HEADER TRANSFERASE 10-APR-12 4EKY
TITLE CRYSTAL STRUCTURE OF GPB IN COMPLEX WITH DK15
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: EUROPEAN RABBIT,JAPANESE WHITE RABBIT,DOMESTIC
SOURCE 4 RABBIT,RABBITS;
SOURCE 5 ORGANISM_TAXID: 9986
KEYWDS ALPHA/BETA PROTEIN, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR A.L.KANTSADI,V.T.SKAMNAKI,D.D.LEONIDAS
REVDAT 5 06-DEC-23 4EKY 1 REMARK
REVDAT 4 13-SEP-23 4EKY 1 REMARK LINK
REVDAT 3 15-NOV-17 4EKY 1 REMARK
REVDAT 2 15-AUG-12 4EKY 1 JRNL
REVDAT 1 25-JUL-12 4EKY 0
JRNL AUTH A.L.KANTSADI,S.MANTA,A.M.PSARRA,A.DIMOPOULOU,C.KIRITSIS,
JRNL AUTH 2 V.PARMENOPOULOU,V.T.SKAMNAKI,P.ZOUMPOULAKIS,S.E.ZOGRAPHOS,
JRNL AUTH 3 D.D.LEONIDAS,D.KOMIOTIS
JRNL TITL THE BINDING OF C5-ALKYNYL AND ALKYLFURANO[2,3-D]PYRIMIDINE
JRNL TITL 2 GLUCOPYRANONUCLEOSIDES TO GLYCOGEN PHOSPHORYLASE B:
JRNL TITL 3 SYNTHESIS, BIOCHEMICAL AND BIOLOGICAL ASSESSMENT.
JRNL REF EUR.J.MED.CHEM. V. 54 740 2012
JRNL REFN ISSN 0223-5234
JRNL PMID 22770609
JRNL DOI 10.1016/J.EJMECH.2012.06.029
REMARK 2
REMARK 2 RESOLUTION. 2.45 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
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) : 2.45
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 13.57
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 92.4
REMARK 3 NUMBER OF REFLECTIONS : 31848
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) : 0.164
REMARK 3 R VALUE (WORKING SET) : 0.161
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1700
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) : 1962
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.02
REMARK 3 BIN R VALUE (WORKING SET) : 0.2410
REMARK 3 BIN FREE R VALUE SET COUNT : 125
REMARK 3 BIN FREE R VALUE : 0.3120
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 6604
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 24
REMARK 3 SOLVENT ATOMS : 149
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.64
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -0.01000
REMARK 3 B22 (A**2) : -0.01000
REMARK 3 B33 (A**2) : 0.03000
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): 0.494
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.272
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.722
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6786 ; 0.018 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9188 ; 1.771 ; 1.957
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 807 ; 6.487 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 348 ;36.087 ;23.534
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1179 ;18.638 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 59 ;22.990 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 994 ; 0.125 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5200 ; 0.008 ; 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): 4035 ; 0.932 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6517 ; 1.813 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2751 ; 2.944 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2671 ; 4.957 ; 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
REMARK 4
REMARK 4 4EKY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-12.
REMARK 100 THE DEPOSITION ID IS D_1000071748.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 07-OCT-11
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 6.7
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 ENHANCE ULTRA
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5419
REMARK 200 MONOCHROMATOR : MIRRORS
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 : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33602
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.450
REMARK 200 RESOLUTION RANGE LOW (A) : 13.700
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : 5.500
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.10900
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.8000
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) : 2.58
REMARK 200 COMPLETENESS FOR SHELL (%) : 82.4
REMARK 200 DATA REDUNDANCY IN SHELL : 4.10
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.49100
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS
REMARK 200 SOFTWARE USED: REFMAC
REMARK 200 STARTING MODEL: PDB ENTRY 3SYM
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 51.30
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM BES BUFFER, PH 6.7, 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 58.28200
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 64.33700
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 64.33700
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 87.42300
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 64.33700
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 64.33700
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 29.14100
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 64.33700
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.33700
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 87.42300
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 64.33700
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.33700
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 29.14100
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 58.28200
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: 4600 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 57530 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 116.56400
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 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 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 CA GLY A 261 O HOH A 1145 2.19
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 68.28 -103.20
REMARK 500 VAL A 21 -45.68 -26.44
REMARK 500 LEU A 131 36.27 -92.15
REMARK 500 TYR A 203 -135.04 63.71
REMARK 500 ASN A 236 15.10 56.17
REMARK 500 ASN A 253 -41.93 68.45
REMARK 500 SER A 313 50.08 -92.84
REMARK 500 ASP A 339 -160.19 65.31
REMARK 500 LEU A 396 55.50 -141.37
REMARK 500 ALA A 435 -81.45 -19.67
REMARK 500 THR A 466 -101.82 -126.38
REMARK 500 LEU A 492 -72.70 -142.43
REMARK 500 ASP A 514 79.75 -158.80
REMARK 500 TYR A 553 24.04 -144.68
REMARK 500 LYS A 554 46.89 30.47
REMARK 500 LYS A 568 171.54 173.79
REMARK 500 SER A 674 -53.06 -138.38
REMARK 500 ASN A 793 77.52 -116.48
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 D1J A 901
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4EJ2 RELATED DB: PDB
REMARK 900 SAME PROTEIN IN COMPLEX WITH DK10
REMARK 900 RELATED ID: 4EKE RELATED DB: PDB
REMARK 900 SAME PROTEIN IN COMPLEX WITH DK11
REMARK 900 RELATED ID: 4EL0 RELATED DB: PDB
REMARK 900 SAME PROTEIN IN COMPLEX WITH DK16
REMARK 900 RELATED ID: 4EL5 RELATED DB: PDB
REMARK 900 SAME PROTEIN IN COMPLEX WITH DK12
DBREF 4EKY A 12 836 UNP P00489 PYGM_RABIT 13 837
SEQRES 1 A 825 GLN ILE SER VAL ARG GLY LEU ALA GLY VAL GLU ASN VAL
SEQRES 2 A 825 THR GLU LEU LYS LYS ASN PHE ASN ARG HIS LEU HIS PHE
SEQRES 3 A 825 THR LEU VAL LYS ASP ARG ASN VAL ALA THR PRO ARG ASP
SEQRES 4 A 825 TYR TYR PHE ALA LEU ALA HIS THR VAL ARG ASP HIS LEU
SEQRES 5 A 825 VAL GLY ARG TRP ILE ARG THR GLN GLN HIS TYR TYR GLU
SEQRES 6 A 825 LYS ASP PRO LYS ARG ILE TYR TYR LEU SER LEU GLU PHE
SEQRES 7 A 825 TYR MET GLY ARG THR LEU GLN ASN THR MET VAL ASN LEU
SEQRES 8 A 825 ALA LEU GLU ASN ALA CYS ASP GLU ALA THR TYR GLN LEU
SEQRES 9 A 825 GLY LEU ASP MET GLU GLU LEU GLU GLU ILE GLU GLU ASP
SEQRES 10 A 825 ALA GLY LEU GLY ASN GLY GLY LEU GLY ARG LEU ALA ALA
SEQRES 11 A 825 CYS PHE LEU ASP SER MET ALA THR LEU GLY LEU ALA ALA
SEQRES 12 A 825 TYR GLY TYR GLY ILE ARG TYR GLU PHE GLY ILE PHE ASN
SEQRES 13 A 825 GLN LYS ILE CYS GLY GLY TRP GLN MET GLU GLU ALA ASP
SEQRES 14 A 825 ASP TRP LEU ARG TYR GLY ASN PRO TRP GLU LYS ALA ARG
SEQRES 15 A 825 PRO GLU PHE THR LEU PRO VAL HIS PHE TYR GLY ARG VAL
SEQRES 16 A 825 GLU HIS THR SER GLN GLY ALA LYS TRP VAL ASP THR GLN
SEQRES 17 A 825 VAL VAL LEU ALA MET PRO TYR ASP THR PRO VAL PRO GLY
SEQRES 18 A 825 TYR ARG ASN ASN VAL VAL ASN THR MET ARG LEU TRP SER
SEQRES 19 A 825 ALA LYS ALA PRO ASN ASP PHE ASN LEU LYS ASP PHE ASN
SEQRES 20 A 825 VAL GLY GLY TYR ILE GLN ALA VAL LEU ASP ARG ASN LEU
SEQRES 21 A 825 ALA GLU ASN ILE SER ARG VAL LEU TYR PRO ASN ASP ASN
SEQRES 22 A 825 PHE PHE GLU GLY LYS GLU LEU ARG LEU LYS GLN GLU TYR
SEQRES 23 A 825 PHE VAL VAL ALA ALA THR LEU GLN ASP ILE ILE ARG ARG
SEQRES 24 A 825 PHE LYS SER SER LYS PHE GLY CYS ARG ASP PRO VAL ARG
SEQRES 25 A 825 THR ASN PHE ASP ALA PHE PRO ASP LYS VAL ALA ILE GLN
SEQRES 26 A 825 LEU ASN ASP THR HIS PRO SER LEU ALA ILE PRO GLU LEU
SEQRES 27 A 825 MET ARG VAL LEU VAL ASP LEU GLU ARG LEU ASP TRP ASP
SEQRES 28 A 825 LYS ALA TRP GLU VAL THR VAL LYS THR CYS ALA TYR THR
SEQRES 29 A 825 ASN HIS THR VAL LEU PRO GLU ALA LEU GLU ARG TRP PRO
SEQRES 30 A 825 VAL HIS LEU LEU GLU THR LEU LEU PRO ARG HIS LEU GLN
SEQRES 31 A 825 ILE ILE TYR GLU ILE ASN GLN ARG PHE LEU ASN ARG VAL
SEQRES 32 A 825 ALA ALA ALA PHE PRO GLY ASP VAL ASP ARG LEU ARG ARG
SEQRES 33 A 825 MET SER LEU VAL GLU GLU GLY ALA VAL LYS ARG ILE ASN
SEQRES 34 A 825 MET ALA HIS LEU CYS ILE ALA GLY SER HIS ALA VAL ASN
SEQRES 35 A 825 GLY VAL ALA ARG ILE HIS SER GLU ILE LEU LYS LYS THR
SEQRES 36 A 825 ILE PHE LYS ASP PHE TYR GLU LEU GLU PRO HIS LYS PHE
SEQRES 37 A 825 GLN ASN LYS THR ASN GLY ILE THR PRO ARG ARG TRP LEU
SEQRES 38 A 825 VAL LEU CYS ASN PRO GLY LEU ALA GLU ILE ILE ALA GLU
SEQRES 39 A 825 ARG ILE GLY GLU GLU TYR ILE SER ASP LEU ASP GLN LEU
SEQRES 40 A 825 ARG LYS LEU LEU SER TYR VAL ASP ASP GLU ALA PHE ILE
SEQRES 41 A 825 ARG ASP VAL ALA LYS VAL LYS GLN GLU ASN LYS LEU LYS
SEQRES 42 A 825 PHE ALA ALA TYR LEU GLU ARG GLU TYR LYS VAL HIS ILE
SEQRES 43 A 825 ASN PRO ASN SER LEU PHE ASP VAL GLN VAL LYS ARG ILE
SEQRES 44 A 825 HIS GLU TYR LYS ARG GLN LEU LEU ASN CYS LEU HIS VAL
SEQRES 45 A 825 ILE THR LEU TYR ASN ARG ILE LYS LYS GLU PRO ASN LYS
SEQRES 46 A 825 PHE VAL VAL PRO ARG THR VAL MET ILE GLY GLY LYS ALA
SEQRES 47 A 825 ALA PRO GLY TYR HIS MET ALA LYS MET ILE ILE LYS LEU
SEQRES 48 A 825 ILE THR ALA ILE GLY ASP VAL VAL ASN HIS ASP PRO VAL
SEQRES 49 A 825 VAL GLY ASP ARG LEU ARG VAL ILE PHE LEU GLU ASN TYR
SEQRES 50 A 825 ARG VAL SER LEU ALA GLU LYS VAL ILE PRO ALA ALA ASP
SEQRES 51 A 825 LEU SER GLU GLN ILE SER THR ALA GLY THR GLU ALA SER
SEQRES 52 A 825 GLY THR GLY ASN MET LLP PHE MET LEU ASN GLY ALA LEU
SEQRES 53 A 825 THR ILE GLY THR MET ASP GLY ALA ASN VAL GLU MET ALA
SEQRES 54 A 825 GLU GLU ALA GLY GLU GLU ASN PHE PHE ILE PHE GLY MET
SEQRES 55 A 825 ARG VAL GLU ASP VAL ASP ARG LEU ASP GLN ARG GLY TYR
SEQRES 56 A 825 ASN ALA GLN GLU TYR TYR ASP ARG ILE PRO GLU LEU ARG
SEQRES 57 A 825 GLN ILE ILE GLU GLN LEU SER SER GLY PHE PHE SER PRO
SEQRES 58 A 825 LYS GLN PRO ASP LEU PHE LYS ASP ILE VAL ASN MET LEU
SEQRES 59 A 825 MET HIS HIS ASP ARG PHE LYS VAL PHE ALA ASP TYR GLU
SEQRES 60 A 825 GLU TYR VAL LYS CYS GLN GLU ARG VAL SER ALA LEU TYR
SEQRES 61 A 825 LYS ASN PRO ARG GLU TRP THR ARG MET VAL ILE ARG ASN
SEQRES 62 A 825 ILE ALA THR SER GLY LYS PHE SER SER ASP ARG THR ILE
SEQRES 63 A 825 ALA GLN TYR ALA ARG GLU ILE TRP GLY VAL GLU PRO SER
SEQRES 64 A 825 ARG GLN ARG LEU PRO ALA
MODRES 4EKY LLP A 680 LYS
HET LLP A 680 24
HET D1J A 901 24
HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-
HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4-
HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID
HETNAM D1J 1-(BETA-D-GLUCOPYRANOSYL)-5-(PENT-1-YN-1-YL)PYRIMIDINE-
HETNAM 2 D1J 2,4(1H,3H)-DIONE
HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE
FORMUL 1 LLP C14 H22 N3 O7 P
FORMUL 2 D1J C15 H20 N2 O7
FORMUL 3 HOH *149(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 TYR A 262 ASP A 268 1 7
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 LEU 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 SER A 449 1 9
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 ASN A 496 GLY A 508 1 13
HELIX 25 25 GLU A 509 VAL A 525 5 17
HELIX 26 26 ASP A 527 LYS A 554 1 28
HELIX 27 27 ARG A 575 GLU A 593 1 19
HELIX 28 28 TYR A 613 ASN A 631 1 19
HELIX 29 29 ARG A 649 ILE A 657 1 9
HELIX 30 30 PRO A 658 ALA A 660 5 3
HELIX 31 31 THR A 676 ASN A 684 1 9
HELIX 32 32 ALA A 695 GLY A 704 1 10
HELIX 33 33 GLU A 705 PHE A 708 5 4
HELIX 34 34 ARG A 714 GLY A 725 1 12
HELIX 35 35 ALA A 728 ILE A 735 1 8
HELIX 36 36 ILE A 735 GLY A 748 1 14
HELIX 37 37 PHE A 758 HIS A 768 1 11
HELIX 38 38 VAL A 773 ALA A 775 5 3
HELIX 39 39 ASP A 776 LYS A 792 1 17
HELIX 40 40 ASN A 793 ALA A 806 1 14
HELIX 41 41 THR A 807 PHE A 811 5 5
HELIX 42 42 SER A 812 ILE A 824 1 13
SHEET 1 A 3 LYS A 191 ALA A 192 0
SHEET 2 A 3 GLY A 212 PRO A 231 -1 O ASP A 227 N LYS A 191
SHEET 3 A 3 LEU A 198 THR A 209 -1 N VAL A 200 O VAL A 221
SHEET 1 B 9 LYS A 191 ALA A 192 0
SHEET 2 B 9 GLY A 212 PRO A 231 -1 O ASP A 227 N LYS A 191
SHEET 3 B 9 VAL A 238 LYS A 247 -1 O SER A 245 N MET A 224
SHEET 4 B 9 ALA A 154 ILE A 159 1 N GLY A 156 O ARG A 242
SHEET 5 B 9 ARG A 81 LEU A 85 1 N TYR A 84 O TYR A 157
SHEET 6 B 9 VAL A 333 ASN A 338 1 O GLN A 336 N TYR A 83
SHEET 7 B 9 CYS A 372 THR A 375 1 O ALA A 373 N LEU A 337
SHEET 8 B 9 ALA A 451 GLY A 454 1 O ALA A 451 N TYR A 374
SHEET 9 B 9 PHE A 479 ASN A 481 1 O GLN A 480 N VAL A 452
SHEET 1 C 2 PHE A 89 GLY A 92 0
SHEET 2 C 2 ALA A 129 LEU A 131 -1 O LEU A 131 N PHE A 89
SHEET 1 D 2 ASN A 167 CYS A 171 0
SHEET 2 D 2 TRP A 174 GLU A 178 -1 O MET A 176 N LYS A 169
SHEET 1 E 3 ARG A 386 PRO A 388 0
SHEET 2 E 3 ARG A 438 ASN A 440 -1 O ILE A 439 N TRP A 387
SHEET 3 E 3 VAL A 431 GLU A 432 -1 N GLU A 432 O ARG A 438
SHEET 1 F 6 LEU A 640 LEU A 645 0
SHEET 2 F 6 ARG A 601 GLY A 606 1 N VAL A 603 O ARG A 641
SHEET 3 F 6 LEU A 562 VAL A 567 1 N ASP A 564 O MET A 604
SHEET 4 F 6 LEU A 662 GLN A 665 1 O LEU A 662 N VAL A 565
SHEET 5 F 6 LEU A 687 GLY A 690 1 O LEU A 687 N SER A 663
SHEET 6 F 6 PHE A 709 ILE A 710 1 O PHE A 709 N THR A 688
LINK C MET A 679 N LLP A 680 1555 1555 1.32
LINK C LLP A 680 N PHE A 681 1555 1555 1.32
SITE 1 AC1 18 GLY A 135 LEU A 136 ASP A 283 ASN A 284
SITE 2 AC1 18 ASP A 339 THR A 340 HIS A 341 HIS A 377
SITE 3 AC1 18 THR A 378 ASN A 484 TYR A 573 GLU A 672
SITE 4 AC1 18 ALA A 673 SER A 674 GLY A 675 HOH A1042
SITE 5 AC1 18 HOH A1069 HOH A1090
CRYST1 128.674 128.674 116.564 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 0.007772 0.000000 0.000000 0.00000
SCALE2 0.000000 0.007772 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008579 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
