HEADER TRANSFERASE 19-JAN-09 2ZYB
TITLE CRYSTAL STRUCTURE OF PHENYLIMIDAZO PYRAZIN 2 BOUND TO THE KINASE
TITLE 2 DOMAIN OF HUMAN LCK, (AUTO-PHOSPHORYLATED ON TYR394)
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE LCK;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 225-509;
COMPND 5 SYNONYM: LYMPHOCYTE CELL-SPECIFIC PROTEIN-TYROSINE KINASE, P56-LCK,
COMPND 6 LSK, T CELL-SPECIFIC PROTEIN-TYROSINE KINASE;
COMPND 7 EC: 2.7.10.2;
COMPND 8 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: LCK;
SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7108;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: SF9;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-19B
KEYWDS TYROSINE-PROTEIN KINASE, ATP-BINDING, PHOSPHORYLATION, SIGNAL
KEYWDS 2 TRANSDUCTION, ALTERNATIVE SPLICING, CHROMOSOMAL REARRANGEMENT,
KEYWDS 3 CYTOPLASM, DISEASE MUTATION, HOST-VIRUS INTERACTION, KINASE,
KEYWDS 4 LIPOPROTEIN, MEMBRANE, MYRISTATE, NUCLEOTIDE-BINDING, PALMITATE,
KEYWDS 5 PHOSPHOPROTEIN, PROTO-ONCOGENE, SH2 DOMAIN, SH3 DOMAIN, TRANSFERASE,
KEYWDS 6 CELL MEMBRANE, POLYMORPHISM
EXPDTA X-RAY DIFFRACTION
AUTHOR E.TSUJI
REVDAT 3 15-NOV-23 2ZYB 1 REMARK
REVDAT 2 01-NOV-23 2ZYB 1 REMARK LINK
REVDAT 1 03-FEB-09 2ZYB 0
JRNL AUTH T.OZAWA,E.TSUJI,M.OZAWA,C.HANDA,H.MUKAIYAMA,T.NISHIMURA,
JRNL AUTH 2 S.KOBAYASHI,K.OKAZAKI
JRNL TITL THE IMPORTANCE OF CH/PI HYDROGEN BONDS IN RATIONAL DRUG
JRNL TITL 2 DESIGN: AN AB INITIO FRAGMENT MOLECULAR ORBITAL STUDY TO
JRNL TITL 3 LEUKOCYTE-SPECIFIC PROTEIN TYROSINE (LCK) KINASE
JRNL REF BIOORG.MED.CHEM. V. 16 10311 2008
JRNL REFN ISSN 0968-0896
JRNL PMID 18977146
JRNL DOI 10.1016/J.BMC.2008.10.041
REMARK 2
REMARK 2 RESOLUTION. 2.55 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.2.0005
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) : 2.55
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3
REMARK 3 NUMBER OF REFLECTIONS : 8763
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) : 0.183
REMARK 3 R VALUE (WORKING SET) : 0.171
REMARK 3 FREE R VALUE : 0.291
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900
REMARK 3 FREE R VALUE TEST SET COUNT : 968
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) : 2.55
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.61
REMARK 3 REFLECTION IN BIN (WORKING SET) : 610
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.60
REMARK 3 BIN R VALUE (WORKING SET) : 0.2560
REMARK 3 BIN FREE R VALUE SET COUNT : 64
REMARK 3 BIN FREE R VALUE : 0.3790
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2205
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 29
REMARK 3 SOLVENT ATOMS : 201
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 26.70
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 8.43
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.04000
REMARK 3 B22 (A**2) : 0.48000
REMARK 3 B33 (A**2) : -0.52000
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): NULL
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.408
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.252
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.722
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.818
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2295 ; 0.020 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3117 ; 1.662 ; 1.983
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 270 ; 8.825 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 108 ;38.147 ;23.796
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 394 ;19.395 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;21.433 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 332 ; 0.138 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1751 ; 0.028 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1134 ; 0.275 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1534 ; 0.335 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 138 ; 0.229 ; 0.200
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): 58 ; 0.302 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 26 ; 0.549 ; 0.200
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): 1407 ; 2.315 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2192 ; 3.324 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1064 ; 4.969 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 925 ; 6.602 ; 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 : 1.20
REMARK 3 ION PROBE RADIUS : 0.80
REMARK 3 SHRINKAGE RADIUS : 0.80
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING
REMARK 3 POSITIONS
REMARK 4
REMARK 4 2ZYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-JAN-09.
REMARK 100 THE DEPOSITION ID IS D_1000028578.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 01-JAN-03
REMARK 200 TEMPERATURE (KELVIN) : 93
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SPRING-8
REMARK 200 BEAMLINE : BL32B2
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.0
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9965
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550
REMARK 200 RESOLUTION RANGE LOW (A) : 28.510
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5
REMARK 200 DATA REDUNDANCY : 3.300
REMARK 200 R MERGE (I) : 0.10100
REMARK 200 R SYM (I) : 0.12000
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69
REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.40
REMARK 200 R MERGE FOR SHELL (I) : 0.21100
REMARK 200 R SYM FOR SHELL (I) : 0.24800
REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.900
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: AMORE
REMARK 200 STARTING MODEL: PDB ENTRY 3LCK
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 43.81
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2SO4, 0.1M SODIUM
REMARK 280 CACODYLATE, 30% PEG8000, PH6.5, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X+1/2,-Y,Z+1/2
REMARK 290 3555 -X,Y+1/2,-Z+1/2
REMARK 290 4555 X+1/2,-Y+1/2,-Z
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 21.07500
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.42850
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.98650
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.42850
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.07500
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.98650
REMARK 290 SMTRY3 4 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 GLN A 225
REMARK 465 THR A 226
REMARK 465 GLN A 227
REMARK 465 LYS A 228
REMARK 465 PRO A 229
REMARK 465 GLN A 230
REMARK 465 GLU A 502
REMARK 465 GLY A 503
REMARK 465 GLN A 504
REMARK 465 TYR A 505
REMARK 465 GLN A 506
REMARK 465 PRO A 507
REMARK 465 GLN A 508
REMARK 465 PRO A 509
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 GLU A 390 CG CD OE1 OE2
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500 O HOH A 605 O HOH A 700 1.14
REMARK 500 OH PTR A 394 O HOH A 677 1.66
REMARK 500 O2P PTR A 394 O HOH A 677 1.84
REMARK 500 P PTR A 394 O HOH A 677 2.01
REMARK 500 NH1 ARG A 458 O TRP A 477 2.07
REMARK 500 CB SER A 274 O HOH A 668 2.09
REMARK 500 O HOH A 549 O HOH A 562 2.17
REMARK 500 O HOH A 608 O HOH A 657 2.17
REMARK 500 O HOH A 551 O HOH A 708 2.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 NH2 ARG A 397 O HOH A 534 4455 1.49
REMARK 500 NH2 ARG A 299 O1 SO4 A 510 3655 2.10
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 CYS A 465 CB CYS A 465 SG -0.109
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 GLN A 309 -135.64 -137.60
REMARK 500 GLU A 310 -101.27 -12.88
REMARK 500 ASN A 359 22.60 81.00
REMARK 500 ARG A 363 -10.36 76.39
REMARK 500 ALA A 381 -162.69 -123.29
REMARK 500 ASP A 382 106.20 28.22
REMARK 500 GLU A 390 -70.62 -57.88
REMARK 500 GLU A 398 -35.31 -26.46
REMARK 500 HIS A 436 -114.60 59.76
REMARK 500 ARG A 461 109.88 -45.24
REMARK 500 LYS A 478 151.71 -45.70
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 GLY A 437 ARG A 438 -137.27
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 PHE A 256 0.06 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 GLN A 294 11.34
REMARK 500 SER A 421 11.62
REMARK 500 TYR A 489 -10.10
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 SO4 A 510
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KSL A 511
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 3LCK RELATED DB: PDB
REMARK 900 STRUCTURAL BASIS FOR ACTIVATION OF HUMAN LYMPHOCYTE KINASE LCK UPON
REMARK 900 TYROSINE PHOSPHORYLATION
REMARK 900 RELATED ID: 2ZOB RELATED DB: PDB
REMARK 900 THIS ENTRY WAS WITHDRAWN
DBREF 2ZYB A 225 509 UNP P06239 LCK_HUMAN 225 509
SEQRES 1 A 285 GLN THR GLN LYS PRO GLN LYS PRO TRP TRP GLU ASP GLU
SEQRES 2 A 285 TRP GLU VAL PRO ARG GLU THR LEU LYS LEU VAL GLU ARG
SEQRES 3 A 285 LEU GLY ALA GLY GLN PHE GLY GLU VAL TRP MET GLY TYR
SEQRES 4 A 285 TYR ASN GLY HIS THR LYS VAL ALA VAL LYS SER LEU LYS
SEQRES 5 A 285 GLN GLY SER MET SER PRO ASP ALA PHE LEU ALA GLU ALA
SEQRES 6 A 285 ASN LEU MET LYS GLN LEU GLN HIS GLN ARG LEU VAL ARG
SEQRES 7 A 285 LEU TYR ALA VAL VAL THR GLN GLU PRO ILE TYR ILE ILE
SEQRES 8 A 285 THR GLU TYR MET GLU ASN GLY SER LEU VAL ASP PHE LEU
SEQRES 9 A 285 LYS THR PRO SER GLY ILE LYS LEU THR ILE ASN LYS LEU
SEQRES 10 A 285 LEU ASP MET ALA ALA GLN ILE ALA GLU GLY MET ALA PHE
SEQRES 11 A 285 ILE GLU GLU ARG ASN TYR ILE HIS ARG ASP LEU ARG ALA
SEQRES 12 A 285 ALA ASN ILE LEU VAL SER ASP THR LEU SER CYS LYS ILE
SEQRES 13 A 285 ALA ASP PHE GLY LEU ALA ARG LEU ILE GLU ASP ASN GLU
SEQRES 14 A 285 PTR THR ALA ARG GLU GLY ALA LYS PHE PRO ILE LYS TRP
SEQRES 15 A 285 THR ALA PRO GLU ALA ILE ASN TYR GLY THR PHE THR ILE
SEQRES 16 A 285 LYS SER ASP VAL TRP SER PHE GLY ILE LEU LEU THR GLU
SEQRES 17 A 285 ILE VAL THR HIS GLY ARG ILE PRO TYR PRO GLY MET THR
SEQRES 18 A 285 ASN PRO GLU VAL ILE GLN ASN LEU GLU ARG GLY TYR ARG
SEQRES 19 A 285 MET VAL ARG PRO ASP ASN CYS PRO GLU GLU LEU TYR GLN
SEQRES 20 A 285 LEU MET ARG LEU CYS TRP LYS GLU ARG PRO GLU ASP ARG
SEQRES 21 A 285 PRO THR PHE ASP TYR LEU ARG SER VAL LEU GLU ASP PHE
SEQRES 22 A 285 PHE THR ALA THR GLU GLY GLN TYR GLN PRO GLN PRO
MODRES 2ZYB PTR A 394 TYR O-PHOSPHOTYROSINE
HET PTR A 394 16
HET SO4 A 510 5
HET KSL A 511 24
HETNAM PTR O-PHOSPHOTYROSINE
HETNAM SO4 SULFATE ION
HETNAM KSL N-(2,6-DIMETHYLPHENYL)-5-PHENYLIMIDAZO[1,5-A]PYRAZIN-8-
HETNAM 2 KSL AMINE
HETSYN PTR PHOSPHONOTYROSINE
FORMUL 1 PTR C9 H12 N O6 P
FORMUL 2 SO4 O4 S 2-
FORMUL 3 KSL C20 H18 N4
FORMUL 4 HOH *201(H2 O)
HELIX 1 1 PRO A 241 GLU A 243 5 3
HELIX 2 2 SER A 281 GLN A 294 1 14
HELIX 3 3 SER A 323 LEU A 328 1 6
HELIX 4 4 THR A 330 LEU A 336 1 7
HELIX 5 5 THR A 337 ARG A 358 1 22
HELIX 6 6 ARG A 366 ALA A 368 5 3
HELIX 7 7 ALA A 408 GLY A 415 1 8
HELIX 8 8 THR A 418 THR A 435 1 18
HELIX 9 9 THR A 445 ARG A 455 1 11
HELIX 10 10 PRO A 466 TRP A 477 1 12
HELIX 11 11 ARG A 480 ARG A 484 5 5
HELIX 12 12 THR A 486 ALA A 500 1 15
SHEET 1 A 5 LEU A 245 GLY A 254 0
SHEET 2 A 5 GLY A 257 TYR A 264 -1 O VAL A 259 N LEU A 251
SHEET 3 A 5 THR A 268 LEU A 275 -1 O VAL A 272 N TRP A 260
SHEET 4 A 5 TYR A 313 THR A 316 -1 O ILE A 314 N LYS A 273
SHEET 5 A 5 LEU A 303 VAL A 307 -1 N ALA A 305 O ILE A 315
SHEET 1 B 2 TYR A 360 ILE A 361 0
SHEET 2 B 2 ARG A 387 LEU A 388 -1 O ARG A 387 N ILE A 361
SHEET 1 C 2 ILE A 370 VAL A 372 0
SHEET 2 C 2 CYS A 378 ILE A 380 -1 O LYS A 379 N LEU A 371
SHEET 1 D 2 PTR A 394 THR A 395 0
SHEET 2 D 2 THR A 416 PHE A 417 -1 O PHE A 417 N PTR A 394
LINK C GLU A 393 N PTR A 394 1555 1555 1.33
LINK C PTR A 394 N THR A 395 1555 1555 1.35
SITE 1 AC1 8 GLN A 298 ARG A 299 SER A 377 LYS A 379
SITE 2 AC1 8 TYR A 457 ARG A 458 ARG A 474 HOH A 618
SITE 1 AC2 9 ALA A 271 GLU A 288 THR A 316 GLU A 317
SITE 2 AC2 9 MET A 319 LEU A 371 ASP A 382 HOH A 552
SITE 3 AC2 9 HOH A 609
CRYST1 42.150 73.973 92.857 90.00 90.00 90.00 P 21 21 21 4
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 0.023725 0.000000 0.000000 0.00000
SCALE2 0.000000 0.013518 0.000000 0.00000
SCALE3 0.000000 0.000000 0.010769 0.00000
(ATOM LINES ARE NOT SHOWN.)
END