HEADER TRANSFERASE 04-DEC-23 8XAM
TITLE CO-CRYSTAL STRUCTURE OF COMPOUND 7 IN COMPLEX WITH MAT2A
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2;
COMPND 3 CHAIN: A, B;
COMPND 4 SYNONYM: ADOMET SYNTHASE 2,METHIONINE ADENOSYLTRANSFERASE 2,MAT 2,
COMPND 5 METHIONINE ADENOSYLTRANSFERASE II,MAT-II;
COMPND 6 EC: 2.5.1.6;
COMPND 7 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: MAT2A, AMS2, MATA2;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECWHH-1;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2419743
KEYWDS MAT2A INHIBITOR, TRANSFERASE
EXPDTA X-RAY DIFFRACTION
AUTHOR F.GAO,X.DING
REVDAT 1 28-FEB-24 8XAM 0
JRNL AUTH F.GAO,X.DING,Z.CAO,W.ZHU,Y.FAN,B.STEURER,H.WANG,X.CAI,
JRNL AUTH 2 M.ZHANG,A.ALIPER,F.REN,X.DING,A.ZHAVORONKOV
JRNL TITL DISCOVERY OF NOVEL MAT2A INHIBITORS BY AN ALLOSTERIC
JRNL TITL 2 SITE-COMPATIBLE FRAGMENT GROWING APPROACH.
JRNL REF BIOORG.MED.CHEM. V. 100 17633 2024
JRNL REFN ESSN 1464-3391
JRNL PMID 38342078
JRNL DOI 10.1016/J.BMC.2024.117633
REMARK 2
REMARK 2 RESOLUTION. 1.30 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0267
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.12
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9
REMARK 3 NUMBER OF REFLECTIONS : 169062
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.121
REMARK 3 FREE R VALUE : 0.143
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.984
REMARK 3 FREE R VALUE TEST SET COUNT : 8426
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.30
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33
REMARK 3 REFLECTION IN BIN (WORKING SET) : 11375
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.18
REMARK 3 BIN R VALUE (WORKING SET) : 0.1630
REMARK 3 BIN FREE R VALUE SET COUNT : 632
REMARK 3 BIN FREE R VALUE : 0.1850
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 5882
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 101
REMARK 3 SOLVENT ATOMS : 1098
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.63
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.49100
REMARK 3 B22 (A**2) : -0.24100
REMARK 3 B33 (A**2) : -0.25000
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.01400
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.038
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.529
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.982
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.975
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6323 ; 0.016 ; 0.013
REMARK 3 BOND LENGTHS OTHERS (A): 5985 ; 0.001 ; 0.017
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8621 ; 1.999 ; 1.666
REMARK 3 BOND ANGLES OTHERS (DEGREES): 13813 ; 1.595 ; 1.597
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 808 ; 6.882 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 321 ;33.957 ;22.212
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1070 ;11.373 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;21.015 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 813 ; 0.118 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7223 ; 0.014 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): 1411 ; 0.005 ; 0.020
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1323 ; 0.233 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): 66 ; 0.204 ; 0.200
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2995 ; 0.178 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 822 ; 0.283 ; 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): 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): 3098 ; 1.007 ; 0.952
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3098 ; 1.007 ; 0.952
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3875 ; 1.462 ; 1.432
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3876 ; 1.462 ; 1.432
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3225 ; 2.157 ; 1.189
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3225 ; 2.157 ; 1.189
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4721 ; 3.184 ; 1.701
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4722 ; 3.183 ; 1.701
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 BULK SOLVENT
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 THEIR
REMARK 3 RIDING POSITIONS
REMARK 4
REMARK 4 8XAM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-DEC-23.
REMARK 100 THE DEPOSITION ID IS D_1300042933.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-MAR-22
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 18-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.1807
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 169065
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300
REMARK 200 RESOLUTION RANGE LOW (A) : 47.020
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 94.1
REMARK 200 DATA REDUNDANCY : 6.900
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.9000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.68
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LICL, 0.1 M TRIS PH 8.0, (18%
REMARK 280 -20%) PEG6000, 10% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING
REMARK 280 DROP, TEMPERATURE 297K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,Y,-Z
REMARK 290 3555 X+1/2,Y+1/2,Z+1/2
REMARK 290 4555 -X+1/2,Y+1/2,-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 0.00000
REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 33.98400
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.02150
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 58.44600
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.98400
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 47.02150
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 58.44600
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: 6660 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 24280 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 375
REMARK 375 SPECIAL POSITION
REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS
REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL
REMARK 375 POSITIONS.
REMARK 375
REMARK 375 ATOM RES CSSEQI
REMARK 375 HOH A 856 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 881 LIES ON A SPECIAL POSITION.
REMARK 375 HOH B 876 LIES ON A SPECIAL POSITION.
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 ARG A 343 NE CZ NH1 NH2
REMARK 470 LYS A 351 CD CE NZ
REMARK 470 LYS A 392 CD CE NZ
REMARK 470 LYS A 394 CD CE NZ
REMARK 470 ARG B 343 NE CZ NH1 NH2
REMARK 470 LYS B 351 CD CE NZ
REMARK 470 LYS B 392 CD CE NZ
REMARK 470 LYS B 394 CD CE NZ
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 608 O HOH A 665 1.45
REMARK 500 O HOH B 586 O HOH B 602 1.46
REMARK 500 O HOH A 594 O HOH A 601 1.55
REMARK 500 O HOH B 636 O HOH B 733 1.58
REMARK 500 O HOH B 583 O HOH B 819 1.58
REMARK 500 O HOH B 507 O HOH B 657 1.59
REMARK 500 O HOH A 504 O HOH A 674 1.59
REMARK 500 O HOH A 572 O HOH A 823 1.60
REMARK 500 CG2 THR B 172 O HOH B 904 1.63
REMARK 500 O HOH B 849 O HOH B 922 1.65
REMARK 500 CG2 THR A 172 O HOH A 911 1.65
REMARK 500 O HOH A 857 O HOH A 885 1.67
REMARK 500 O HOH A 732 O HOH A 822 1.70
REMARK 500 O HOH A 874 O HOH A 989 1.75
REMARK 500 O HOH B 906 O HOH B 922 1.76
REMARK 500 O HOH A 989 O HOH A 1012 1.80
REMARK 500 O HOH B 869 O HOH B 985 1.83
REMARK 500 O HOH B 535 O HOH B 791 1.84
REMARK 500 NZ LYS A 350 O HOH A 501 1.84
REMARK 500 O HOH A 537 O HOH A 787 1.85
REMARK 500 O HOH A 608 O HOH A 722 1.86
REMARK 500 O HOH A 876 O HOH B 887 1.86
REMARK 500 O HOH B 586 O HOH B 709 1.87
REMARK 500 O HOH A 835 O HOH A 1020 1.90
REMARK 500 O HOH A 890 O HOH B 864 1.91
REMARK 500 O HOH B 651 O HOH B 863 1.92
REMARK 500 O HOH A 836 O HOH A 860 1.92
REMARK 500 O HOH B 985 O HOH B 1005 1.95
REMARK 500 NH2 ARG B 177 O HOH B 501 1.96
REMARK 500 O HOH B 838 O HOH B 1022 1.97
REMARK 500 O HOH A 1043 O HOH A 1045 1.98
REMARK 500 O HOH B 739 O HOH B 838 1.99
REMARK 500 O HOH B 820 O HOH B 1020 1.99
REMARK 500 O HOH A 644 O HOH A 865 2.00
REMARK 500 O HOH B 1022 O HOH B 1041 2.01
REMARK 500 O HOH B 523 O HOH B 936 2.01
REMARK 500 OE1 GLU B 347 O HOH B 502 2.02
REMARK 500 OG1 THR B 143 O HOH B 503 2.03
REMARK 500 O HOH B 814 O HOH B 856 2.03
REMARK 500 O HOH A 846 O HOH A 866 2.04
REMARK 500 OH TYR B 287 O HOH B 504 2.05
REMARK 500 NZ LYS B 350 O HOH B 505 2.06
REMARK 500 OH TYR A 287 O HOH A 502 2.06
REMARK 500 O HOH B 501 O HOH B 748 2.06
REMARK 500 O HOH B 719 O HOH B 963 2.07
REMARK 500 O HOH A 701 O HOH A 835 2.08
REMARK 500 O HOH A 928 O HOH A 1030 2.10
REMARK 500 OG1 THR A 143 O HOH A 503 2.11
REMARK 500 O HOH B 887 O HOH B 943 2.12
REMARK 500 OH TYR B 235 O HOH B 506 2.12
REMARK 500
REMARK 500 THIS ENTRY HAS 63 CLOSE CONTACTS
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 O HOH A 984 O HOH B 1013 4354 1.90
REMARK 500 O HOH A 1015 O HOH B 980 4454 1.90
REMARK 500 O HOH A 1020 O HOH B 1041 2455 2.08
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 HIS A 326 CE1 HIS A 326 NE2 -0.081
REMARK 500 HIS B 326 CE1 HIS B 326 NE2 -0.070
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 ARG A 177 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES
REMARK 500 ARG A 177 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES
REMARK 500 ARG A 199 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES
REMARK 500 ARG A 199 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES
REMARK 500 ARG A 219 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES
REMARK 500 ARG B 177 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES
REMARK 500 ARG B 219 NE - CZ - NH2 ANGL. DEV. = -5.6 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 VAL A 226 -70.41 -107.23
REMARK 500 THR A 270 -98.55 -117.11
REMARK 500 ARG A 292 -61.87 -93.18
REMARK 500 TYR A 335 18.73 59.05
REMARK 500 VAL B 226 -69.80 -106.84
REMARK 500 THR B 270 -99.00 -115.82
REMARK 500 ARG B 292 -60.53 -92.74
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 A1045 DISTANCE = 5.82 ANGSTROMS
REMARK 525 HOH A1046 DISTANCE = 5.97 ANGSTROMS
REMARK 525 HOH A1047 DISTANCE = 6.08 ANGSTROMS
REMARK 525 HOH A1048 DISTANCE = 6.55 ANGSTROMS
REMARK 525 HOH A1049 DISTANCE = 7.08 ANGSTROMS
REMARK 525 HOH B1044 DISTANCE = 5.81 ANGSTROMS
REMARK 525 HOH B1045 DISTANCE = 5.96 ANGSTROMS
REMARK 525 HOH B1046 DISTANCE = 6.01 ANGSTROMS
REMARK 525 HOH B1047 DISTANCE = 6.34 ANGSTROMS
REMARK 525 HOH B1048 DISTANCE = 6.60 ANGSTROMS
REMARK 525 HOH B1049 DISTANCE = 7.07 ANGSTROMS
DBREF 8XAM A 16 395 UNP P31153 METK2_HUMAN 16 395
DBREF 8XAM B 16 395 UNP P31153 METK2_HUMAN 16 395
SEQRES 1 A 380 GLY THR PHE LEU PHE THR SER GLU SER VAL GLY GLU GLY
SEQRES 2 A 380 HIS PRO ASP LYS ILE CYS ASP GLN ILE SER ASP ALA VAL
SEQRES 3 A 380 LEU ASP ALA HIS LEU GLN GLN ASP PRO ASP ALA LYS VAL
SEQRES 4 A 380 ALA CYS GLU THR VAL ALA LYS THR GLY MET ILE LEU LEU
SEQRES 5 A 380 ALA GLY GLU ILE THR SER ARG ALA ALA VAL ASP TYR GLN
SEQRES 6 A 380 LYS VAL VAL ARG GLU ALA VAL LYS HIS ILE GLY TYR ASP
SEQRES 7 A 380 ASP SER SER LYS GLY PHE ASP TYR LYS THR CYS ASN VAL
SEQRES 8 A 380 LEU VAL ALA LEU GLU GLN GLN SER PRO ASP ILE ALA GLN
SEQRES 9 A 380 GLY VAL HIS LEU ASP ARG ASN GLU GLU ASP ILE GLY ALA
SEQRES 10 A 380 GLY ASP GLN GLY LEU MET PHE GLY TYR ALA THR ASP GLU
SEQRES 11 A 380 THR GLU GLU CYS MET PRO LEU THR ILE VAL LEU ALA HIS
SEQRES 12 A 380 LYS LEU ASN ALA LYS LEU ALA GLU LEU ARG ARG ASN GLY
SEQRES 13 A 380 THR LEU PRO TRP LEU ARG PRO ASP SER LYS THR GLN VAL
SEQRES 14 A 380 THR VAL GLN TYR MET GLN ASP ARG GLY ALA VAL LEU PRO
SEQRES 15 A 380 ILE ARG VAL HIS THR ILE VAL ILE SER VAL GLN HIS ASP
SEQRES 16 A 380 GLU GLU VAL CYS LEU ASP GLU MET ARG ASP ALA LEU LYS
SEQRES 17 A 380 GLU LYS VAL ILE LYS ALA VAL VAL PRO ALA LYS TYR LEU
SEQRES 18 A 380 ASP GLU ASP THR ILE TYR HIS LEU GLN PRO SER GLY ARG
SEQRES 19 A 380 PHE VAL ILE GLY GLY PRO GLN GLY ASP ALA GLY LEU THR
SEQRES 20 A 380 GLY ARG LYS ILE ILE VAL ASP THR TYR GLY GLY TRP GLY
SEQRES 21 A 380 ALA HIS GLY GLY GLY ALA PHE SER GLY LYS ASP TYR THR
SEQRES 22 A 380 LYS VAL ASP ARG SER ALA ALA TYR ALA ALA ARG TRP VAL
SEQRES 23 A 380 ALA LYS SER LEU VAL LYS GLY GLY LEU CYS ARG ARG VAL
SEQRES 24 A 380 LEU VAL GLN VAL SER TYR ALA ILE GLY VAL SER HIS PRO
SEQRES 25 A 380 LEU SER ILE SER ILE PHE HIS TYR GLY THR SER GLN LYS
SEQRES 26 A 380 SER GLU ARG GLU LEU LEU GLU ILE VAL LYS LYS ASN PHE
SEQRES 27 A 380 ASP LEU ARG PRO GLY VAL ILE VAL ARG ASP LEU ASP LEU
SEQRES 28 A 380 LYS LYS PRO ILE TYR GLN ARG THR ALA ALA TYR GLY HIS
SEQRES 29 A 380 PHE GLY ARG ASP SER PHE PRO TRP GLU VAL PRO LYS LYS
SEQRES 30 A 380 LEU LYS TYR
SEQRES 1 B 380 GLY THR PHE LEU PHE THR SER GLU SER VAL GLY GLU GLY
SEQRES 2 B 380 HIS PRO ASP LYS ILE CYS ASP GLN ILE SER ASP ALA VAL
SEQRES 3 B 380 LEU ASP ALA HIS LEU GLN GLN ASP PRO ASP ALA LYS VAL
SEQRES 4 B 380 ALA CYS GLU THR VAL ALA LYS THR GLY MET ILE LEU LEU
SEQRES 5 B 380 ALA GLY GLU ILE THR SER ARG ALA ALA VAL ASP TYR GLN
SEQRES 6 B 380 LYS VAL VAL ARG GLU ALA VAL LYS HIS ILE GLY TYR ASP
SEQRES 7 B 380 ASP SER SER LYS GLY PHE ASP TYR LYS THR CYS ASN VAL
SEQRES 8 B 380 LEU VAL ALA LEU GLU GLN GLN SER PRO ASP ILE ALA GLN
SEQRES 9 B 380 GLY VAL HIS LEU ASP ARG ASN GLU GLU ASP ILE GLY ALA
SEQRES 10 B 380 GLY ASP GLN GLY LEU MET PHE GLY TYR ALA THR ASP GLU
SEQRES 11 B 380 THR GLU GLU CYS MET PRO LEU THR ILE VAL LEU ALA HIS
SEQRES 12 B 380 LYS LEU ASN ALA LYS LEU ALA GLU LEU ARG ARG ASN GLY
SEQRES 13 B 380 THR LEU PRO TRP LEU ARG PRO ASP SER LYS THR GLN VAL
SEQRES 14 B 380 THR VAL GLN TYR MET GLN ASP ARG GLY ALA VAL LEU PRO
SEQRES 15 B 380 ILE ARG VAL HIS THR ILE VAL ILE SER VAL GLN HIS ASP
SEQRES 16 B 380 GLU GLU VAL CYS LEU ASP GLU MET ARG ASP ALA LEU LYS
SEQRES 17 B 380 GLU LYS VAL ILE LYS ALA VAL VAL PRO ALA LYS TYR LEU
SEQRES 18 B 380 ASP GLU ASP THR ILE TYR HIS LEU GLN PRO SER GLY ARG
SEQRES 19 B 380 PHE VAL ILE GLY GLY PRO GLN GLY ASP ALA GLY LEU THR
SEQRES 20 B 380 GLY ARG LYS ILE ILE VAL ASP THR TYR GLY GLY TRP GLY
SEQRES 21 B 380 ALA HIS GLY GLY GLY ALA PHE SER GLY LYS ASP TYR THR
SEQRES 22 B 380 LYS VAL ASP ARG SER ALA ALA TYR ALA ALA ARG TRP VAL
SEQRES 23 B 380 ALA LYS SER LEU VAL LYS GLY GLY LEU CYS ARG ARG VAL
SEQRES 24 B 380 LEU VAL GLN VAL SER TYR ALA ILE GLY VAL SER HIS PRO
SEQRES 25 B 380 LEU SER ILE SER ILE PHE HIS TYR GLY THR SER GLN LYS
SEQRES 26 B 380 SER GLU ARG GLU LEU LEU GLU ILE VAL LYS LYS ASN PHE
SEQRES 27 B 380 ASP LEU ARG PRO GLY VAL ILE VAL ARG ASP LEU ASP LEU
SEQRES 28 B 380 LYS LYS PRO ILE TYR GLN ARG THR ALA ALA TYR GLY HIS
SEQRES 29 B 380 PHE GLY ARG ASP SER PHE PRO TRP GLU VAL PRO LYS LYS
SEQRES 30 B 380 LEU LYS TYR
HET SAM A 401 27
HET XRH B 401 94
HET SAM B 402 27
HETNAM SAM S-ADENOSYLMETHIONINE
HETNAM XRH 2-[3-[7-CHLORANYL-4-(DIMETHYLAMINO)-2-OXIDANYLIDENE-
HETNAM 2 XRH QUINAZOLIN-1-YL]PHENOXY]-~{N}-[3-[7-CHLORANYL-4-
HETNAM 3 XRH (DIMETHYLAMINO)-2-OXIDANYLIDENE-QUINAZOLIN-1-
HETNAM 4 XRH YL]PHENYL]ETHANAMIDE
HETSYN XRH 3-CARBAMIMIDOYL-1-(PYRIDIN-3-YLCARBAMOYLMETHYL)-1H-
HETSYN 2 XRH INDOLE-7-CARBOXYLIC ACID PYRIDIN-3-YLAMIDE
FORMUL 3 SAM 2(C15 H22 N6 O5 S)
FORMUL 4 XRH C34 H29 CL2 N7 O4
FORMUL 6 HOH *1098(H2 O)
HELIX 1 AA1 HIS A 29 ASP A 49 1 21
HELIX 2 AA2 ASP A 78 GLY A 91 1 14
HELIX 3 AA3 SER A 95 GLY A 98 5 4
HELIX 4 AA4 SER A 114 HIS A 122 1 9
HELIX 5 AA5 ASN A 126 ILE A 130 5 5
HELIX 6 AA6 PRO A 151 ASN A 170 1 20
HELIX 7 AA7 CYS A 214 LYS A 225 1 12
HELIX 8 AA8 VAL A 226 VAL A 231 1 6
HELIX 9 AA9 PRO A 232 LEU A 236 5 5
HELIX 10 AB1 GLY A 253 GLY A 257 5 5
HELIX 11 AB2 LYS A 289 GLY A 308 1 20
HELIX 12 AB3 SER A 341 PHE A 353 1 13
HELIX 13 AB4 ARG A 356 LEU A 364 1 9
HELIX 14 AB5 ILE A 370 ALA A 375 1 6
HELIX 15 AB6 PHE A 385 VAL A 389 5 5
HELIX 16 AB7 HIS B 29 ASP B 49 1 21
HELIX 17 AB8 ASP B 78 GLY B 91 1 14
HELIX 18 AB9 SER B 95 GLY B 98 5 4
HELIX 19 AC1 SER B 114 HIS B 122 1 9
HELIX 20 AC2 ASN B 126 ILE B 130 5 5
HELIX 21 AC3 PRO B 151 ASN B 170 1 20
HELIX 22 AC4 CYS B 214 LYS B 225 1 12
HELIX 23 AC5 VAL B 226 VAL B 231 1 6
HELIX 24 AC6 PRO B 232 LEU B 236 5 5
HELIX 25 AC7 GLY B 253 GLY B 257 5 5
HELIX 26 AC8 LYS B 289 GLY B 308 1 20
HELIX 27 AC9 SER B 341 PHE B 353 1 13
HELIX 28 AD1 ARG B 356 LEU B 364 1 9
HELIX 29 AD2 ILE B 370 ALA B 375 1 6
HELIX 30 AD3 PHE B 385 VAL B 389 5 5
SHEET 1 AA1 4 THR A 17 VAL A 25 0
SHEET 2 AA1 4 LEU A 176 ASP A 191 -1 O TYR A 188 N PHE A 18
SHEET 3 AA1 4 ALA A 194 HIS A 209 -1 O ILE A 198 N GLN A 187
SHEET 4 AA1 4 ILE A 241 LEU A 244 1 O HIS A 243 N ILE A 203
SHEET 1 AA2 4 ASN A 105 GLU A 111 0
SHEET 2 AA2 4 MET A 64 THR A 72 1 N LEU A 67 O ALA A 109
SHEET 3 AA2 4 LYS A 53 LYS A 61 -1 N LYS A 53 O THR A 72
SHEET 4 AA2 4 GLY A 260 LEU A 261 -1 O GLY A 260 N ALA A 60
SHEET 1 AA3 2 ASP A 93 ASP A 94 0
SHEET 2 AA3 2 PHE A 99 ASP A 100 -1 O PHE A 99 N ASP A 94
SHEET 1 AA4 3 GLY A 136 THR A 143 0
SHEET 2 AA4 3 ARG A 313 TYR A 320 -1 O VAL A 316 N GLY A 140
SHEET 3 AA4 3 SER A 329 PHE A 333 -1 O PHE A 333 N LEU A 315
SHEET 1 AA5 4 THR B 17 VAL B 25 0
SHEET 2 AA5 4 LEU B 176 ASP B 191 -1 O TYR B 188 N PHE B 18
SHEET 3 AA5 4 ALA B 194 HIS B 209 -1 O ILE B 198 N GLN B 187
SHEET 4 AA5 4 ILE B 241 LEU B 244 1 O HIS B 243 N ILE B 203
SHEET 1 AA6 4 ASN B 105 GLU B 111 0
SHEET 2 AA6 4 MET B 64 THR B 72 1 N LEU B 67 O ALA B 109
SHEET 3 AA6 4 LYS B 53 LYS B 61 -1 N LYS B 53 O THR B 72
SHEET 4 AA6 4 GLY B 260 LEU B 261 -1 O GLY B 260 N ALA B 60
SHEET 1 AA7 2 ASP B 93 ASP B 94 0
SHEET 2 AA7 2 PHE B 99 ASP B 100 -1 O PHE B 99 N ASP B 94
SHEET 1 AA8 3 GLY B 136 THR B 143 0
SHEET 2 AA8 3 ARG B 313 TYR B 320 -1 O VAL B 316 N GLY B 140
SHEET 3 AA8 3 SER B 329 PHE B 333 -1 O PHE B 333 N LEU B 315
CRYST1 67.968 94.043 116.892 90.00 90.00 90.00 I 1 2 1 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 0.014713 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010633 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008555 0.00000