HEADER OXIDOREDUCTASE 14-FEB-17 5N6C TITLE CRYSTAL STRUCTURE OF HUMAN 3-PHOSPHOGLYCERATE DEHYDROGENASE IN COMPLEX TITLE 2 WITH NAD AND L-TARTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-3-PHOSPHOGLYCERATE DEHYDROGENASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3-PGDH; COMPND 5 EC: 1.1.1.95; COMPND 6 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: PHGDH, PGDH3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DEHYDROGENASE, SERINE METABOLISM, ENZYMOLOGY, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR J.E.UNTERLASS,A.BASLE,J.TUCKER,C.CANO,M.E.M.NOBLE,N.J.CURTIN REVDAT 5 17-JAN-24 5N6C 1 REMARK REVDAT 4 10-JUL-19 5N6C 1 REMARK REVDAT 3 20-FEB-19 5N6C 1 REMARK LINK REVDAT 2 03-JAN-18 5N6C 1 JRNL REVDAT 1 22-NOV-17 5N6C 0 JRNL AUTH J.E.UNTERLASS,R.J.WOOD,A.BASLE,J.TUCKER,C.CANO,M.M.E.NOBLE, JRNL AUTH 2 N.J.CURTIN JRNL TITL STRUCTURAL INSIGHTS INTO THE ENZYMATIC ACTIVITY AND JRNL TITL 2 POTENTIAL SUBSTRATE PROMISCUITY OF HUMAN 3-PHOSPHOGLYCERATE JRNL TITL 3 DEHYDROGENASE (PHGDH). JRNL REF ONCOTARGET V. 8 04478 2017 JRNL REFN ESSN 1949-2553 JRNL PMID 29262655 JRNL DOI 10.18632/ONCOTARGET.22327 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 66.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 26108 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 + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.255 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1319 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1911 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.2830 REMARK 3 BIN FREE R VALUE SET COUNT : 89 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4392 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 98 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.38000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -3.50000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.08000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.387 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.251 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.239 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.384 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.918 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4597 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4311 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6255 ; 2.217 ; 2.002 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10019 ; 1.176 ; 2.999 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 613 ; 6.236 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;40.980 ;25.491 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 787 ;15.806 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;16.540 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 750 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5132 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 828 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 8 305 B 8 305 17298 0.120 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 95 REMARK 3 ORIGIN FOR THE GROUP (A): 40.2580 54.5910 29.0390 REMARK 3 T TENSOR REMARK 3 T11: 0.3560 T22: 0.8037 REMARK 3 T33: 1.0856 T12: -0.1552 REMARK 3 T13: 0.2750 T23: 0.1915 REMARK 3 L TENSOR REMARK 3 L11: 3.0010 L22: 4.4569 REMARK 3 L33: 5.5624 L12: 0.8139 REMARK 3 L13: -0.8869 L23: -0.2768 REMARK 3 S TENSOR REMARK 3 S11: -0.4767 S12: 0.9632 S13: 0.2513 REMARK 3 S21: -0.9727 S22: 0.3081 S23: -0.5416 REMARK 3 S31: -0.3558 S32: 0.6028 S33: 0.1686 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 96 A 306 REMARK 3 ORIGIN FOR THE GROUP (A): 24.2980 50.8650 54.5540 REMARK 3 T TENSOR REMARK 3 T11: 0.0065 T22: 0.2887 REMARK 3 T33: 0.8108 T12: -0.0174 REMARK 3 T13: 0.0482 T23: -0.0303 REMARK 3 L TENSOR REMARK 3 L11: 2.9755 L22: 2.2773 REMARK 3 L33: 0.8531 L12: 0.3592 REMARK 3 L13: 0.0086 L23: 0.0803 REMARK 3 S TENSOR REMARK 3 S11: 0.0010 S12: -0.1063 S13: 0.2927 REMARK 3 S21: 0.0123 S22: 0.0183 S23: 0.0250 REMARK 3 S31: -0.0426 S32: 0.0097 S33: -0.0192 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 95 REMARK 3 ORIGIN FOR THE GROUP (A): 14.9410 26.8520 90.1970 REMARK 3 T TENSOR REMARK 3 T11: 1.0783 T22: 0.3466 REMARK 3 T33: 0.7574 T12: 0.0209 REMARK 3 T13: 0.0517 T23: -0.1097 REMARK 3 L TENSOR REMARK 3 L11: 5.8532 L22: 9.5068 REMARK 3 L33: 9.9070 L12: -2.6553 REMARK 3 L13: 2.5235 L23: -5.2964 REMARK 3 S TENSOR REMARK 3 S11: -0.4916 S12: -0.2328 S13: 0.2135 REMARK 3 S21: 2.2738 S22: 0.3071 S23: -0.0329 REMARK 3 S31: -2.6979 S32: -0.3620 S33: 0.1846 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 96 B 306 REMARK 3 ORIGIN FOR THE GROUP (A): 26.0540 27.1380 59.1010 REMARK 3 T TENSOR REMARK 3 T11: 0.0350 T22: 0.3552 REMARK 3 T33: 0.9397 T12: -0.0180 REMARK 3 T13: 0.0584 T23: 0.0407 REMARK 3 L TENSOR REMARK 3 L11: 2.5193 L22: 2.5274 REMARK 3 L33: 0.4375 L12: 0.2851 REMARK 3 L13: -0.0110 L23: -0.3021 REMARK 3 S TENSOR REMARK 3 S11: -0.0302 S12: -0.2695 S13: -0.4471 REMARK 3 S21: 0.1783 S22: 0.0323 S23: -0.0274 REMARK 3 S31: 0.0491 S32: 0.0023 S33: -0.0022 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5N6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1200003529. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27448 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 66.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.880 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 2.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 3.85 REMARK 200 R MERGE FOR SHELL (I) : 0.62700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 2G76 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, PH 8.5 0.2 M MGCL2 REMARK 280 HEXAHYDRATE 20 % (W/V) PEG 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K 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 54.85950 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -40.0 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 ALA B 7 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 LYS A 8 CG CD CE NZ REMARK 470 LYS A 33 CD CE NZ REMARK 470 LYS A 38 CD CE NZ REMARK 470 GLN A 46 CG CD OE1 NE2 REMARK 470 LYS A 136 CD CE NZ REMARK 470 LYS A 137 CE NZ REMARK 470 LYS A 227 NZ REMARK 470 ARG A 268 NE CZ NH1 NH2 REMARK 470 ARG B 20 CZ NH1 NH2 REMARK 470 LYS B 21 CG CD CE NZ REMARK 470 GLN B 29 CD OE1 NE2 REMARK 470 LYS B 33 CD CE NZ REMARK 470 LYS B 38 CD CE NZ REMARK 470 GLU B 39 CG CD OE1 OE2 REMARK 470 GLN B 46 CG CD OE1 NE2 REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 ARG B 54 NE CZ NH1 NH2 REMARK 470 ASP B 62 OD1 OD2 REMARK 470 LYS B 69 CE NZ REMARK 470 GLU B 86 CD OE1 OE2 REMARK 470 LYS B 136 CD CE NZ REMARK 470 LYS B 227 CD CE NZ REMARK 470 ARG B 268 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 289 CD CE NZ REMARK 470 MET B 306 CB CG SD CE 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 OD1 ASP B 260 SG CYS B 281 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 SER A 166 CB SER A 166 OG 0.101 REMARK 500 GLU A 297 CD GLU A 297 OE1 0.072 REMARK 500 GLY B 131 C GLY B 131 O -0.101 REMARK 500 ARG B 135 CD ARG B 135 NE -0.109 REMARK 500 GLU B 181 CD GLU B 181 OE1 0.068 REMARK 500 GLU B 195 CD GLU B 195 OE1 0.074 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 ASP A 62 CB - CG - OD1 ANGL. DEV. = -8.0 DEGREES REMARK 500 MET A 115 CG - SD - CE ANGL. DEV. = 13.1 DEGREES REMARK 500 ASP A 130 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ASP A 130 CB - CG - OD2 ANGL. DEV. = -7.8 DEGREES REMARK 500 ASP A 201 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 236 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 236 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ASP A 241 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ASP A 274 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 LYS A 289 CB - CG - CD ANGL. DEV. = 15.9 DEGREES REMARK 500 ASP B 81 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP B 130 CB - CG - OD1 ANGL. DEV. = -10.3 DEGREES REMARK 500 ASP B 130 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 ARG B 135 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ASP B 201 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG B 236 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 GLU B 290 OE1 - CD - OE2 ANGL. DEV. = -8.8 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 ASN A 35 97.38 56.42 REMARK 500 ARG A 54 -108.44 -117.15 REMARK 500 ASP A 62 -78.24 -49.34 REMARK 500 VAL A 80 36.41 -143.30 REMARK 500 GLU A 134 74.51 -115.38 REMARK 500 HIS A 206 46.70 -151.68 REMARK 500 ALA A 235 -86.01 -106.06 REMARK 500 LYS B 33 119.20 178.62 REMARK 500 GLN B 34 -164.39 -106.89 REMARK 500 ASN B 35 27.80 43.28 REMARK 500 ARG B 54 -102.91 -121.05 REMARK 500 VAL B 80 33.08 -141.23 REMARK 500 GLU B 134 77.66 -117.55 REMARK 500 HIS B 206 50.69 -148.78 REMARK 500 ALA B 235 -86.30 -109.10 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 TLA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAD B 401 DBREF 5N6C A 8 306 UNP O43175 SERA_HUMAN 8 306 DBREF 5N6C B 8 306 UNP O43175 SERA_HUMAN 8 306 SEQADV 5N6C ALA A 7 UNP O43175 EXPRESSION TAG SEQADV 5N6C ALA B 7 UNP O43175 EXPRESSION TAG SEQRES 1 A 300 ALA LYS VAL LEU ILE SER ASP SER LEU ASP PRO CYS CYS SEQRES 2 A 300 ARG LYS ILE LEU GLN ASP GLY GLY LEU GLN VAL VAL GLU SEQRES 3 A 300 LYS GLN ASN LEU SER LYS GLU GLU LEU ILE ALA GLU LEU SEQRES 4 A 300 GLN ASP CYS GLU GLY LEU ILE VAL ARG SER ALA THR LYS SEQRES 5 A 300 VAL THR ALA ASP VAL ILE ASN ALA ALA GLU LYS LEU GLN SEQRES 6 A 300 VAL VAL GLY ARG ALA GLY THR GLY VAL ASP ASN VAL ASP SEQRES 7 A 300 LEU GLU ALA ALA THR ARG LYS GLY ILE LEU VAL MET ASN SEQRES 8 A 300 THR PRO ASN GLY ASN SER LEU SER ALA ALA GLU LEU THR SEQRES 9 A 300 CYS GLY MET ILE MET CYS LEU ALA ARG GLN ILE PRO GLN SEQRES 10 A 300 ALA THR ALA SER MET LYS ASP GLY LYS TRP GLU ARG LYS SEQRES 11 A 300 LYS PHE MET GLY THR GLU LEU ASN GLY LYS THR LEU GLY SEQRES 12 A 300 ILE LEU GLY LEU GLY ARG ILE GLY ARG GLU VAL ALA THR SEQRES 13 A 300 ARG MET GLN SER PHE GLY MET LYS THR ILE GLY TYR ASP SEQRES 14 A 300 PRO ILE ILE SER PRO GLU VAL SER ALA SER PHE GLY VAL SEQRES 15 A 300 GLN GLN LEU PRO LEU GLU GLU ILE TRP PRO LEU CYS ASP SEQRES 16 A 300 PHE ILE THR VAL HIS THR PRO LEU LEU PRO SER THR THR SEQRES 17 A 300 GLY LEU LEU ASN ASP ASN THR PHE ALA GLN CYS LYS LYS SEQRES 18 A 300 GLY VAL ARG VAL VAL ASN CYS ALA ARG GLY GLY ILE VAL SEQRES 19 A 300 ASP GLU GLY ALA LEU LEU ARG ALA LEU GLN SER GLY GLN SEQRES 20 A 300 CYS ALA GLY ALA ALA LEU ASP VAL PHE THR GLU GLU PRO SEQRES 21 A 300 PRO ARG ASP ARG ALA LEU VAL ASP HIS GLU ASN VAL ILE SEQRES 22 A 300 SER CYS PRO HIS LEU GLY ALA SER THR LYS GLU ALA GLN SEQRES 23 A 300 SER ARG CYS GLY GLU GLU ILE ALA VAL GLN PHE VAL ASP SEQRES 24 A 300 MET SEQRES 1 B 300 ALA LYS VAL LEU ILE SER ASP SER LEU ASP PRO CYS CYS SEQRES 2 B 300 ARG LYS ILE LEU GLN ASP GLY GLY LEU GLN VAL VAL GLU SEQRES 3 B 300 LYS GLN ASN LEU SER LYS GLU GLU LEU ILE ALA GLU LEU SEQRES 4 B 300 GLN ASP CYS GLU GLY LEU ILE VAL ARG SER ALA THR LYS SEQRES 5 B 300 VAL THR ALA ASP VAL ILE ASN ALA ALA GLU LYS LEU GLN SEQRES 6 B 300 VAL VAL GLY ARG ALA GLY THR GLY VAL ASP ASN VAL ASP SEQRES 7 B 300 LEU GLU ALA ALA THR ARG LYS GLY ILE LEU VAL MET ASN SEQRES 8 B 300 THR PRO ASN GLY ASN SER LEU SER ALA ALA GLU LEU THR SEQRES 9 B 300 CYS GLY MET ILE MET CYS LEU ALA ARG GLN ILE PRO GLN SEQRES 10 B 300 ALA THR ALA SER MET LYS ASP GLY LYS TRP GLU ARG LYS SEQRES 11 B 300 LYS PHE MET GLY THR GLU LEU ASN GLY LYS THR LEU GLY SEQRES 12 B 300 ILE LEU GLY LEU GLY ARG ILE GLY ARG GLU VAL ALA THR SEQRES 13 B 300 ARG MET GLN SER PHE GLY MET LYS THR ILE GLY TYR ASP SEQRES 14 B 300 PRO ILE ILE SER PRO GLU VAL SER ALA SER PHE GLY VAL SEQRES 15 B 300 GLN GLN LEU PRO LEU GLU GLU ILE TRP PRO LEU CYS ASP SEQRES 16 B 300 PHE ILE THR VAL HIS THR PRO LEU LEU PRO SER THR THR SEQRES 17 B 300 GLY LEU LEU ASN ASP ASN THR PHE ALA GLN CYS LYS LYS SEQRES 18 B 300 GLY VAL ARG VAL VAL ASN CYS ALA ARG GLY GLY ILE VAL SEQRES 19 B 300 ASP GLU GLY ALA LEU LEU ARG ALA LEU GLN SER GLY GLN SEQRES 20 B 300 CYS ALA GLY ALA ALA LEU ASP VAL PHE THR GLU GLU PRO SEQRES 21 B 300 PRO ARG ASP ARG ALA LEU VAL ASP HIS GLU ASN VAL ILE SEQRES 22 B 300 SER CYS PRO HIS LEU GLY ALA SER THR LYS GLU ALA GLN SEQRES 23 B 300 SER ARG CYS GLY GLU GLU ILE ALA VAL GLN PHE VAL ASP SEQRES 24 B 300 MET HET TLA A 401 10 HET NAD A 402 44 HET NAD B 401 44 HETNAM TLA L(+)-TARTARIC ACID HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 3 TLA C4 H6 O6 FORMUL 4 NAD 2(C21 H27 N7 O14 P2) FORMUL 6 HOH *74(H2 O) HELIX 1 AA1 PRO A 17 GLY A 27 1 11 HELIX 2 AA2 SER A 37 GLN A 46 1 10 HELIX 3 AA3 THR A 60 ALA A 67 1 8 HELIX 4 AA4 ASP A 84 LYS A 91 1 8 HELIX 5 AA5 ASN A 102 GLN A 120 1 19 HELIX 6 AA6 GLN A 120 ASP A 130 1 11 HELIX 7 AA7 ARG A 135 MET A 139 5 5 HELIX 8 AA8 GLY A 154 SER A 166 1 13 HELIX 9 AA9 SER A 179 PHE A 186 1 8 HELIX 10 AB1 PRO A 192 TRP A 197 1 6 HELIX 11 AB2 PRO A 198 CYS A 200 5 3 HELIX 12 AB3 ASN A 218 CYS A 225 1 8 HELIX 13 AB4 ASP A 241 GLY A 252 1 12 HELIX 14 AB5 ARG A 270 HIS A 275 1 6 HELIX 15 AB6 THR A 288 MET A 306 1 19 HELIX 16 AB7 PRO B 17 GLY B 27 1 11 HELIX 17 AB8 SER B 37 GLN B 46 1 10 HELIX 18 AB9 THR B 60 ALA B 67 1 8 HELIX 19 AC1 ASP B 84 LYS B 91 1 8 HELIX 20 AC2 ASN B 102 GLN B 120 1 19 HELIX 21 AC3 GLN B 120 ASP B 130 1 11 HELIX 22 AC4 ARG B 135 MET B 139 5 5 HELIX 23 AC5 GLY B 154 SER B 166 1 13 HELIX 24 AC6 SER B 179 PHE B 186 1 8 HELIX 25 AC7 PRO B 192 TRP B 197 1 6 HELIX 26 AC8 PRO B 198 CYS B 200 5 3 HELIX 27 AC9 ASN B 218 CYS B 225 1 8 HELIX 28 AD1 ASP B 241 GLY B 252 1 12 HELIX 29 AD2 ARG B 270 HIS B 275 1 6 HELIX 30 AD3 THR B 288 MET B 306 1 19 SHEET 1 AA1 5 GLN A 29 GLU A 32 0 SHEET 2 AA1 5 LYS A 8 ILE A 11 1 N ILE A 11 O VAL A 31 SHEET 3 AA1 5 GLY A 50 VAL A 53 1 O GLY A 50 N LEU A 10 SHEET 4 AA1 5 VAL A 72 ARG A 75 1 O GLY A 74 N VAL A 53 SHEET 5 AA1 5 LEU A 94 MET A 96 1 O MET A 96 N VAL A 73 SHEET 1 AA2 7 GLN A 189 GLN A 190 0 SHEET 2 AA2 7 LYS A 170 TYR A 174 1 N THR A 171 O GLN A 189 SHEET 3 AA2 7 THR A 147 LEU A 151 1 N LEU A 148 O LYS A 170 SHEET 4 AA2 7 PHE A 202 VAL A 205 1 O PHE A 202 N GLY A 149 SHEET 5 AA2 7 ARG A 230 ASN A 233 1 O VAL A 232 N ILE A 203 SHEET 6 AA2 7 GLY A 256 LEU A 259 1 O ALA A 258 N ASN A 233 SHEET 7 AA2 7 VAL A 278 SER A 280 1 O ILE A 279 N ALA A 257 SHEET 1 AA3 5 VAL B 30 GLU B 32 0 SHEET 2 AA3 5 VAL B 9 ILE B 11 1 N ILE B 11 O VAL B 31 SHEET 3 AA3 5 GLY B 50 VAL B 53 1 O GLY B 50 N LEU B 10 SHEET 4 AA3 5 VAL B 72 ARG B 75 1 O GLY B 74 N LEU B 51 SHEET 5 AA3 5 LEU B 94 MET B 96 1 O MET B 96 N VAL B 73 SHEET 1 AA4 7 GLN B 189 GLN B 190 0 SHEET 2 AA4 7 LYS B 170 TYR B 174 1 N GLY B 173 O GLN B 189 SHEET 3 AA4 7 THR B 147 LEU B 151 1 N LEU B 148 O LYS B 170 SHEET 4 AA4 7 PHE B 202 VAL B 205 1 O PHE B 202 N GLY B 149 SHEET 5 AA4 7 ARG B 230 ASN B 233 1 O VAL B 232 N ILE B 203 SHEET 6 AA4 7 GLY B 256 LEU B 259 1 O ALA B 258 N ASN B 233 SHEET 7 AA4 7 VAL B 278 SER B 280 1 O ILE B 279 N ALA B 257 CISPEP 1 GLU A 265 PRO A 266 0 5.33 CISPEP 2 GLU B 265 PRO B 266 0 -1.07 SITE 1 AC1 11 ARG A 54 SER A 55 ARG A 75 THR A 78 SITE 2 AC1 11 ARG A 236 HIS A 283 ALA A 286 GLN A 292 SITE 3 AC1 11 NAD A 402 HOH A 514 ARG B 135 SITE 1 AC2 26 THR A 78 ASN A 102 GLY A 152 GLY A 154 SITE 2 AC2 26 ARG A 155 ILE A 156 TYR A 174 ASP A 175 SITE 3 AC2 26 PRO A 176 ILE A 177 HIS A 206 THR A 207 SITE 4 AC2 26 PRO A 208 THR A 213 CYS A 234 ALA A 235 SITE 5 AC2 26 ARG A 236 ASP A 260 HIS A 283 GLY A 285 SITE 6 AC2 26 ALA A 286 TLA A 401 HOH A 505 HOH A 509 SITE 7 AC2 26 HOH A 520 HOH A 524 SITE 1 AC3 21 GLY B 152 GLY B 154 ARG B 155 ILE B 156 SITE 2 AC3 21 TYR B 174 ASP B 175 PRO B 176 ILE B 177 SITE 3 AC3 21 HIS B 206 THR B 207 PRO B 208 THR B 213 SITE 4 AC3 21 CYS B 234 ALA B 235 ARG B 236 ASP B 260 SITE 5 AC3 21 HIS B 283 GLY B 285 ALA B 286 HOH B 503 SITE 6 AC3 21 HOH B 514 CRYST1 43.523 109.719 66.923 90.00 94.40 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 0.022976 0.000000 0.001769 0.00000 SCALE2 0.000000 0.009114 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014987 0.00000