PDB Short entry for 1KHE HEADER LYASE 29-NOV-01 1KHE TITLE PEPCK COMPLEX WITH NONHYDROLYZABLE GTP ANALOG, MAD DATA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOENOLPYRUVATE CARBOXYKINASE, CYTOSOLIC (GTP); COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOENOLPYRUVATE CARBOXYLASE, PEPCK, PEPCK-C; COMPND 5 EC: 4.1.1.32; 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: PCK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLUCONEOGENESIS, P-LOOP, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR P.DUNTEN,C.BELUNIS,R.CROWTHER,K.HOLLFELDER,U.KAMMLOTT,W.LEVIN, AUTHOR 2 H.MICHEL,G.B.RAMSEY,A.SWAIN,D.WEBER,S.J.WERTHEIMER REVDAT 3 11-OCT-17 1KHE 1 REMARK REVDAT 2 24-FEB-09 1KHE 1 VERSN REVDAT 1 27-FEB-02 1KHE 0 JRNL AUTH P.DUNTEN,C.BELUNIS,R.CROWTHER,K.HOLLFELDER,U.KAMMLOTT, JRNL AUTH 2 W.LEVIN,H.MICHEL,G.B.RAMSEY,A.SWAIN,D.WEBER,S.J.WERTHEIMER JRNL TITL CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC PHOSPHOENOLPYRUVATE JRNL TITL 2 CARBOXYKINASE REVEALS A NEW GTP-BINDING SITE. JRNL REF J.MOL.BIOL. V. 316 257 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11851336 JRNL DOI 10.1006/JMBI.2001.5364 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 22522 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.170 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1125 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4721 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 34 REMARK 3 SOLVENT ATOMS : 145 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.06000 REMARK 3 B13 (A**2) : 0.09000 REMARK 3 B23 (A**2) : -0.57000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.693 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.289 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.299 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.035 ; 0.021 REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.438 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.466 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.443 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.515 ; 4.500 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HIGH-ENERGY REMOTE DATA USED FOR REMARK 3 REFINEMENT REMARK 4 REMARK 4 1KHE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000014963. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-98 REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.971270, 0.978947, 0.978838 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22522 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG1500, MES, DTT, PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 GLY A -2 REMARK 465 GLU A -1 REMARK 465 LEU A 0 REMARK 465 MSE A 1 REMARK 465 PRO A 2 REMARK 465 PRO A 3 REMARK 465 GLN A 4 REMARK 465 LEU A 5 REMARK 465 GLN A 6 REMARK 465 ASN A 7 REMARK 465 GLY A 8 REMARK 465 LEU A 9 REMARK 465 THR A 465 REMARK 465 ALA A 466 REMARK 465 ALA A 467 REMARK 465 ALA A 468 REMARK 465 GLU A 469 REMARK 465 HIS A 470 REMARK 465 LYS A 471 REMARK 465 GLY A 472 REMARK 465 LYS A 547 REMARK 465 ALA A 548 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 SER A 90 NH1 ARG A 115 2.02 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 TYR A 72 CE2 TYR A 72 CD2 0.096 REMARK 500 ARG A 83 CZ ARG A 83 NH1 0.078 REMARK 500 MSE A 139 SE MSE A 139 CE -0.553 REMARK 500 GLU A 159 CD GLU A 159 OE1 0.067 REMARK 500 VAL A 196 CB VAL A 196 CG2 0.129 REMARK 500 ALA A 247 CA ALA A 247 CB 0.126 REMARK 500 ARG A 253 CZ ARG A 253 NH1 0.080 REMARK 500 ALA A 282 CA ALA A 282 CB 0.153 REMARK 500 MSE A 296 SE MSE A 296 CE -0.535 REMARK 500 LYS A 304 CD LYS A 304 CE 0.152 REMARK 500 VAL A 454 CB VAL A 454 CG2 0.208 REMARK 500 PHE A 530 CB PHE A 530 CG 0.103 REMARK 500 PHE A 578 CE1 PHE A 578 CZ 0.139 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 73 CB - CG - OD1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 83 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ASP A 84 CB - CG - OD2 ANGL. DEV. = 10.3 DEGREES REMARK 500 VAL A 85 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ASP A 186 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 224 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 249 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 253 NE - CZ - NH2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 318 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES REMARK 500 ARG A 324 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ASP A 395 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 405 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 405 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 ASP A 417 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 ARG A 461 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 543 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 586 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 LYS A 587 CD - CE - NZ ANGL. DEV. = 15.6 DEGREES REMARK 500 ASP A 603 CB - CG - OD2 ANGL. DEV. = 7.7 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 84 53.50 -111.69 REMARK 500 LYS A 91 21.65 -77.88 REMARK 500 LEU A 149 109.86 -50.85 REMARK 500 SER A 151 142.29 -28.38 REMARK 500 ASN A 208 41.26 38.93 REMARK 500 SER A 239 -37.39 -131.42 REMARK 500 LYS A 244 -45.16 -138.87 REMARK 500 SER A 286 138.31 -39.15 REMARK 500 ASP A 311 -38.77 -138.90 REMARK 500 PHE A 333 72.88 -104.60 REMARK 500 ASN A 344 70.95 -153.76 REMARK 500 ASN A 388 38.98 73.12 REMARK 500 PHE A 480 18.08 50.30 REMARK 500 PHE A 530 -131.16 58.36 REMARK 500 ASN A 601 -116.67 51.43 REMARK 500 REMARK 500 REMARK: NULL 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 701 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 291 OG1 REMARK 620 2 GCP A 703 O3G 173.8 REMARK 620 3 HOH A 802 O 78.8 95.0 REMARK 620 4 HOH A 803 O 83.8 96.1 96.8 REMARK 620 5 GCP A 703 O2B 87.9 98.3 166.7 82.8 REMARK 620 6 HOH A 785 O 92.8 88.3 91.7 170.0 87.6 REMARK 620 N 1 2 3 4 5 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 ASP A 311 OD1 REMARK 620 2 GCP A 703 O1G 85.4 REMARK 620 3 HOH A 733 O 80.7 76.7 REMARK 620 4 LYS A 244 NZ 99.4 172.4 98.1 REMARK 620 5 HOH A 797 O 162.0 81.1 84.6 92.9 REMARK 620 6 HIS A 264 NE2 95.2 100.9 175.4 84.7 99.0 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 GCP A 703 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KHB RELATED DB: PDB REMARK 900 PEPCK COMPLEX WITH NONHYDROLYZABLE GTP ANALOG, NATIVE DATA REMARK 900 RELATED ID: 1KHF RELATED DB: PDB REMARK 900 PEPCK COMPLEX WITH PEP REMARK 900 RELATED ID: 1KHG RELATED DB: PDB REMARK 900 PEPCK DBREF 1KHE A 1 622 UNP P35558 PPCKC_HUMAN 1 622 SEQADV 1KHE GLY A -2 UNP P35558 CLONING ARTIFACT SEQADV 1KHE GLU A -1 UNP P35558 CLONING ARTIFACT SEQADV 1KHE LEU A 0 UNP P35558 CLONING ARTIFACT SEQADV 1KHE MSE A 1 UNP P35558 MET 1 MODIFIED RESIDUE SEQADV 1KHE MSE A 60 UNP P35558 MET 60 MODIFIED RESIDUE SEQADV 1KHE MSE A 117 UNP P35558 MET 117 MODIFIED RESIDUE SEQADV 1KHE MSE A 134 UNP P35558 MET 134 MODIFIED RESIDUE SEQADV 1KHE MSE A 139 UNP P35558 MET 139 MODIFIED RESIDUE SEQADV 1KHE MSE A 146 UNP P35558 MET 146 MODIFIED RESIDUE SEQADV 1KHE MSE A 170 UNP P35558 MET 170 MODIFIED RESIDUE SEQADV 1KHE MSE A 173 UNP P35558 MET 173 MODIFIED RESIDUE SEQADV 1KHE MSE A 176 UNP P35558 MET 176 MODIFIED RESIDUE SEQADV 1KHE MSE A 250 UNP P35558 MET 250 MODIFIED RESIDUE SEQADV 1KHE MSE A 265 UNP P35558 MET 265 MODIFIED RESIDUE SEQADV 1KHE VAL A 267 UNP P35558 ILE 267 VARIANT SEQADV 1KHE MSE A 295 UNP P35558 MET 295 MODIFIED RESIDUE SEQADV 1KHE MSE A 296 UNP P35558 MET 296 MODIFIED RESIDUE SEQADV 1KHE MSE A 315 UNP P35558 MET 315 MODIFIED RESIDUE SEQADV 1KHE MSE A 460 UNP P35558 MET 460 MODIFIED RESIDUE SEQADV 1KHE MSE A 476 UNP P35558 MET 476 MODIFIED RESIDUE SEQADV 1KHE MSE A 482 UNP P35558 MET 482 MODIFIED RESIDUE SEQADV 1KHE MSE A 500 UNP P35558 MET 500 MODIFIED RESIDUE SEQADV 1KHE MSE A 540 UNP P35558 MET 540 MODIFIED RESIDUE SEQADV 1KHE MSE A 574 UNP P35558 MET 574 MODIFIED RESIDUE SEQADV 1KHE MSE A 575 UNP P35558 MET 575 MODIFIED RESIDUE SEQADV 1KHE ASP A 586 UNP P35558 GLU 586 VARIANT SEQADV 1KHE VAL A 597 UNP P35558 GLU 597 VARIANT SEQADV 1KHE MSE A 622 UNP P35558 MET 622 MODIFIED RESIDUE SEQRES 1 A 625 GLY GLU LEU MSE PRO PRO GLN LEU GLN ASN GLY LEU ASN SEQRES 2 A 625 LEU SER ALA LYS VAL VAL GLN GLY SER LEU ASP SER LEU SEQRES 3 A 625 PRO GLN ALA VAL ARG GLU PHE LEU GLU ASN ASN ALA GLU SEQRES 4 A 625 LEU CYS GLN PRO ASP HIS ILE HIS ILE CYS ASP GLY SER SEQRES 5 A 625 GLU GLU GLU ASN GLY ARG LEU LEU GLY GLN MSE GLU GLU SEQRES 6 A 625 GLU GLY ILE LEU ARG ARG LEU LYS LYS TYR ASP ASN CYS SEQRES 7 A 625 TRP LEU ALA LEU THR ASP PRO ARG ASP VAL ALA ARG ILE SEQRES 8 A 625 GLU SER LYS THR VAL ILE VAL THR GLN GLU GLN ARG ASP SEQRES 9 A 625 THR VAL PRO ILE PRO LYS THR GLY LEU SER GLN LEU GLY SEQRES 10 A 625 ARG TRP MSE SER GLU GLU ASP PHE GLU LYS ALA PHE ASN SEQRES 11 A 625 ALA ARG PHE PRO GLY CYS MSE LYS GLY ARG THR MSE TYR SEQRES 12 A 625 VAL ILE PRO PHE SER MSE GLY PRO LEU GLY SER PRO LEU SEQRES 13 A 625 SER LYS ILE GLY ILE GLU LEU THR ASP SER PRO TYR VAL SEQRES 14 A 625 VAL ALA SER MSE ARG ILE MSE THR ARG MSE GLY THR PRO SEQRES 15 A 625 VAL LEU GLU ALA LEU GLY ASP GLY GLU PHE VAL LYS CYS SEQRES 16 A 625 LEU HIS SER VAL GLY CYS PRO LEU PRO LEU GLN LYS PRO SEQRES 17 A 625 LEU VAL ASN ASN TRP PRO CYS ASN PRO GLU LEU THR LEU SEQRES 18 A 625 ILE ALA HIS LEU PRO ASP ARG ARG GLU ILE ILE SER PHE SEQRES 19 A 625 GLY SER GLY TYR GLY GLY ASN SER LEU LEU GLY LYS LYS SEQRES 20 A 625 CYS PHE ALA LEU ARG MSE ALA SER ARG LEU ALA LYS GLU SEQRES 21 A 625 GLU GLY TRP LEU ALA GLU HIS MSE LEU VAL LEU GLY ILE SEQRES 22 A 625 THR ASN PRO GLU GLY GLU LYS LYS TYR LEU ALA ALA ALA SEQRES 23 A 625 PHE PRO SER ALA CYS GLY LYS THR ASN LEU ALA MSE MSE SEQRES 24 A 625 ASN PRO SER LEU PRO GLY TRP LYS VAL GLU CYS VAL GLY SEQRES 25 A 625 ASP ASP ILE ALA TRP MSE LYS PHE ASP ALA GLN GLY HIS SEQRES 26 A 625 LEU ARG ALA ILE ASN PRO GLU ASN GLY PHE PHE GLY VAL SEQRES 27 A 625 ALA PRO GLY THR SER VAL LYS THR ASN PRO ASN ALA ILE SEQRES 28 A 625 LYS THR ILE GLN LYS ASN THR ILE PHE THR ASN VAL ALA SEQRES 29 A 625 GLU THR SER ASP GLY GLY VAL TYR TRP GLU GLY ILE ASP SEQRES 30 A 625 GLU PRO LEU ALA SER GLY VAL THR ILE THR SER TRP LYS SEQRES 31 A 625 ASN LYS GLU TRP SER SER GLU ASP GLY GLU PRO CYS ALA SEQRES 32 A 625 HIS PRO ASN SER ARG PHE CYS THR PRO ALA SER GLN CYS SEQRES 33 A 625 PRO ILE ILE ASP ALA ALA TRP GLU SER PRO GLU GLY VAL SEQRES 34 A 625 PRO ILE GLU GLY ILE ILE PHE GLY GLY ARG ARG PRO ALA SEQRES 35 A 625 GLY VAL PRO LEU VAL TYR GLU ALA LEU SER TRP GLN HIS SEQRES 36 A 625 GLY VAL PHE VAL GLY ALA ALA MSE ARG SER GLU ALA THR SEQRES 37 A 625 ALA ALA ALA GLU HIS LYS GLY LYS ILE ILE MSE HIS ASP SEQRES 38 A 625 PRO PHE ALA MSE ARG PRO PHE PHE GLY TYR ASN PHE GLY SEQRES 39 A 625 LYS TYR LEU ALA HIS TRP LEU SER MSE ALA GLN HIS PRO SEQRES 40 A 625 ALA ALA LYS LEU PRO LYS ILE PHE HIS VAL ASN TRP PHE SEQRES 41 A 625 ARG LYS ASP LYS GLU GLY LYS PHE LEU TRP PRO GLY PHE SEQRES 42 A 625 GLY GLU ASN SER ARG VAL LEU GLU TRP MSE PHE ASN ARG SEQRES 43 A 625 ILE ASP GLY LYS ALA SER THR LYS LEU THR PRO ILE GLY SEQRES 44 A 625 TYR ILE PRO LYS GLU ASP ALA LEU ASN LEU LYS GLY LEU SEQRES 45 A 625 GLY HIS ILE ASN MSE MSE GLU LEU PHE SER ILE SER LYS SEQRES 46 A 625 GLU PHE TRP ASP LYS GLU VAL GLU ASP ILE GLU LYS TYR SEQRES 47 A 625 LEU VAL ASP GLN VAL ASN ALA ASP LEU PRO CYS GLU ILE SEQRES 48 A 625 GLU ARG GLU ILE LEU ALA LEU LYS GLN ARG ILE SER GLN SEQRES 49 A 625 MSE MODRES 1KHE MSE A 60 MET SELENOMETHIONINE MODRES 1KHE MSE A 117 MET SELENOMETHIONINE MODRES 1KHE MSE A 134 MET SELENOMETHIONINE MODRES 1KHE MSE A 139 MET SELENOMETHIONINE MODRES 1KHE MSE A 146 MET SELENOMETHIONINE MODRES 1KHE MSE A 170 MET SELENOMETHIONINE MODRES 1KHE MSE A 173 MET SELENOMETHIONINE MODRES 1KHE MSE A 176 MET SELENOMETHIONINE MODRES 1KHE MSE A 250 MET SELENOMETHIONINE MODRES 1KHE MSE A 265 MET SELENOMETHIONINE MODRES 1KHE MSE A 295 MET SELENOMETHIONINE MODRES 1KHE MSE A 296 MET SELENOMETHIONINE MODRES 1KHE MSE A 315 MET SELENOMETHIONINE MODRES 1KHE MSE A 460 MET SELENOMETHIONINE MODRES 1KHE MSE A 476 MET SELENOMETHIONINE MODRES 1KHE MSE A 482 MET SELENOMETHIONINE MODRES 1KHE MSE A 500 MET SELENOMETHIONINE MODRES 1KHE MSE A 540 MET SELENOMETHIONINE MODRES 1KHE MSE A 574 MET SELENOMETHIONINE MODRES 1KHE MSE A 575 MET SELENOMETHIONINE MODRES 1KHE MSE A 622 MET SELENOMETHIONINE HET MSE A 60 8 HET MSE A 117 8 HET MSE A 134 8 HET MSE A 139 8 HET MSE A 146 8 HET MSE A 170 8 HET MSE A 173 8 HET MSE A 176 8 HET MSE A 250 8 HET MSE A 265 8 HET MSE A 295 8 HET MSE A 296 8 HET MSE A 315 8 HET MSE A 460 8 HET MSE A 476 8 HET MSE A 482 8 HET MSE A 500 12 HET MSE A 540 8 HET MSE A 574 8 HET MSE A 575 8 HET MSE A 622 8 HET MN A 701 1 HET MN A 702 1 HET GCP A 703 32 HETNAM MSE SELENOMETHIONINE HETNAM MN MANGANESE (II) ION HETNAM GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER FORMUL 1 MSE 21(C5 H11 N O2 SE) FORMUL 2 MN 2(MN 2+) FORMUL 4 GCP C11 H18 N5 O13 P3 FORMUL 5 HOH *145(H2 O) HELIX 1 1 LEU A 11 ALA A 13 5 3 HELIX 2 2 SER A 19 LEU A 23 5 5 HELIX 3 3 PRO A 24 GLN A 39 1 16 HELIX 4 4 SER A 49 GLU A 63 1 15 HELIX 5 5 ASP A 81 VAL A 85 5 5 HELIX 6 6 GLU A 98 VAL A 103 1 6 HELIX 7 7 SER A 118 ALA A 128 1 11 HELIX 8 8 SER A 163 THR A 174 1 12 HELIX 9 9 GLY A 177 GLY A 185 1 9 HELIX 10 10 ASN A 213 THR A 217 5 5 HELIX 11 11 TYR A 235 LEU A 240 1 6 HELIX 12 12 LEU A 248 GLY A 259 1 12 HELIX 13 13 GLY A 289 MSE A 295 1 7 HELIX 14 14 ASN A 344 ILE A 351 1 8 HELIX 15 15 SER A 411 CYS A 413 5 3 HELIX 16 16 SER A 449 ALA A 459 1 11 HELIX 17 17 PRO A 479 MSE A 482 5 4 HELIX 18 18 ASN A 489 MSE A 500 1 12 HELIX 19 19 ALA A 501 HIS A 503 5 3 HELIX 20 20 GLY A 529 GLY A 531 5 3 HELIX 21 21 GLU A 532 ASP A 545 1 14 HELIX 22 22 ASN A 573 SER A 579 1 7 HELIX 23 23 SER A 581 ASN A 601 1 21 HELIX 24 24 ALA A 602 LEU A 604 5 3 HELIX 25 25 PRO A 605 GLN A 621 1 17 SHEET 1 A 9 TRP A 116 MSE A 117 0 SHEET 2 A 9 THR A 92 VAL A 95 1 N ILE A 94 O MSE A 117 SHEET 3 A 9 LEU A 218 LEU A 222 1 O ILE A 219 N VAL A 93 SHEET 4 A 9 GLU A 227 PHE A 231 -1 O ILE A 229 N ALA A 220 SHEET 5 A 9 VAL A 190 SER A 195 1 N LYS A 191 O ILE A 228 SHEET 6 A 9 LYS A 155 THR A 161 1 N LEU A 160 O CYS A 192 SHEET 7 A 9 THR A 138 MSE A 146 -1 N MSE A 146 O LYS A 155 SHEET 8 A 9 HIS A 42 ILE A 45 1 N HIS A 42 O MSE A 139 SHEET 9 A 9 VAL A 15 GLN A 17 1 N GLN A 17 O ILE A 45 SHEET 1 B 8 TRP A 116 MSE A 117 0 SHEET 2 B 8 THR A 92 VAL A 95 1 N ILE A 94 O MSE A 117 SHEET 3 B 8 LEU A 218 LEU A 222 1 O ILE A 219 N VAL A 93 SHEET 4 B 8 GLU A 227 PHE A 231 -1 O ILE A 229 N ALA A 220 SHEET 5 B 8 VAL A 190 SER A 195 1 N LYS A 191 O ILE A 228 SHEET 6 B 8 LYS A 155 THR A 161 1 N LEU A 160 O CYS A 192 SHEET 7 B 8 THR A 138 MSE A 146 -1 N MSE A 146 O LYS A 155 SHEET 8 B 8 ARG A 175 MSE A 176 -1 O ARG A 175 N SER A 145 SHEET 1 C 5 ARG A 67 ARG A 68 0 SHEET 2 C 5 ASP A 73 ALA A 78 -1 O LEU A 77 N ARG A 67 SHEET 3 C 5 LYS A 353 THR A 358 1 O PHE A 357 N TRP A 76 SHEET 4 C 5 ARG A 405 PRO A 409 -1 O ARG A 405 N THR A 358 SHEET 5 C 5 GLY A 331 VAL A 335 -1 N GLY A 334 O PHE A 406 SHEET 1 D 7 LYS A 304 GLY A 309 0 SHEET 2 D 7 LEU A 266 THR A 271 -1 N GLY A 269 O GLU A 306 SHEET 3 D 7 LYS A 277 ALA A 283 -1 O LYS A 278 N ILE A 270 SHEET 4 D 7 VAL A 426 GLY A 434 1 O GLY A 430 N ALA A 281 SHEET 5 D 7 LEU A 323 ILE A 326 -1 N ALA A 325 O VAL A 426 SHEET 6 D 7 ALA A 313 PHE A 317 -1 N LYS A 316 O ARG A 324 SHEET 7 D 7 LEU A 261 GLU A 263 -1 N GLU A 263 O ALA A 313 SHEET 1 E 6 LYS A 304 GLY A 309 0 SHEET 2 E 6 LEU A 266 THR A 271 -1 N GLY A 269 O GLU A 306 SHEET 3 E 6 LYS A 277 ALA A 283 -1 O LYS A 278 N ILE A 270 SHEET 4 E 6 VAL A 426 GLY A 434 1 O GLY A 430 N ALA A 281 SHEET 5 E 6 LYS A 510 VAL A 514 1 O PHE A 512 N PHE A 433 SHEET 6 E 6 VAL A 444 GLU A 446 -1 N TYR A 445 O HIS A 513 SHEET 1 F 3 VAL A 368 TYR A 369 0 SHEET 2 F 3 ALA A 361 THR A 363 -1 N ALA A 361 O TYR A 369 SHEET 3 F 3 ILE A 383 THR A 384 -1 O THR A 384 N GLU A 362 SHEET 1 G 2 ARG A 461 GLU A 463 0 SHEET 2 G 2 ILE A 475 HIS A 477 -1 O MSE A 476 N SER A 462 SHEET 1 H 2 THR A 550 THR A 553 0 SHEET 2 H 2 GLY A 556 PRO A 559 -1 O ILE A 558 N LYS A 551 LINK C GLN A 59 N MSE A 60 1555 1555 1.34 LINK C MSE A 60 N GLU A 61 1555 1555 1.32 LINK C TRP A 116 N MSE A 117 1555 1555 1.33 LINK C MSE A 117 N SER A 118 1555 1555 1.35 LINK C CYS A 133 N MSE A 134 1555 1555 1.30 LINK C MSE A 134 N LYS A 135 1555 1555 1.30 LINK C THR A 138 N MSE A 139 1555 1555 1.33 LINK C MSE A 139 N TYR A 140 1555 1555 1.35 LINK C SER A 145 N MSE A 146 1555 1555 1.33 LINK C MSE A 146 N GLY A 147 1555 1555 1.33 LINK C SER A 169 N MSE A 170 1555 1555 1.32 LINK C MSE A 170 N ARG A 171 1555 1555 1.33 LINK C ILE A 172 N MSE A 173 1555 1555 1.32 LINK C MSE A 173 N THR A 174 1555 1555 1.32 LINK C ARG A 175 N MSE A 176 1555 1555 1.32 LINK C MSE A 176 N GLY A 177 1555 1555 1.32 LINK C ARG A 249 N MSE A 250 1555 1555 1.34 LINK C MSE A 250 N ALA A 251 1555 1555 1.34 LINK C HIS A 264 N MSE A 265 1555 1555 1.33 LINK C MSE A 265 N LEU A 266 1555 1555 1.34 LINK C ALA A 294 N MSE A 295 1555 1555 1.31 LINK C MSE A 295 N MSE A 296 1555 1555 1.31 LINK C MSE A 296 N ASN A 297 1555 1555 1.29 LINK C TRP A 314 N MSE A 315 1555 1555 1.28 LINK C MSE A 315 N LYS A 316 1555 1555 1.32 LINK C ALA A 459 N MSE A 460 1555 1555 1.35 LINK C MSE A 460 N ARG A 461 1555 1555 1.32 LINK C ILE A 475 N MSE A 476 1555 1555 1.30 LINK C MSE A 476 N HIS A 477 1555 1555 1.31 LINK C ALA A 481 N MSE A 482 1555 1555 1.32 LINK C MSE A 482 N ARG A 483 1555 1555 1.35 LINK C SER A 499 N MSE A 500 1555 1555 1.32 LINK C MSE A 500 N ALA A 501 1555 1555 1.31 LINK C TRP A 539 N MSE A 540 1555 1555 1.33 LINK C MSE A 540 N PHE A 541 1555 1555 1.31 LINK C ASN A 573 N MSE A 574 1555 1555 1.32 LINK C MSE A 574 N MSE A 575 1555 1555 1.33 LINK C MSE A 575 N GLU A 576 1555 1555 1.32 LINK C GLN A 621 N MSE A 622 1555 1555 1.31 LINK MN MN A 701 OG1 THR A 291 1555 1555 2.06 LINK MN MN A 701 O3G GCP A 703 1555 1555 2.18 LINK MN MN A 701 O HOH A 802 1555 1555 2.03 LINK MN MN A 701 O HOH A 803 1555 1555 2.11 LINK MN MN A 701 O2B GCP A 703 1555 1555 2.06 LINK MN MN A 701 O HOH A 785 1555 1555 2.16 LINK MN MN A 702 OD1 ASP A 311 1555 1555 2.22 LINK MN MN A 702 O1G GCP A 703 1555 1555 2.13 LINK MN MN A 702 O HOH A 733 1555 1555 2.06 LINK MN MN A 702 NZ LYS A 244 1555 1555 2.32 LINK MN MN A 702 O HOH A 797 1555 1555 2.31 LINK MN MN A 702 NE2 HIS A 264 1555 1555 2.31 CISPEP 1 LEU A 200 PRO A 201 0 6.60 SITE 1 AC1 5 THR A 291 GCP A 703 HOH A 785 HOH A 802 SITE 2 AC1 5 HOH A 803 SITE 1 AC2 6 LYS A 244 HIS A 264 ASP A 311 GCP A 703 SITE 2 AC2 6 HOH A 733 HOH A 797 SITE 1 AC3 28 HIS A 264 PRO A 285 ALA A 287 CYS A 288 SITE 2 AC3 28 GLY A 289 LYS A 290 THR A 291 ASN A 292 SITE 3 AC3 28 ASP A 311 VAL A 335 ARG A 405 ARG A 436 SITE 4 AC3 28 TRP A 516 PHE A 517 PHE A 525 GLY A 529 SITE 5 AC3 28 PHE A 530 ASN A 533 MN A 701 MN A 702 SITE 6 AC3 28 HOH A 728 HOH A 729 HOH A 733 HOH A 784 SITE 7 AC3 28 HOH A 785 HOH A 797 HOH A 803 HOH A 844 CRYST1 45.386 60.540 61.833 88.36 70.39 72.37 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.022033 -0.007004 -0.008450 0.00000 SCALE2 0.000000 0.017333 0.001416 0.00000 SCALE3 0.000000 0.000000 0.017226 0.00000