HEADER TRANSFERASE 21-NOV-12 3ZCS
TITLE RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-(1-NAPHTHOYL)
TITLE 2 -N-BETA-D-GLUCOPYRANOSYL UREA DETERMINED AT 2.07 A RESOLUTION
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;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS;
SOURCE 3 ORGANISM_COMMON: RABBIT;
SOURCE 4 ORGANISM_TAXID: 9986;
SOURCE 5 TISSUE: SKELETAL MUSCLE
KEYWDS TRANSFERASE, INHIBITOR, HYPOGLYCAEMIC AGENTS, STRUCTURE-BASED LIGAND
KEYWDS 2 DESIGN
EXPDTA X-RAY DIFFRACTION
AUTHOR E.D.CHRYSINA,V.NAGY,N.FELFOLDI,B.KONYA,K.TELEPO,J.P.PRALY,T.DOCSA,
AUTHOR 2 P.GERGELY,K.M.ALEXACOU,J.M.HAYES,M.KONSTANTAKAKI,R.KARDAKARIS,
AUTHOR 3 D.D.LEONIDAS,S.E.ZOGRAPHOS,N.G.OIKONOMAKOS,L.SOMSAK
REVDAT 3 20-DEC-23 3ZCS 1 REMARK LINK
REVDAT 2 17-JUL-19 3ZCS 1 REMARK LINK
REVDAT 1 11-DEC-13 3ZCS 0
JRNL AUTH E.D.CHRYSINA,V.NAGY,N.FELFOLDI,B.KONYA,K.TELEPO,J.P.PRALY,
JRNL AUTH 2 T.DOCSA,P.GERGELY,K.M.ALEXACOU,J.M.HAYES,M.KONSTANTAKAKI,
JRNL AUTH 3 R.KARDAKARIS,D.D.LEONIDAS,S.E.ZOGRAPHOS,N.G.OIKONOMAKOS,
JRNL AUTH 4 L.SOMSAK
JRNL TITL SYNTHESIS, KINETIC, COMPUTATIONAL AND CRYSTALLOGRAPHIC
JRNL TITL 2 EVALUATION OF N-ACYL-N-BETA-D- GLUCOPYRANOSYL)UREAS,
JRNL TITL 3 NANOMOLAR GLUCOSE ANALOGUE INHIBITORS OF GLYCOGEN
JRNL TITL 4 PHOSPHORYLASE, POTENTIAL ANTIDIABETIC AGENTS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH N.G.OIKONOMAKOS,M.KOSMOPOULOU,S.E.ZOGRAPHOS,D.D.LEONIDAS,
REMARK 1 AUTH 2 E.D.CHRYSINA,L.SOMSAK,V.NAGY,J.PRALY,T.DOCSA,B.TOTH,
REMARK 1 AUTH 3 P.GERGELY
REMARK 1 TITL BINDING OF N-ACETYL-N '-BETA-D-GLUCOPYRANOSYL UREA AND
REMARK 1 TITL 2 N-BENZOYL-N '-BETA-D-GLUCOPYRANOSYL UREA TO GLYCOGEN
REMARK 1 TITL 3 PHOSPHORYLASE B: KINETIC AND CRYSTALLOGRAPHIC STUDIES.
REMARK 1 REF EUR.J.BIOCHEM. V. 269 1684 2002
REMARK 1 REFN ISSN 0014-2956
REMARK 1 PMID 11895439
REMARK 1 DOI 10.1046/J.1432-1327.2002.02813.X
REMARK 2
REMARK 2 RESOLUTION. 2.03 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.5.0072
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.03
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.50
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 3 NUMBER OF REFLECTIONS : 58787
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) : 0.193
REMARK 3 R VALUE (WORKING SET) : 0.192
REMARK 3 FREE R VALUE : 0.217
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 3138
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) : 2.03
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.08
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4249
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.15
REMARK 3 BIN R VALUE (WORKING SET) : 0.2340
REMARK 3 BIN FREE R VALUE SET COUNT : 262
REMARK 3 BIN FREE R VALUE : 0.2790
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6558
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 65
REMARK 3 SOLVENT ATOMS : 275
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.23
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): 0.187
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.154
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.749
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6774 ; 0.007 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9176 ; 0.999 ; 1.962
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 804 ; 5.095 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 344 ;33.836 ;23.517
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1171 ;13.928 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 59 ;19.008 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 983 ; 0.070 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5184 ; 0.004 ; 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): 4018 ; 0.482 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6487 ; 0.938 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2756 ; 1.256 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2689 ; 2.201 ; 4.500
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 : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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. THE FOLLOWING RESIDUES WERE NOT INCLUDED IN THE
REMARK 3 STRUCTURE SINCE THERE WAS NOT SUFFICIENT DENSITY TO INDICATE
REMARK 3 THEIR POSITION 1-11, 252-260, 315-323, 837-842
REMARK 4
REMARK 4 3ZCS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-12.
REMARK 100 THE DEPOSITION ID IS D_1290054825.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-JUL-02
REMARK 200 TEMPERATURE (KELVIN) : 298
REMARK 200 PH : 6.8
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG
REMARK 200 BEAMLINE : BW7B
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.84410
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC CCD
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61970
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.030
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0
REMARK 200 DATA REDUNDANCY : 4.000
REMARK 200 R MERGE (I) : 0.06000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.03
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.2
REMARK 200 DATA REDUNDANCY IN SHELL : 4.10
REMARK 200 R MERGE FOR SHELL (I) : 0.27000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.700
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: PDB ENTRY 2QNB
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 50.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: PH 6.8
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 58.25650
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.14150
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.14150
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.38475
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.14150
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.14150
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.12825
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.14150
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.14150
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.38475
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.14150
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.14150
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.12825
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 58.25650
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: 8590 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 57060 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.5 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 116.51300
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 PHE A 252
REMARK 465 ASN A 253
REMARK 465 LEU A 254
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 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 GLN A 12 CG CD OE1 NE2
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 72.54 -110.44
REMARK 500 LEU A 131 39.74 -90.64
REMARK 500 TYR A 203 -135.11 64.08
REMARK 500 GLN A 211 42.82 -99.85
REMARK 500 ASP A 339 -171.85 69.19
REMARK 500 THR A 466 -87.41 -122.94
REMARK 500 LEU A 492 -64.10 -139.22
REMARK 500 ASP A 514 73.11 -153.23
REMARK 500 LYS A 554 55.01 -98.87
REMARK 500 LYS A 568 164.73 171.71
REMARK 500 SER A 674 -58.42 -140.51
REMARK 500 SER A 751 76.03 -158.16
REMARK 500 HIS A 768 54.16 -149.31
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 PLP A 1837
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMP A 1838
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CAW A 1839
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3ZCP RELATED DB: PDB
REMARK 900 RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-
REMARK 900 CYCLOHEXANCARBONYL-N-BETA-D-GLUCOPYRANOSYL UREA DETERMINED AT 1.83
REMARK 900 A RESOLUTION
REMARK 900 RELATED ID: 3ZCQ RELATED DB: PDB
REMARK 900 RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-(4-
REMARK 900 TRIFLUOROMETHYL-BENZOYL)-N-BETA-D-GLUCOPYRANOSYL UREA DETERMINED AT
REMARK 900 2.15 A RESOLUTION
REMARK 900 RELATED ID: 3ZCR RELATED DB: PDB
REMARK 900 RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-(4-TERT-
REMARK 900 BUTYL-BENZOYL)-N-BETA-D-GLUCOPYRANOSYL UREA DETERMINED AT 2.07 A
REMARK 900 RESOLUTION
REMARK 900 RELATED ID: 3ZCT RELATED DB: PDB
REMARK 900 RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-(2-
REMARK 900 NAPHTHOYL)-N-BETA-D-GLUCOPYRANOSYL UREA DETERMINED AT 2.0 A
REMARK 900 RESOLUTION
REMARK 900 RELATED ID: 3ZCU RELATED DB: PDB
REMARK 900 RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-(PYRIDYL-2-
REMARK 900 CARBONYL)-N-BETA-D-GLUCOPYRANOSYL UREA DETERMINED AT 2.05 A
REMARK 900 RESOLUTION
REMARK 900 RELATED ID: 3ZCV RELATED DB: PDB
REMARK 900 RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH N-(INDOL-2-
REMARK 900 CARBONYL)-N-BETA-D-GLUCOPYRANOSYL UREA DETERMINED AT 1.8 A
REMARK 900 RESOLUTION
DBREF 3ZCS A 0 842 UNP P00489 PYGM_RABIT 1 843
SEQADV 3ZCS ILE A 380 UNP P00489 LEU 381 ENGINEERED MUTATION
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 ILE 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 A1837 15
HET IMP A1838 23
HET CAW A1839 27
HETNAM PLP PYRIDOXAL-5'-PHOSPHATE
HETNAM IMP INOSINIC ACID
HETNAM CAW N-[[(2R,3R,4S,5S,6R)-6-(HYDROXYMETHYL)-3,4,5-
HETNAM 2 CAW TRIS(OXIDANYL)OXAN-2-YL]CARBAMOYL]NAPHTHALENE-1-
HETNAM 3 CAW CARBOXAMIDE
HETSYN PLP VITAMIN B6 PHOSPHATE
FORMUL 2 PLP C8 H10 N O6 P
FORMUL 3 IMP C10 H13 N4 O8 P
FORMUL 4 CAW C18 H20 N2 O7
FORMUL 5 HOH *275(H2 O)
HELIX 1 1 ILE A 13 GLY A 17 5 5
HELIX 2 2 GLY A 20 THR A 38 1 19
HELIX 3 3 THR A 47 ASP A 78 1 32
HELIX 4 4 THR A 94 LEU A 102 1 9
HELIX 5 5 LEU A 104 LEU A 115 1 12
HELIX 6 6 ASP A 118 GLU A 124 1 7
HELIX 7 7 GLY A 134 LEU A 150 1 17
HELIX 8 8 PRO A 194 THR A 197 5 4
HELIX 9 9 GLY A 261 ASP A 268 1 8
HELIX 10 10 ARG A 269 ASN A 274 1 6
HELIX 11 11 ILE A 275 ARG A 277 5 3
HELIX 12 12 LYS A 289 SER A 313 1 25
HELIX 13 13 ASN A 325 ASP A 327 5 3
HELIX 14 14 ALA A 328 LYS A 332 1 5
HELIX 15 15 LEU A 344 LEU A 356 1 13
HELIX 16 16 ASP A 360 THR A 371 1 12
HELIX 17 17 ILE A 380 LEU A 384 5 5
HELIX 18 18 VAL A 389 LEU A 396 1 8
HELIX 19 19 LEU A 396 PHE A 418 1 23
HELIX 20 20 ASP A 421 SER A 429 1 9
HELIX 21 21 MET A 441 GLY A 448 1 8
HELIX 22 22 ALA A 456 THR A 466 1 11
HELIX 23 23 PHE A 468 GLU A 475 1 8
HELIX 24 24 PRO A 488 CYS A 495 1 8
HELIX 25 25 ASN A 496 GLY A 508 1 13
HELIX 26 26 GLU A 509 ASP A 514 5 6
HELIX 27 27 ASP A 514 VAL A 525 5 12
HELIX 28 28 ASP A 527 TYR A 553 1 27
HELIX 29 29 ARG A 575 GLU A 593 1 19
HELIX 30 30 TYR A 613 ASN A 631 1 19
HELIX 31 31 ARG A 649 ILE A 657 1 9
HELIX 32 32 PRO A 658 ALA A 660 5 3
HELIX 33 33 THR A 676 ASN A 684 1 9
HELIX 34 34 ALA A 695 GLY A 704 1 10
HELIX 35 35 GLU A 705 PHE A 708 5 4
HELIX 36 36 ARG A 714 GLY A 725 1 12
HELIX 37 37 ASN A 727 ILE A 735 1 9
HELIX 38 38 ILE A 735 GLY A 748 1 14
HELIX 39 39 PHE A 758 HIS A 768 1 11
HELIX 40 40 LYS A 772 LYS A 792 1 21
HELIX 41 41 ASN A 793 THR A 807 1 15
HELIX 42 42 SER A 808 PHE A 811 5 4
HELIX 43 43 SER A 812 ILE A 824 1 13
SHEET 1 AA 2 LYS A 191 ALA A 192 0
SHEET 2 AA 2 GLN A 219 PRO A 231 -1 O ASP A 227 N LYS A 191
SHEET 1 AB 2 LEU A 198 PHE A 202 0
SHEET 2 AB 2 GLN A 219 PRO A 231 -1 O GLN A 219 N PHE A 202
SHEET 1 AC 9 PHE A 479 ASN A 481 0
SHEET 2 AC 9 ALA A 451 GLY A 454 1 O VAL A 452 N GLN A 480
SHEET 3 AC 9 CYS A 372 THR A 375 1 O TYR A 374 N ASN A 453
SHEET 4 AC 9 VAL A 333 ASN A 338 1 O ILE A 335 N ALA A 373
SHEET 5 AC 9 ARG A 81 LEU A 85 1 O ARG A 81 N ALA A 334
SHEET 6 AC 9 ALA A 154 ILE A 159 1 O TYR A 155 N TYR A 84
SHEET 7 AC 9 VAL A 238 LYS A 247 1 O THR A 240 N GLY A 156
SHEET 8 AC 9 GLN A 219 PRO A 231 -1 O LEU A 222 N LYS A 247
SHEET 9 AC 9 LEU A 198 PHE A 202 -1 O LEU A 198 N ALA A 223
SHEET 1 AD 9 PHE A 479 ASN A 481 0
SHEET 2 AD 9 ALA A 451 GLY A 454 1 O VAL A 452 N GLN A 480
SHEET 3 AD 9 CYS A 372 THR A 375 1 O TYR A 374 N ASN A 453
SHEET 4 AD 9 VAL A 333 ASN A 338 1 O ILE A 335 N ALA A 373
SHEET 5 AD 9 ARG A 81 LEU A 85 1 O ARG A 81 N ALA A 334
SHEET 6 AD 9 ALA A 154 ILE A 159 1 O TYR A 155 N TYR A 84
SHEET 7 AD 9 VAL A 238 LYS A 247 1 O THR A 240 N GLY A 156
SHEET 8 AD 9 GLN A 219 PRO A 231 -1 O LEU A 222 N LYS A 247
SHEET 9 AD 9 LYS A 191 ALA A 192 -1 O LYS A 191 N ASP A 227
SHEET 1 AE 2 PHE A 89 GLY A 92 0
SHEET 2 AE 2 ALA A 129 LEU A 131 -1 O ALA A 129 N GLY A 92
SHEET 1 AF 2 ASN A 167 CYS A 171 0
SHEET 2 AF 2 TRP A 174 GLU A 178 -1 O TRP A 174 N CYS A 171
SHEET 1 AG 2 ARG A 205 THR A 209 0
SHEET 2 AG 2 GLY A 212 VAL A 216 -1 O GLY A 212 N THR A 209
SHEET 1 AH 3 ARG A 386 PRO A 388 0
SHEET 2 AH 3 ARG A 438 ASN A 440 -1 O ILE A 439 N TRP A 387
SHEET 3 AH 3 VAL A 431 GLU A 432 -1 O GLU A 432 N ARG A 438
SHEET 1 AI 6 LEU A 640 LEU A 645 0
SHEET 2 AI 6 ARG A 601 GLY A 606 1 O ARG A 601 N ARG A 641
SHEET 3 AI 6 LEU A 562 VAL A 567 1 O LEU A 562 N THR A 602
SHEET 4 AI 6 LEU A 662 GLN A 665 1 O LEU A 662 N VAL A 565
SHEET 5 AI 6 LEU A 687 GLY A 690 1 O LEU A 687 N SER A 663
SHEET 6 AI 6 PHE A 709 ILE A 710 1 O PHE A 709 N GLY A 690
LINK NZ LYS A 680 C4A PLP A1837 1555 1555 1.33
SITE 1 AC1 15 LYS A 568 LYS A 574 TYR A 648 ARG A 649
SITE 2 AC1 15 VAL A 650 GLY A 675 THR A 676 GLY A 677
SITE 3 AC1 15 LYS A 680 HOH A2036 HOH A2193 HOH A2194
SITE 4 AC1 15 HOH A2196 HOH A2228 HOH A2234
SITE 1 AC2 7 ASP A 42 VAL A 45 GLN A 72 TYR A 75
SITE 2 AC2 7 ARG A 309 ARG A 310 HOH A2022
SITE 1 AC3 22 GLU A 88 ASN A 133 GLY A 135 LEU A 136
SITE 2 AC3 22 ASN A 282 ASP A 283 HIS A 341 HIS A 377
SITE 3 AC3 22 ALA A 383 ASN A 484 TYR A 573 GLU A 672
SITE 4 AC3 22 ALA A 673 SER A 674 GLY A 675 HOH A2033
SITE 5 AC3 22 HOH A2112 HOH A2136 HOH A2137 HOH A2203
SITE 6 AC3 22 HOH A2204 HOH A2234
CRYST1 128.283 128.283 116.513 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 0.007795 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007795 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008583 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
