HEADER LYASE/INHIBITOR 30-MAY-19 6P5O TITLE THE STRUCTURE OF RAT CYTOSOLIC PEPCK IN COMPLEX WITH 3- TITLE 2 (CARBOXYMETHYLTHIOL)-PICOLINIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC [GTP]; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEPCK-C; COMPND 5 EC: 4.1.1.32; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: PCK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PESUMOSTAR KEYWDS KINASE, GLUCONEOGENESIS, LYASE, LYASE-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.J.MCLEOD,T.HOLYOAK REVDAT 4 11-OCT-23 6P5O 1 LINK REVDAT 3 08-JAN-20 6P5O 1 REMARK REVDAT 2 02-OCT-19 6P5O 1 JRNL REVDAT 1 18-SEP-19 6P5O 0 JRNL AUTH M.J.MCLEOD,A.P.KRISMANICH,A.ASSOUD,G.I.DMITRIENKO,T.HOLYOAK JRNL TITL CHARACTERIZATION OF 3-[(CARBOXYMETHYL)THIO]PICOLINIC ACID: A JRNL TITL 2 NOVEL INHIBITOR OF PHOSPHOENOLPYRUVATE CARBOXYKINASE. JRNL REF BIOCHEMISTRY V. 58 3918 2019 JRNL REFN ISSN 0006-2960 JRNL PMID 31461616 JRNL DOI 10.1021/ACS.BIOCHEM.9B00583 REMARK 2 REMARK 2 RESOLUTION. 1.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.35 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 90874 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) : 0.160 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4915 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) : 1.49 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.53 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6734 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.99 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 379 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4860 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 633 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.069 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.068 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.048 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.320 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.971 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5076 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4721 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6884 ; 1.443 ; 1.647 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11014 ; 1.358 ; 1.576 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 639 ; 7.059 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 257 ;30.311 ;22.568 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 882 ;12.290 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;17.951 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 637 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5692 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1057 ; 0.001 ; 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6P5O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-19. REMARK 100 THE DEPOSITION ID IS D_1000241928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97952 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94702 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.490 REMARK 200 RESOLUTION RANGE LOW (A) : 60.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 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: MOLREP REMARK 200 STARTING MODEL: 2QEW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M HEPES PH 7.4, 8MM REMARK 280 MNCL2, 1MM CMP, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 59.35350 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 MET A 1 REMARK 465 PRO A 2 REMARK 465 GLU A 469 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 885 O HOH A 1001 1.70 REMARK 500 NE2 GLN A 110 O HOH A 801 1.77 REMARK 500 O HOH A 830 O HOH A 1347 2.01 REMARK 500 O ALA A 287 O HOH A 802 2.06 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 HIS A 6 -132.15 -135.78 REMARK 500 ASN A 7 27.44 -146.79 REMARK 500 ARG A 129 -58.48 -122.31 REMARK 500 LYS A 244 -43.38 -135.20 REMARK 500 PRO A 285 -170.28 -68.25 REMARK 500 ASP A 311 -52.27 -146.84 REMARK 500 PHE A 333 72.00 -113.53 REMARK 500 ASN A 344 73.26 -159.56 REMARK 500 PHE A 480 15.25 58.84 REMARK 500 ALA A 505 -12.78 84.75 REMARK 500 PHE A 530 -129.84 50.92 REMARK 500 LYS A 560 159.58 -49.83 REMARK 500 ASN A 601 -122.60 52.97 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 A1432 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A1433 DISTANCE = 6.47 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 MN A 702 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 63 OE2 REMARK 620 2 HIS A 502 NE2 9.3 REMARK 620 3 GLU A 607 OE2 8.7 4.1 REMARK 620 4 HOH A 903 O 168.6 159.3 160.6 REMARK 620 5 HOH A1127 O 112.0 120.0 120.7 77.6 REMARK 620 6 HOH A1276 O 92.2 83.7 83.5 77.8 155.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 704 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 79 O REMARK 620 2 ASN A 208 O 104.1 REMARK 620 3 HOH A1050 O 94.8 160.8 REMARK 620 4 HOH A1075 O 96.4 89.1 86.0 REMARK 620 5 HOH A1294 O 105.5 94.3 83.1 156.3 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 701 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 244 NZ REMARK 620 2 HIS A 264 NE2 86.5 REMARK 620 3 ASP A 311 OD1 95.9 90.5 REMARK 620 4 O2Y A 703 N2 93.4 170.1 99.4 REMARK 620 5 O2Y A 703 O9 89.8 94.2 172.9 75.9 REMARK 620 6 HOH A1113 O 175.9 89.8 82.5 90.6 92.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue O2Y A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 704 DBREF 6P5O A 1 622 UNP P07379 PCKGC_RAT 1 622 SEQRES 1 A 622 MET PRO PRO GLN LEU HIS ASN GLY LEU ASP PHE SER ALA SEQRES 2 A 622 LYS VAL ILE GLN GLY SER LEU ASP SER LEU PRO GLN GLU SEQRES 3 A 622 VAL ARG LYS PHE VAL GLU GLY ASN ALA GLN LEU CYS GLN SEQRES 4 A 622 PRO GLU TYR ILE HIS ILE CYS ASP GLY SER GLU GLU GLU SEQRES 5 A 622 TYR GLY ARG LEU LEU ALA HIS MET GLN GLU GLU GLY VAL SEQRES 6 A 622 ILE ARG LYS LEU LYS LYS TYR ASP ASN CYS TRP LEU ALA SEQRES 7 A 622 LEU THR ASP PRO ARG ASP VAL ALA ARG ILE GLU SER LYS SEQRES 8 A 622 THR VAL ILE ILE THR GLN GLU GLN ARG ASP THR VAL PRO SEQRES 9 A 622 ILE PRO LYS SER GLY GLN SER GLN LEU GLY ARG TRP MET SEQRES 10 A 622 SER GLU GLU ASP PHE GLU LYS ALA PHE ASN ALA ARG PHE SEQRES 11 A 622 PRO GLY CYS MET LYS GLY ARG THR MET TYR VAL ILE PRO SEQRES 12 A 622 PHE SER MET GLY PRO LEU GLY SER PRO LEU ALA LYS ILE SEQRES 13 A 622 GLY ILE GLU LEU THR ASP SER PRO TYR VAL VAL ALA SER SEQRES 14 A 622 MET ARG ILE MET THR ARG MET GLY THR SER VAL LEU GLU SEQRES 15 A 622 ALA LEU GLY ASP GLY GLU PHE ILE LYS CYS LEU HIS SER SEQRES 16 A 622 VAL GLY CYS PRO LEU PRO LEU LYS LYS PRO LEU VAL ASN SEQRES 17 A 622 ASN TRP ALA CYS ASN PRO GLU LEU THR LEU ILE ALA HIS SEQRES 18 A 622 LEU PRO ASP ARG ARG GLU ILE ILE SER PHE GLY SER GLY SEQRES 19 A 622 TYR GLY GLY ASN SER LEU LEU GLY LYS LYS CYS PHE ALA SEQRES 20 A 622 LEU ARG ILE ALA SER ARG LEU ALA LYS GLU GLU GLY TRP SEQRES 21 A 622 LEU ALA GLU HIS MET LEU ILE LEU GLY ILE THR ASN PRO SEQRES 22 A 622 GLU GLY LYS LYS LYS TYR LEU ALA ALA ALA PHE PRO SER SEQRES 23 A 622 ALA CYS GLY LYS THR ASN LEU ALA MET MET ASN PRO THR SEQRES 24 A 622 LEU PRO GLY TRP LYS VAL GLU CYS VAL GLY ASP ASP ILE SEQRES 25 A 622 ALA TRP MET LYS PHE ASP ALA GLN GLY ASN LEU ARG ALA SEQRES 26 A 622 ILE ASN PRO GLU ASN GLY PHE PHE GLY VAL ALA PRO GLY SEQRES 27 A 622 THR SER VAL LYS THR ASN PRO ASN ALA ILE LYS THR ILE SEQRES 28 A 622 GLN LYS ASN THR ILE PHE THR ASN VAL ALA GLU THR SER SEQRES 29 A 622 ASP GLY GLY VAL TYR TRP GLU GLY ILE ASP GLU PRO LEU SEQRES 30 A 622 ALA PRO GLY VAL THR ILE THR SER TRP LYS ASN LYS GLU SEQRES 31 A 622 TRP ARG PRO GLN ASP GLU GLU PRO CYS ALA HIS PRO ASN SEQRES 32 A 622 SER ARG PHE CYS THR PRO ALA SER GLN CYS PRO ILE ILE SEQRES 33 A 622 ASP PRO ALA TRP GLU SER PRO GLU GLY VAL PRO ILE GLU SEQRES 34 A 622 GLY ILE ILE PHE GLY GLY ARG ARG PRO ALA GLY VAL PRO SEQRES 35 A 622 LEU VAL TYR GLU ALA LEU SER TRP GLN HIS GLY VAL PHE SEQRES 36 A 622 VAL GLY ALA ALA MET ARG SER GLU ALA THR ALA ALA ALA SEQRES 37 A 622 GLU HIS LYS GLY LYS VAL ILE MET HIS ASP PRO PHE ALA SEQRES 38 A 622 MET ARG PRO PHE PHE GLY TYR ASN PHE GLY LYS TYR LEU SEQRES 39 A 622 ALA HIS TRP LEU SER MET ALA HIS ARG PRO ALA ALA LYS SEQRES 40 A 622 LEU PRO LYS ILE PHE HIS VAL ASN TRP PHE ARG LYS ASP SEQRES 41 A 622 LYS ASN GLY LYS PHE LEU TRP PRO GLY PHE GLY GLU ASN SEQRES 42 A 622 SER ARG VAL LEU GLU TRP MET PHE GLY ARG ILE GLU GLY SEQRES 43 A 622 GLU ASP SER ALA LYS LEU THR PRO ILE GLY TYR VAL PRO SEQRES 44 A 622 LYS GLU ASP ALA LEU ASN LEU LYS GLY LEU GLY ASP VAL SEQRES 45 A 622 ASN VAL GLU GLU LEU PHE GLY ILE SER LYS GLU PHE TRP SEQRES 46 A 622 GLU LYS GLU VAL GLU GLU ILE ASP LYS TYR LEU GLU ASP SEQRES 47 A 622 GLN VAL ASN ALA ASP LEU PRO TYR GLU ILE GLU ARG GLU SEQRES 48 A 622 LEU ARG ALA LEU LYS GLN ARG ILE SER GLN MET HET MN A 701 1 HET MN A 702 1 HET O2Y A 703 14 HET NA A 704 1 HETNAM MN MANGANESE (II) ION HETNAM O2Y 3-[(CARBOXYMETHYL)SULFANYL]PYRIDINE-2-CARBOXYLIC ACID HETNAM NA SODIUM ION HETSYN O2Y 3-(CARBOXYMETHYLTHIO)PICOLINIC ACID FORMUL 2 MN 2(MN 2+) FORMUL 4 O2Y C8 H7 N O4 S FORMUL 5 NA NA 1+ FORMUL 6 HOH *633(H2 O) HELIX 1 AA1 PHE A 11 ALA A 13 5 3 HELIX 2 AA2 PRO A 24 GLN A 39 1 16 HELIX 3 AA3 SER A 49 GLU A 63 1 15 HELIX 4 AA4 ILE A 88 SER A 90 5 3 HELIX 5 AA5 GLU A 98 THR A 102 5 5 HELIX 6 AA6 SER A 118 ALA A 128 1 11 HELIX 7 AA7 SER A 163 THR A 174 1 12 HELIX 8 AA8 GLY A 177 GLY A 185 1 9 HELIX 9 AA9 ASN A 213 THR A 217 5 5 HELIX 10 AB1 PRO A 223 ARG A 225 5 3 HELIX 11 AB2 TYR A 235 LEU A 240 1 6 HELIX 12 AB3 LEU A 248 GLY A 259 1 12 HELIX 13 AB4 GLY A 289 MET A 295 1 7 HELIX 14 AB5 ASN A 344 ILE A 351 1 8 HELIX 15 AB6 SER A 411 CYS A 413 5 3 HELIX 16 AB7 SER A 449 ALA A 459 1 11 HELIX 17 AB8 PRO A 479 MET A 482 5 4 HELIX 18 AB9 ASN A 489 MET A 500 1 12 HELIX 19 AC1 ALA A 501 ARG A 503 5 3 HELIX 20 AC2 GLY A 529 GLU A 532 5 4 HELIX 21 AC3 ASN A 533 GLU A 545 1 13 HELIX 22 AC4 ASN A 573 PHE A 578 1 6 HELIX 23 AC5 SER A 581 VAL A 600 1 20 HELIX 24 AC6 ASN A 601 LEU A 604 5 4 HELIX 25 AC7 PRO A 605 GLN A 621 1 17 SHEET 1 AA1 9 VAL A 15 GLN A 17 0 SHEET 2 AA1 9 TYR A 42 ILE A 45 1 O ILE A 43 N ILE A 16 SHEET 3 AA1 9 THR A 138 MET A 146 1 O MET A 139 N TYR A 42 SHEET 4 AA1 9 LYS A 155 THR A 161 -1 O THR A 161 N TYR A 140 SHEET 5 AA1 9 ILE A 190 SER A 195 1 O CYS A 192 N ILE A 158 SHEET 6 AA1 9 GLU A 227 PHE A 231 1 O SER A 230 N LEU A 193 SHEET 7 AA1 9 LEU A 218 LEU A 222 -1 N LEU A 222 O GLU A 227 SHEET 8 AA1 9 THR A 92 ILE A 95 1 N ILE A 95 O HIS A 221 SHEET 9 AA1 9 TRP A 116 MET A 117 1 O MET A 117 N ILE A 94 SHEET 1 AA2 4 VAL A 15 GLN A 17 0 SHEET 2 AA2 4 TYR A 42 ILE A 45 1 O ILE A 43 N ILE A 16 SHEET 3 AA2 4 THR A 138 MET A 146 1 O MET A 139 N TYR A 42 SHEET 4 AA2 4 ARG A 175 MET A 176 -1 O ARG A 175 N SER A 145 SHEET 1 AA3 5 ARG A 67 LEU A 69 0 SHEET 2 AA3 5 CYS A 75 ALA A 78 -1 O CYS A 75 N LEU A 69 SHEET 3 AA3 5 ILE A 356 THR A 358 1 O PHE A 357 N TRP A 76 SHEET 4 AA3 5 ARG A 405 PRO A 409 -1 O ARG A 405 N THR A 358 SHEET 5 AA3 5 GLY A 331 VAL A 335 -1 N PHE A 332 O THR A 408 SHEET 1 AA4 7 LEU A 261 GLU A 263 0 SHEET 2 AA4 7 ALA A 313 PHE A 317 -1 O ALA A 313 N GLU A 263 SHEET 3 AA4 7 LEU A 323 ILE A 326 -1 O ILE A 326 N TRP A 314 SHEET 4 AA4 7 VAL A 426 GLY A 434 -1 O ILE A 428 N LEU A 323 SHEET 5 AA4 7 LYS A 277 ALA A 283 1 N TYR A 279 O GLU A 429 SHEET 6 AA4 7 LEU A 266 THR A 271 -1 N ILE A 270 O LYS A 278 SHEET 7 AA4 7 LYS A 304 GLY A 309 -1 O GLU A 306 N GLY A 269 SHEET 1 AA5 6 LEU A 261 GLU A 263 0 SHEET 2 AA5 6 ALA A 313 PHE A 317 -1 O ALA A 313 N GLU A 263 SHEET 3 AA5 6 LEU A 323 ILE A 326 -1 O ILE A 326 N TRP A 314 SHEET 4 AA5 6 VAL A 426 GLY A 434 -1 O ILE A 428 N LEU A 323 SHEET 5 AA5 6 LYS A 510 VAL A 514 1 O PHE A 512 N PHE A 433 SHEET 6 AA5 6 VAL A 444 GLU A 446 -1 N TYR A 445 O HIS A 513 SHEET 1 AA6 4 VAL A 368 TYR A 369 0 SHEET 2 AA6 4 ALA A 361 THR A 363 -1 N ALA A 361 O TYR A 369 SHEET 3 AA6 4 ILE A 383 THR A 384 -1 O THR A 384 N GLU A 362 SHEET 4 AA6 4 GLU A 390 TRP A 391 -1 O TRP A 391 N ILE A 383 SHEET 1 AA7 2 ARG A 461 GLU A 463 0 SHEET 2 AA7 2 ILE A 475 HIS A 477 -1 O MET A 476 N SER A 462 SHEET 1 AA8 2 ALA A 550 THR A 553 0 SHEET 2 AA8 2 GLY A 556 PRO A 559 -1 O VAL A 558 N LYS A 551 LINK OE2 GLU A 63 MN MN A 702 1555 1555 2.09 LINK O LEU A 79 NA NA A 704 1555 1555 2.30 LINK O ASN A 208 NA NA A 704 1555 1555 2.14 LINK NZ LYS A 244 MN MN A 701 1555 1555 2.30 LINK NE2 HIS A 264 MN MN A 701 1555 1555 2.22 LINK OD1 ASP A 311 MN MN A 701 1555 1555 2.11 LINK NE2 HIS A 502 MN MN A 702 1555 2555 2.19 LINK OE2 GLU A 607 MN MN A 702 1555 2555 2.10 LINK MN MN A 701 N2 O2Y A 703 1555 1555 2.17 LINK MN MN A 701 O9 O2Y A 703 1555 1555 2.15 LINK MN MN A 701 O HOH A1113 1555 1555 2.18 LINK MN MN A 702 O HOH A 903 1555 2545 2.57 LINK MN MN A 702 O HOH A1127 1555 2545 2.07 LINK MN MN A 702 O HOH A1276 1555 2545 2.25 LINK NA NA A 704 O HOH A1050 1555 1555 2.47 LINK NA NA A 704 O HOH A1075 1555 1555 2.39 LINK NA NA A 704 O HOH A1294 1555 1555 2.32 CISPEP 1 LEU A 200 PRO A 201 0 -0.62 SITE 1 AC1 5 LYS A 244 HIS A 264 ASP A 311 O2Y A 703 SITE 2 AC1 5 HOH A1113 SITE 1 AC2 1 GLU A 63 SITE 1 AC3 16 ALA A 86 ARG A 87 TYR A 235 GLY A 236 SITE 2 AC3 16 GLY A 237 LYS A 243 LYS A 244 HIS A 264 SITE 3 AC3 16 ASP A 311 PHE A 333 ASN A 403 ARG A 405 SITE 4 AC3 16 MN A 701 HOH A1113 HOH A1130 HOH A1272 SITE 1 AC4 5 LEU A 79 ASN A 208 HOH A1050 HOH A1075 SITE 2 AC4 5 HOH A1294 CRYST1 44.409 118.707 60.863 90.00 109.61 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 0.022518 0.000000 0.008023 0.00000 SCALE2 0.000000 0.008424 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017442 0.00000