HEADER TRANSFERASE 31-MAY-17 5O56 TITLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH 29B COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOGEN PHOSPHORYLASE, MUSCLE FORM; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MYOPHOSPHORYLASE; COMPND 5 EC: 2.4.1.1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986 KEYWDS TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.G.A.SOLOVOU,E.KYRIAKIS,G.A.STRAVODIMOS,A.L.KANTSADI, AUTHOR 2 D.S.CHATZILEONTIADOU,V.T.SKAMNAKI,D.D.LEONIDAS REVDAT 2 29-NOV-17 5O56 1 JRNL REVDAT 1 27-SEP-17 5O56 0 JRNL AUTH E.BOKOR,E.KYRIAKIS,T.G.A.SOLOVOU,C.KOPPANY,A.L.KANTSADI, JRNL AUTH 2 K.E.SZABO,A.SZAKACS,G.A.STRAVODIMOS,T.DOCSA,V.T.SKAMNAKI, JRNL AUTH 3 S.E.ZOGRAPHOS,P.GERGELY,D.D.LEONIDAS,L.SOMSAK JRNL TITL NANOMOLAR INHIBITORS OF GLYCOGEN PHOSPHORYLASE BASED ON JRNL TITL 2 BETA-D-GLUCOSAMINYL HETEROCYCLES: A COMBINED SYNTHETIC, JRNL TITL 3 ENZYME KINETIC, AND PROTEIN CRYSTALLOGRAPHY STUDY. JRNL REF J. MED. CHEM. V. 60 9251 2017 JRNL REFN ISSN 1520-4804 JRNL PMID 28925695 JRNL DOI 10.1021/ACS.JMEDCHEM.7B01056 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 33683 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1776 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2349 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 93.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 136 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6589 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 41 REMARK 3 SOLVENT ATOMS : 199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.07000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : 0.14000 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): 0.432 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.260 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.200 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.130 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6809 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9225 ; 2.213 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 813 ; 6.990 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 350 ;38.338 ;23.486 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1178 ;17.683 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 60 ;21.484 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 995 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5232 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3243 ; 1.293 ; 1.763 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4050 ; 2.254 ; 2.635 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3566 ; 2.030 ; 2.010 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): 10042 ; 5.045 ;22.975 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 : 1 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 12 A 836 REMARK 3 ORIGIN FOR THE GROUP (A): 28.3000 21.2870 31.5670 REMARK 3 T TENSOR REMARK 3 T11: 0.0422 T22: 0.0722 REMARK 3 T33: 0.0116 T12: -0.0341 REMARK 3 T13: 0.0005 T23: -0.0178 REMARK 3 L TENSOR REMARK 3 L11: 0.5723 L22: 0.4320 REMARK 3 L33: 0.8843 L12: 0.0338 REMARK 3 L13: -0.0102 L23: -0.1265 REMARK 3 S TENSOR REMARK 3 S11: -0.0360 S12: 0.0283 S13: 0.0500 REMARK 3 S21: -0.0074 S22: 0.0070 S23: 0.0097 REMARK 3 S31: 0.0510 S32: -0.1013 S33: 0.0290 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5O56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005204. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-FEB-17 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : OXFORD DIFFRACTION NOVA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35487 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450 REMARK 200 RESOLUTION RANGE LOW (A) : 13.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12200 REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.56 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.79300 REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM BES BUFFER, PH 6.8, SMALL TUBES, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 58.07050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.27400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.27400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.10575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.27400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.27400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.03525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.27400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.27400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.10575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.27400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.27400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.03525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.07050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5680 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 56850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 116.14100 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 0 REMARK 465 SER A 1 REMARK 465 ARG A 2 REMARK 465 PRO A 3 REMARK 465 LEU A 4 REMARK 465 SER A 5 REMARK 465 ASP A 6 REMARK 465 GLN A 7 REMARK 465 GLU A 8 REMARK 465 LYS A 9 REMARK 465 ARG A 10 REMARK 465 LYS A 11 REMARK 465 LYS A 255 REMARK 465 ASP A 256 REMARK 465 PHE A 257 REMARK 465 ASN A 258 REMARK 465 VAL A 259 REMARK 465 GLY A 260 REMARK 465 LYS A 315 REMARK 465 PHE A 316 REMARK 465 GLY A 317 REMARK 465 CYS A 318 REMARK 465 ARG A 319 REMARK 465 ASP A 320 REMARK 465 PRO A 321 REMARK 465 VAL A 322 REMARK 465 ARG A 323 REMARK 465 PRO A 837 REMARK 465 ASP A 838 REMARK 465 GLU A 839 REMARK 465 LYS A 840 REMARK 465 ILE A 841 REMARK 465 PRO A 842 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 OE1 GLN A 539 O HOH A 1001 2.15 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 90 CE1 TYR A 90 CZ 0.078 REMARK 500 TRP A 797 CE3 TRP A 797 CZ3 0.104 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 LEU A 85 CB - CG - CD2 ANGL. DEV. = -15.0 DEGREES REMARK 500 ASP A 109 CB - CG - OD1 ANGL. DEV. = 7.8 DEGREES REMARK 500 CYS A 171 CA - CB - SG ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 205 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 269 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ASP A 339 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 355 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 LEU A 384 CB - CG - CD1 ANGL. DEV. = -11.7 DEGREES REMARK 500 ARG A 424 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 424 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 427 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ASP A 470 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 519 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 569 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 739 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ARG A 770 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 786 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 786 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 815 NE - CZ - NH2 ANGL. DEV. = -3.3 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 ALA A 19 68.94 -117.30 REMARK 500 ALA A 129 97.86 -68.71 REMARK 500 LEU A 131 42.34 -88.36 REMARK 500 TYR A 203 -128.22 66.86 REMARK 500 TYR A 233 99.39 -67.62 REMARK 500 ASN A 253 -23.56 72.14 REMARK 500 SER A 313 48.62 -101.55 REMARK 500 ASP A 339 -162.43 64.08 REMARK 500 THR A 466 -84.73 -131.18 REMARK 500 LEU A 492 -65.18 -148.59 REMARK 500 ASN A 496 59.57 -146.83 REMARK 500 GLN A 517 -19.50 -47.87 REMARK 500 LYS A 554 52.71 26.24 REMARK 500 LYS A 568 164.38 175.62 REMARK 500 SER A 674 -54.76 -133.22 REMARK 500 HIS A 768 40.53 -140.93 REMARK 500 ASN A 793 79.23 -108.70 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 A1198 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A1199 DISTANCE = 7.73 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9L8 A 902 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5O50 RELATED DB: PDB REMARK 900 RELATED ID: 5O52 RELATED DB: PDB REMARK 900 RELATED ID: 5O54 RELATED DB: PDB DBREF 5O56 A 0 842 UNP P00489 PYGM_RABIT 1 843 SEQRES 1 A 843 MET SER ARG PRO LEU SER ASP GLN GLU LYS ARG LYS GLN SEQRES 2 A 843 ILE SER VAL ARG GLY LEU ALA GLY VAL GLU ASN VAL THR SEQRES 3 A 843 GLU LEU LYS LYS ASN PHE ASN ARG HIS LEU HIS PHE THR SEQRES 4 A 843 LEU VAL LYS ASP ARG ASN VAL ALA THR PRO ARG ASP TYR SEQRES 5 A 843 TYR PHE ALA LEU ALA HIS THR VAL ARG ASP HIS LEU VAL SEQRES 6 A 843 GLY ARG TRP ILE ARG THR GLN GLN HIS TYR TYR GLU LYS SEQRES 7 A 843 ASP PRO LYS ARG ILE TYR TYR LEU SER LEU GLU PHE TYR SEQRES 8 A 843 MET GLY ARG THR LEU GLN ASN THR MET VAL ASN LEU ALA SEQRES 9 A 843 LEU GLU ASN ALA CYS ASP GLU ALA THR TYR GLN LEU GLY SEQRES 10 A 843 LEU ASP MET GLU GLU LEU GLU GLU ILE GLU GLU ASP ALA SEQRES 11 A 843 GLY LEU GLY ASN GLY GLY LEU GLY ARG LEU ALA ALA CYS SEQRES 12 A 843 PHE LEU ASP SER MET ALA THR LEU GLY LEU ALA ALA TYR SEQRES 13 A 843 GLY TYR GLY ILE ARG TYR GLU PHE GLY ILE PHE ASN GLN SEQRES 14 A 843 LYS ILE CYS GLY GLY TRP GLN MET GLU GLU ALA ASP ASP SEQRES 15 A 843 TRP LEU ARG TYR GLY ASN PRO TRP GLU LYS ALA ARG PRO SEQRES 16 A 843 GLU PHE THR LEU PRO VAL HIS PHE TYR GLY ARG VAL GLU SEQRES 17 A 843 HIS THR SER GLN GLY ALA LYS TRP VAL ASP THR GLN VAL SEQRES 18 A 843 VAL LEU ALA MET PRO TYR ASP THR PRO VAL PRO GLY TYR SEQRES 19 A 843 ARG ASN ASN VAL VAL ASN THR MET ARG LEU TRP SER ALA SEQRES 20 A 843 LYS ALA PRO ASN ASP PHE ASN LEU LYS ASP PHE ASN VAL SEQRES 21 A 843 GLY GLY TYR ILE GLN ALA VAL LEU ASP ARG ASN LEU ALA SEQRES 22 A 843 GLU ASN ILE SER ARG VAL LEU TYR PRO ASN ASP ASN PHE SEQRES 23 A 843 PHE GLU GLY LYS GLU LEU ARG LEU LYS GLN GLU TYR PHE SEQRES 24 A 843 VAL VAL ALA ALA THR LEU GLN ASP ILE ILE ARG ARG PHE SEQRES 25 A 843 LYS SER SER LYS PHE GLY CYS ARG ASP PRO VAL ARG THR SEQRES 26 A 843 ASN PHE ASP ALA PHE PRO ASP LYS VAL ALA ILE GLN LEU SEQRES 27 A 843 ASN ASP THR HIS PRO SER LEU ALA ILE PRO GLU LEU MET SEQRES 28 A 843 ARG VAL LEU VAL ASP LEU GLU ARG LEU ASP TRP ASP LYS SEQRES 29 A 843 ALA TRP GLU VAL THR VAL LYS THR CYS ALA TYR THR ASN SEQRES 30 A 843 HIS THR VAL LEU PRO GLU ALA LEU GLU ARG TRP PRO VAL SEQRES 31 A 843 HIS LEU LEU GLU THR LEU LEU PRO ARG HIS LEU GLN ILE SEQRES 32 A 843 ILE TYR GLU ILE ASN GLN ARG PHE LEU ASN ARG VAL ALA SEQRES 33 A 843 ALA ALA PHE PRO GLY ASP VAL ASP ARG LEU ARG ARG MET SEQRES 34 A 843 SER LEU VAL GLU GLU GLY ALA VAL LYS ARG ILE ASN MET SEQRES 35 A 843 ALA HIS LEU CYS ILE ALA GLY SER HIS ALA VAL ASN GLY SEQRES 36 A 843 VAL ALA ARG ILE HIS SER GLU ILE LEU LYS LYS THR ILE SEQRES 37 A 843 PHE LYS ASP PHE TYR GLU LEU GLU PRO HIS LYS PHE GLN SEQRES 38 A 843 ASN LYS THR ASN GLY ILE THR PRO ARG ARG TRP LEU VAL SEQRES 39 A 843 LEU CYS ASN PRO GLY LEU ALA GLU ILE ILE ALA GLU ARG SEQRES 40 A 843 ILE GLY GLU GLU TYR ILE SER ASP LEU ASP GLN LEU ARG SEQRES 41 A 843 LYS LEU LEU SER TYR VAL ASP ASP GLU ALA PHE ILE ARG SEQRES 42 A 843 ASP VAL ALA LYS VAL LYS GLN GLU ASN LYS LEU LYS PHE SEQRES 43 A 843 ALA ALA TYR LEU GLU ARG GLU TYR LYS VAL HIS ILE ASN SEQRES 44 A 843 PRO ASN SER LEU PHE ASP VAL GLN VAL LYS ARG ILE HIS SEQRES 45 A 843 GLU TYR LYS ARG GLN LEU LEU ASN CYS LEU HIS VAL ILE SEQRES 46 A 843 THR LEU TYR ASN ARG ILE LYS LYS GLU PRO ASN LYS PHE SEQRES 47 A 843 VAL VAL PRO ARG THR VAL MET ILE GLY GLY LYS ALA ALA SEQRES 48 A 843 PRO GLY TYR HIS MET ALA LYS MET ILE ILE LYS LEU ILE SEQRES 49 A 843 THR ALA ILE GLY ASP VAL VAL ASN HIS ASP PRO VAL VAL SEQRES 50 A 843 GLY ASP ARG LEU ARG VAL ILE PHE LEU GLU ASN TYR ARG SEQRES 51 A 843 VAL SER LEU ALA GLU LYS VAL ILE PRO ALA ALA ASP LEU SEQRES 52 A 843 SER GLU GLN ILE SER THR ALA GLY THR GLU ALA SER GLY SEQRES 53 A 843 THR GLY ASN MET LYS PHE MET LEU ASN GLY ALA LEU THR SEQRES 54 A 843 ILE GLY THR MET ASP GLY ALA ASN VAL GLU MET ALA GLU SEQRES 55 A 843 GLU ALA GLY GLU GLU ASN PHE PHE ILE PHE GLY MET ARG SEQRES 56 A 843 VAL GLU ASP VAL ASP ARG LEU ASP GLN ARG GLY TYR ASN SEQRES 57 A 843 ALA GLN GLU TYR TYR ASP ARG ILE PRO GLU LEU ARG GLN SEQRES 58 A 843 ILE ILE GLU GLN LEU SER SER GLY PHE PHE SER PRO LYS SEQRES 59 A 843 GLN PRO ASP LEU PHE LYS ASP ILE VAL ASN MET LEU MET SEQRES 60 A 843 HIS HIS ASP ARG PHE LYS VAL PHE ALA ASP TYR GLU GLU SEQRES 61 A 843 TYR VAL LYS CYS GLN GLU ARG VAL SER ALA LEU TYR LYS SEQRES 62 A 843 ASN PRO ARG GLU TRP THR ARG MET VAL ILE ARG ASN ILE SEQRES 63 A 843 ALA THR SER GLY LYS PHE SER SER ASP ARG THR ILE ALA SEQRES 64 A 843 GLN TYR ALA ARG GLU ILE TRP GLY VAL GLU PRO SER ARG SEQRES 65 A 843 GLN ARG LEU PRO ALA PRO ASP GLU LYS ILE PRO HET PLP A 901 15 HET 9L8 A 902 26 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETNAM 9L8 (2~{R},3~{S},4~{R},5~{R},6~{R})-5-AZANYL-2- HETNAM 2 9L8 (HYDROXYMETHYL)-6-(3-NAPHTHALEN-2-YL-1~{H}-1,2,4- HETNAM 3 9L8 TRIAZOL-5-YL)OXANE-3,4-DIOL HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 9L8 C18 H20 N4 O4 FORMUL 4 HOH *199(H2 O) HELIX 1 AA1 ILE A 13 GLY A 17 5 5 HELIX 2 AA2 GLY A 20 THR A 38 1 19 HELIX 3 AA3 THR A 47 ASP A 78 1 32 HELIX 4 AA4 THR A 94 LEU A 102 1 9 HELIX 5 AA5 LEU A 104 LEU A 115 1 12 HELIX 6 AA6 ASP A 118 GLU A 124 1 7 HELIX 7 AA7 GLY A 134 LEU A 150 1 17 HELIX 8 AA8 PRO A 194 THR A 197 5 4 HELIX 9 AA9 TYR A 262 ASP A 268 1 7 HELIX 10 AB1 ARG A 269 ASN A 274 1 6 HELIX 11 AB2 ILE A 275 ARG A 277 5 3 HELIX 12 AB3 LYS A 289 SER A 313 1 25 HELIX 13 AB4 ASN A 325 ASP A 327 5 3 HELIX 14 AB5 ALA A 328 LYS A 332 1 5 HELIX 15 AB6 LEU A 344 LEU A 356 1 13 HELIX 16 AB7 ASP A 360 THR A 371 1 12 HELIX 17 AB8 LEU A 380 LEU A 384 5 5 HELIX 18 AB9 VAL A 389 LEU A 396 1 8 HELIX 19 AC1 LEU A 396 PHE A 418 1 23 HELIX 20 AC2 ASP A 421 SER A 429 1 9 HELIX 21 AC3 MET A 441 SER A 449 1 9 HELIX 22 AC4 ALA A 456 THR A 466 1 11 HELIX 23 AC5 PHE A 468 GLU A 475 1 8 HELIX 24 AC6 ASN A 496 GLY A 508 1 13 HELIX 25 AC7 GLU A 509 VAL A 525 5 17 HELIX 26 AC8 ASP A 527 LYS A 554 1 28 HELIX 27 AC9 ARG A 575 GLU A 593 1 19 HELIX 28 AD1 TYR A 613 ASN A 631 1 19 HELIX 29 AD2 ARG A 649 ILE A 657 1 9 HELIX 30 AD3 THR A 676 ASN A 684 1 9 HELIX 31 AD4 ALA A 695 GLY A 704 1 10 HELIX 32 AD5 GLU A 705 PHE A 708 5 4 HELIX 33 AD6 ARG A 714 GLY A 725 1 12 HELIX 34 AD7 ALA A 728 ILE A 735 1 8 HELIX 35 AD8 ILE A 735 GLY A 748 1 14 HELIX 36 AD9 PHE A 758 HIS A 768 1 11 HELIX 37 AE1 VAL A 773 ALA A 775 5 3 HELIX 38 AE2 ASP A 776 LYS A 792 1 17 HELIX 39 AE3 ASN A 793 THR A 807 1 15 HELIX 40 AE4 SER A 808 PHE A 811 5 4 HELIX 41 AE5 SER A 812 ILE A 824 1 13 SHEET 1 AA1 3 LYS A 191 ALA A 192 0 SHEET 2 AA1 3 ALA A 213 PRO A 231 -1 O ASP A 227 N LYS A 191 SHEET 3 AA1 3 LEU A 198 HIS A 208 -1 N LEU A 198 O ALA A 223 SHEET 1 AA2 9 LYS A 191 ALA A 192 0 SHEET 2 AA2 9 ALA A 213 PRO A 231 -1 O ASP A 227 N LYS A 191 SHEET 3 AA2 9 VAL A 238 LYS A 247 -1 O MET A 241 N THR A 228 SHEET 4 AA2 9 ALA A 154 ILE A 159 1 N GLY A 156 O ARG A 242 SHEET 5 AA2 9 ARG A 81 LEU A 85 1 N ILE A 82 O TYR A 155 SHEET 6 AA2 9 VAL A 333 ASN A 338 1 O GLN A 336 N TYR A 83 SHEET 7 AA2 9 CYS A 372 THR A 375 1 O ALA A 373 N LEU A 337 SHEET 8 AA2 9 ALA A 451 GLY A 454 1 O ALA A 451 N TYR A 374 SHEET 9 AA2 9 PHE A 479 ASN A 481 1 O GLN A 480 N VAL A 452 SHEET 1 AA3 2 PHE A 89 GLY A 92 0 SHEET 2 AA3 2 ALA A 129 LEU A 131 -1 O LEU A 131 N PHE A 89 SHEET 1 AA4 2 ASN A 167 CYS A 171 0 SHEET 2 AA4 2 TRP A 174 GLU A 178 -1 O MET A 176 N LYS A 169 SHEET 1 AA5 3 ARG A 386 PRO A 388 0 SHEET 2 AA5 3 ARG A 438 ASN A 440 -1 O ILE A 439 N TRP A 387 SHEET 3 AA5 3 VAL A 431 GLU A 432 -1 N GLU A 432 O ARG A 438 SHEET 1 AA6 6 LEU A 640 LEU A 645 0 SHEET 2 AA6 6 ARG A 601 GLY A 606 1 N VAL A 603 O ILE A 643 SHEET 3 AA6 6 LEU A 562 VAL A 567 1 N ASP A 564 O MET A 604 SHEET 4 AA6 6 LEU A 662 GLN A 665 1 O LEU A 662 N PHE A 563 SHEET 5 AA6 6 LEU A 687 GLY A 690 1 O ILE A 689 N SER A 663 SHEET 6 AA6 6 PHE A 709 ILE A 710 1 O PHE A 709 N THR A 688 LINK NZ LYS A 680 C4A PLP A 901 1555 1555 1.44 SITE 1 AC1 17 GLY A 134 GLY A 135 TRP A 491 LYS A 568 SITE 2 AC1 17 LYS A 574 TYR A 648 ARG A 649 VAL A 650 SITE 3 AC1 17 GLY A 675 THR A 676 GLY A 677 LYS A 680 SITE 4 AC1 17 HOH A1028 HOH A1035 HOH A1047 HOH A1050 SITE 5 AC1 17 HOH A1124 SITE 1 AC2 18 GLU A 88 LEU A 136 LEU A 139 ASN A 282 SITE 2 AC2 18 ASN A 284 PHE A 285 ARG A 292 HIS A 341 SITE 3 AC2 18 HIS A 377 ALA A 383 ASN A 484 TYR A 573 SITE 4 AC2 18 GLU A 672 ALA A 673 SER A 674 GLY A 675 SITE 5 AC2 18 HOH A1045 HOH A1050 CRYST1 128.548 128.548 116.141 90.00 90.00 90.00 P 43 21 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 0.007779 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007779 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008610 0.00000