 REMARK 465 GLN A 18 REMARK 465 PHE A 19 REMARK 465 GLU A 20 REMARK 465 LYS A 21 REMARK 465 GLY A 22 REMARK 465 SER A 23 REMARK 465 GLN A 24 REMARK 465 GLY A 25 REMARK 465 GLY A 26 REMARK 465 LYS A 335 REMARK 465 GLU A 336 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 HOH A 613 O HOH A 916 2.07 REMARK 500 OE2 GLU A 320 O HOH A 601 2.10 REMARK 500 O HOH A 886 O HOH A 899 2.11 REMARK 500 O HOH A 932 O HOH A 954 2.11 REMARK 500 O HOH A 667 O HOH A 899 2.12 REMARK 500 O THR A 145 NH1 ARG A 148 2.13 REMARK 500 O HOH A 813 O HOH A 924 2.15 REMARK 500 O HOH A 861 O HOH A 879 2.16 REMARK 500 O HOH A 719 O HOH A 977 2.16 REMARK 500 O HOH A 613 O HOH A 819 2.18 REMARK 500 O HOH A 637 O HOH A 950 2.19 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 O HOH A 722 O HOH A 816 2665 2.08 REMARK 500 O HOH A 619 O HOH A 619 4565 2.13 REMARK 500 O HOH A 623 O HOH A 875 2665 2.15 REMARK 500 O HOH A 703 O HOH A 912 2665 2.16 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 LYS A 362 CD - CE - NZ ANGL. DEV. = -18.2 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 ASP A 57 -139.14 -122.85 REMARK 500 ASP A 149 -10.62 87.81 REMARK 500 SER A 173 -153.55 -130.35 REMARK 500 LYS A 362 -156.89 -96.31 REMARK 500 ASP A 367 35.19 -161.91 REMARK 500 GLU A 442 -32.45 -154.52 REMARK 500 VAL A 483 -64.25 74.29 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 A 292 LEU A 293 140.26 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 A1058 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A1059 DISTANCE = 7.21 ANGSTROMS DBREF 8JDQ A 22 484 UNP Q7TNG8 LDHD_MOUSE 22 484 SEQADV 8JDQ TRP A 14 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ SER A 15 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ HIS A 16 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ PRO A 17 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ GLN A 18 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ PHE A 19 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ GLU A 20 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ LYS A 21 UNP Q7TNG8 EXPRESSION TAG SEQADV 8JDQ ALA A 405 UNP Q7TNG8 HIS 405 ENGINEERED MUTATION SEQRES 1 A 471 TRP SER HIS PRO GLN PHE GLU LYS GLY SER GLN GLY GLY SEQRES 2 A 471 LEU SER GLN ASP PHE VAL GLU ALA LEU LYS ALA VAL VAL SEQRES 3 A 471 GLY SER PRO HIS VAL SER THR ALA SER ALA VAL ARG GLU SEQRES 4 A 471 GLN HIS GLY HIS ASP GLU SER MET HIS ARG CYS GLN PRO SEQRES 5 A 471 PRO ASP ALA VAL VAL TRP PRO GLN ASN VAL ASP GLN VAL SEQRES 6 A 471 SER ARG VAL ALA SER LEU CYS TYR ASN GLN GLY VAL PRO SEQRES 7 A 471 ILE ILE PRO PHE GLY THR GLY THR GLY VAL GLU GLY GLY SEQRES 8 A 471 VAL CYS ALA VAL GLN GLY GLY VAL CYS ILE ASN LEU THR SEQRES 9 A 471 HIS MET ASP GLN ILE THR GLU LEU ASN THR GLU ASP PHE SEQRES 10 A 471 SER VAL VAL VAL GLU PRO GLY VAL THR ARG LYS ALA LEU SEQRES 11 A 471 ASN THR HIS LEU ARG ASP SER GLY LEU TRP PHE PRO VAL SEQRES 12 A 471 ASP PRO GLY ALA ASP ALA SER LEU CYS GLY MET ALA ALA SEQRES 13 A 471 THR GLY ALA SER GLY THR ASN ALA VAL ARG TYR GLY THR SEQRES 14 A 471 MET ARG ASP ASN VAL ILE ASN LEU GLU VAL VAL LEU PRO SEQRES 15 A 471 ASP GLY ARG LEU LEU HIS THR ALA GLY ARG GLY ARG HIS SEQRES 16 A 471 TYR ARG LYS SER ALA ALA GLY TYR ASN LEU THR GLY LEU SEQRES 17 A 471 PHE VAL GLY SER GLU GLY THR LEU GLY ILE ILE THR SER SEQRES 18 A 471 THR THR LEU ARG LEU HIS PRO ALA PRO GLU ALA THR VAL SEQRES 19 A 471 ALA ALA THR CYS ALA PHE PRO SER VAL GLN ALA ALA VAL SEQRES 20 A 471 ASP SER THR VAL GLN ILE LEU GLN ALA ALA VAL PRO VAL SEQRES 21 A 471 ALA ARG ILE GLU PHE LEU ASP ASP VAL MET MET ASP ALA SEQRES 22 A 471 CYS ASN ARG HIS SER LYS LEU ASN CYS PRO VAL ALA PRO SEQRES 23 A 471 THR LEU PHE LEU GLU PHE HIS GLY SER GLN GLN THR LEU SEQRES 24 A 471 ALA GLU GLN LEU GLN ARG THR GLU ALA ILE THR GLN ASP SEQRES 25 A 471 ASN GLY GLY SER HIS PHE SER TRP ALA LYS GLU ALA GLU SEQRES 26 A 471 LYS ARG ASN GLU LEU TRP ALA ALA ARG HIS ASN ALA TRP SEQRES 27 A 471 TYR ALA ALA LEU ALA LEU SER PRO GLY SER LYS ALA TYR SEQRES 28 A 471 SER THR ASP VAL CYS VAL PRO ILE SER ARG LEU PRO GLU SEQRES 29 A 471 ILE LEU VAL GLU THR LYS GLU GLU ILE LYS ALA SER LYS SEQRES 30 A 471 LEU THR GLY ALA ILE VAL GLY HIS VAL GLY ASP GLY ASN SEQRES 31 A 471 PHE ALA CYS ILE LEU LEU VAL ASP PRO ASP ASP ALA GLU SEQRES 32 A 471 GLU GLN ARG ARG VAL LYS ALA PHE ALA GLU ASN LEU GLY SEQRES 33 A 471 ARG ARG ALA LEU ALA LEU GLY GLY THR CYS THR GLY GLU SEQRES 34 A 471 HIS GLY ILE GLY LEU GLY LYS ARG GLN LEU LEU GLN GLU SEQRES 35 A 471 GLU VAL GLY PRO VAL GLY VAL GLU THR MET ARG GLN LEU SEQRES 36 A 471 LYS ASN THR LEU ASP PRO ARG GLY LEU MET ASN PRO GLY SEQRES 37 A 471 LYS VAL LEU HET FAD A 501 53 HET 2RH A 502 9 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM 2RH (2R)-2-HYDROXY-4-METHYLPENTANOIC ACID HETSYN 2RH (R)-2-HYDROXYISOCAPROATE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 2RH C6 H12 O3 FORMUL 4 HOH *459(H2 O) HELIX 1 AA1 SER A 28 GLY A 40 1 13 HELIX 2 AA2 ALA A 47 HIS A 54 1 8 HELIX 3 AA3 ASN A 74 GLN A 88 1 15 HELIX 4 AA4 THR A 127 ASP A 129 5 3 HELIX 5 AA5 THR A 139 LEU A 147 1 9 HELIX 6 AA6 SER A 163 GLY A 171 1 9 HELIX 7 AA7 ASN A 176 GLY A 181 1 6 HELIX 8 AA8 THR A 182 ASN A 186 1 5 HELIX 9 AA9 LEU A 218 VAL A 223 1 6 HELIX 10 AB1 SER A 255 ALA A 269 1 15 HELIX 11 AB2 ASP A 280 LYS A 292 1 13 HELIX 12 AB3 SER A 308 ASN A 326 1 19 HELIX 13 AB4 GLU A 338 ASN A 349 1 12 HELIX 14 AB5 ASN A 349 LEU A 357 1 9 HELIX 15 AB6 PRO A 371 SER A 373 5 3 HELIX 16 AB7 ARG A 374 SER A 389 1 16 HELIX 17 AB8 HIS A 398 GLY A 402 5 5 HELIX 18 AB9 ASP A 414 LEU A 435 1 22 HELIX 19 AC1 LYS A 449 ASP A 473 1 25 SHEET 1 AA1 4 VAL A 44 SER A 45 0 SHEET 2 AA1 4 ALA A 68 VAL A 70 -1 O VAL A 69 N SER A 45 SHEET 3 AA1 4 VAL A 112 ASN A 115 1 O CYS A 113 N ALA A 68 SHEET 4 AA1 4 ILE A 92 PHE A 95 1 N ILE A 93 O VAL A 112 SHEET 1 AA2 5 ILE A 122 ASN A 126 0 SHEET 2 AA2 5 SER A 131 VAL A 134 -1 O SER A 131 N ASN A 126 SHEET 3 AA2 5 ILE A 231 ARG A 238 -1 O LEU A 237 N VAL A 132 SHEET 4 AA2 5 VAL A 187 VAL A 193 -1 N VAL A 193 O ILE A 231 SHEET 5 AA2 5 LEU A 199 HIS A 201 -1 O LEU A 200 N VAL A 192 SHEET 1 AA3 2 LEU A 152 TRP A 153 0 SHEET 2 AA3 2 HIS A 240 PRO A 241 -1 O HIS A 240 N TRP A 153 SHEET 1 AA4 7 SER A 332 ALA A 334 0 SHEET 2 AA4 7 ALA A 245 ALA A 252 -1 N ALA A 248 O ALA A 334 SHEET 3 AA4 7 THR A 300 GLY A 307 -1 O LEU A 303 N ALA A 249 SHEET 4 AA4 7 ARG A 275 LEU A 279 -1 N LEU A 279 O THR A 300 SHEET 5 AA4 7 ALA A 394 GLY A 397 -1 O GLY A 397 N PHE A 278 SHEET 6 AA4 7 ALA A 405 VAL A 410 -1 O ALA A 405 N VAL A 396 SHEET 7 AA4 7 LYS A 362 SER A 365 -1 N TYR A 364 O LEU A 408 CRYST1 81.320 103.010 122.470 90.00 90.00 90.00 I 2 2 2 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 0.012297 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008165 0.00000