HEADER TRANSFERASE 30-APR-15 5A1G
TITLE THE STRUCTURE OF HUMAN MAT2A IN COMPLEX WITH S-ADENOSYLETHIONINE AND
TITLE 2 PPNP.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE SYNTHASE ISOFORM TYPE-2;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ADOMET SYNTHASE 2, METHIONINE ADENOSYLTRANSFERASE 2, MAT 2,
COMPND 5 METHIONINE ADENOSYLTRANSFERASE II, MAT-II, METHIONINE
COMPND 6 ADENOSYLTRANSFERASE 2A;
COMPND 7 EC: 2.5.1.6;
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 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4
KEYWDS TRANSFERASE, METHIONINE ADENOSYLTRANSFERASE, CELL GROWTH, LIVER
KEYWDS 2 CANCER, METHYLATION
EXPDTA X-RAY DIFFRACTION
AUTHOR B.MURRAY,S.V.ANTONYUK,A.MARINA,S.C.LU,J.M.MATO,S.S.HASNAIN,A.L.ROJAS
REVDAT 3 10-JAN-24 5A1G 1 COMPND REMARK HETNAM LINK
REVDAT 2 09-MAR-16 5A1G 1 JRNL
REVDAT 1 17-FEB-16 5A1G 0
JRNL AUTH B.MURRAY,S.V.ANTONYUK,A.MARINA,S.C.LU,J.M.MATO,S.S.HASNAIN,
JRNL AUTH 2 A.L.ROJAS
JRNL TITL CRYSTALLOGRAPHY CAPTURES CATALYTIC STEPS IN HUMAN METHIONINE
JRNL TITL 2 ADENOSYLTRANSFERASE ENZYMES.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 113 2104 2016
JRNL REFN ISSN 0027-8424
JRNL PMID 26858410
JRNL DOI 10.1073/PNAS.1510959113
REMARK 2
REMARK 2 RESOLUTION. 1.83 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0135
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) : 1.83
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.69
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 3 NUMBER OF REFLECTIONS : 32055
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) : 0.122
REMARK 3 R VALUE (WORKING SET) : 0.120
REMARK 3 FREE R VALUE : 0.175
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 1633
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) : 1.83
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88
REMARK 3 REFLECTION IN BIN (WORKING SET) : 2356
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.72
REMARK 3 BIN R VALUE (WORKING SET) : 0.1770
REMARK 3 BIN FREE R VALUE SET COUNT : 133
REMARK 3 BIN FREE R VALUE : 0.2640
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2954
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 65
REMARK 3 SOLVENT ATOMS : 278
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.78
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 3.06000
REMARK 3 B22 (A**2) : -0.38000
REMARK 3 B33 (A**2) : -2.68000
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): 0.297
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.260
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3134 ; 0.008 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3033 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4254 ; 1.376 ; 1.984
REMARK 3 BOND ANGLES OTHERS (DEGREES): 6975 ; 0.913 ; 3.000
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 391 ; 6.268 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;36.702 ;23.453
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 540 ;12.279 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 25 ;20.264 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 471 ; 0.081 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3524 ; 0.004 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 710 ; 0.002 ; 0.020
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): 1540 ; 1.592 ; 1.847
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1539 ; 1.591 ; 1.846
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1930 ; 1.966 ; 2.772
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1931 ; 1.966 ; 2.774
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1594 ; 2.178 ; 2.139
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1595 ; 2.178 ; 2.140
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2322 ; 2.664 ; 3.111
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3571 ; 3.773 ;15.829
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3572 ; 3.772 ;15.831
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6164 ; 1.150 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 88 ;35.870 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 6296 ; 9.726 ; 5.000
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. U VALUES REFINED INDIVIDUALLY
REMARK 4
REMARK 4 5A1G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 30-APR-15.
REMARK 100 THE DEPOSITION ID IS D_1290063718.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-AUG-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 7.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : DIAMOND
REMARK 200 BEAMLINE : I04-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.92
REMARK 200 MONOCHROMATOR : SI111
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : XDS
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32401
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830
REMARK 200 RESOLUTION RANGE LOW (A) : 29.340
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 200 DATA REDUNDANCY : 13.30
REMARK 200 R MERGE (I) : 0.10000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.5000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5
REMARK 200 DATA REDUNDANCY IN SHELL : 12.50
REMARK 200 R MERGE FOR SHELL (I) : 0.81000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.400
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: MOLREP
REMARK 200 STARTING MODEL: PDB ENTRY 2P02
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 39.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE PH 7.0, 50 % MPD
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2
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,Y,-Z
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z+1/2
REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2
REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2
REMARK 290 8555 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 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.19500
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 47.19500
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.69500
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.19500
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 47.19500
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.69500
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.19500
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 47.19500
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.69500
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.19500
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 47.19500
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.69500
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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 23850 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 45230 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -230.1 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 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 117.39000
REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 117.39000
REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000
REMARK 350 BIOMT3 4 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 A2207 LIES ON A SPECIAL POSITION.
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 1
REMARK 465 ASN A 2
REMARK 465 GLY A 3
REMARK 465 GLN A 4
REMARK 465 LEU A 5
REMARK 465 ASN A 6
REMARK 465 GLY A 7
REMARK 465 PHE A 8
REMARK 465 HIS A 9
REMARK 465 GLU A 10
REMARK 465 ALA A 11
REMARK 465 PHE A 12
REMARK 465 ILE A 13
REMARK 465 GLU A 14
REMARK 465 GLU A 15
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 THR A 62 115.19 -38.70
REMARK 500 VAL A 226 -68.15 -107.33
REMARK 500 PHE A 250 61.03 -157.60
REMARK 500 THR A 270 -100.45 -119.15
REMARK 500 ARG A 292 -64.47 -90.01
REMARK 500
REMARK 500 REMARK: NULL
REMARK 620
REMARK 620 METAL COORDINATION
REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 406 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 31 OD2
REMARK 620 2 PPK A 402 O2A 83.5
REMARK 620 3 PPK A 402 O1B 173.3 89.8
REMARK 620 4 PPK A 402 O2G 92.2 90.7 88.2
REMARK 620 5 HOH A2014 O 92.7 167.5 93.7 101.4
REMARK 620 6 HOH A2015 O 88.5 86.3 90.7 176.8 81.7
REMARK 620 N 1 2 3 4 5
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 K A 405 K
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU A 57 OE2
REMARK 620 2 ASP A 258 OD1 157.8
REMARK 620 3 ALA A 259 O 104.5 85.5
REMARK 620 4 PPK A 402 O1B 95.6 97.2 117.6
REMARK 620 5 HOH A2014 O 66.5 135.7 71.2 64.4
REMARK 620 6 HOH A2015 O 120.5 81.6 57.5 61.3 54.1
REMARK 620 7 HOH A2035 O 81.3 77.5 98.8 142.8 141.6 149.7
REMARK 620 N 1 2 3 4 5 6
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 MG A 407 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 PPK A 402 O4A
REMARK 620 2 PPK A 402 O1G 88.5
REMARK 620 3 HOH A2006 O 84.3 155.0
REMARK 620 4 HOH A2008 O 82.0 78.0 77.3
REMARK 620 5 HOH A2273 O 90.7 119.9 84.1 160.6
REMARK 620 6 HOH A2276 O 160.6 96.7 83.2 80.8 102.7
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD A 400
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PPK A 402
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE IMD A 403
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE S7M A 404
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 405
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 406
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 407
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5A19 RELATED DB: PDB
REMARK 900 THE STRUCTURE OF MAT2A IN COMPLEX WITH PPNP.
REMARK 900 RELATED ID: 5A1I RELATED DB: PDB
REMARK 900 THE STRUCTURE OF HUMAB MAT2A IN COMPLEX WITH SAME, ADENOSINE,
REMARK 900 METHIONINE AND PPNP.
DBREF 5A1G A 1 395 UNP P31153 METK2_HUMAN 1 395
SEQRES 1 A 395 MET ASN GLY GLN LEU ASN GLY PHE HIS GLU ALA PHE ILE
SEQRES 2 A 395 GLU GLU GLY THR PHE LEU PHE THR SER GLU SER VAL GLY
SEQRES 3 A 395 GLU GLY HIS PRO ASP LYS ILE CYS ASP GLN ILE SER ASP
SEQRES 4 A 395 ALA VAL LEU ASP ALA HIS LEU GLN GLN ASP PRO ASP ALA
SEQRES 5 A 395 LYS VAL ALA CYS GLU THR VAL ALA LYS THR GLY MET ILE
SEQRES 6 A 395 LEU LEU ALA GLY GLU ILE THR SER ARG ALA ALA VAL ASP
SEQRES 7 A 395 TYR GLN LYS VAL VAL ARG GLU ALA VAL LYS HIS ILE GLY
SEQRES 8 A 395 TYR ASP ASP SER SER LYS GLY PHE ASP TYR LYS THR CYS
SEQRES 9 A 395 ASN VAL LEU VAL ALA LEU GLU GLN GLN SER PRO ASP ILE
SEQRES 10 A 395 ALA GLN GLY VAL HIS LEU ASP ARG ASN GLU GLU ASP ILE
SEQRES 11 A 395 GLY ALA GLY ASP GLN GLY LEU MET PHE GLY TYR ALA THR
SEQRES 12 A 395 ASP GLU THR GLU GLU CYS MET PRO LEU THR ILE VAL LEU
SEQRES 13 A 395 ALA HIS LYS LEU ASN ALA LYS LEU ALA GLU LEU ARG ARG
SEQRES 14 A 395 ASN GLY THR LEU PRO TRP LEU ARG PRO ASP SER LYS THR
SEQRES 15 A 395 GLN VAL THR VAL GLN TYR MET GLN ASP ARG GLY ALA VAL
SEQRES 16 A 395 LEU PRO ILE ARG VAL HIS THR ILE VAL ILE SER VAL GLN
SEQRES 17 A 395 HIS ASP GLU GLU VAL CYS LEU ASP GLU MET ARG ASP ALA
SEQRES 18 A 395 LEU LYS GLU LYS VAL ILE LYS ALA VAL VAL PRO ALA LYS
SEQRES 19 A 395 TYR LEU ASP GLU ASP THR ILE TYR HIS LEU GLN PRO SER
SEQRES 20 A 395 GLY ARG PHE VAL ILE GLY GLY PRO GLN GLY ASP ALA GLY
SEQRES 21 A 395 LEU THR GLY ARG LYS ILE ILE VAL ASP THR TYR GLY GLY
SEQRES 22 A 395 TRP GLY ALA HIS GLY GLY GLY ALA PHE SER GLY LYS ASP
SEQRES 23 A 395 TYR THR LYS VAL ASP ARG SER ALA ALA TYR ALA ALA ARG
SEQRES 24 A 395 TRP VAL ALA LYS SER LEU VAL LYS GLY GLY LEU CYS ARG
SEQRES 25 A 395 ARG VAL LEU VAL GLN VAL SER TYR ALA ILE GLY VAL SER
SEQRES 26 A 395 HIS PRO LEU SER ILE SER ILE PHE HIS TYR GLY THR SER
SEQRES 27 A 395 GLN LYS SER GLU ARG GLU LEU LEU GLU ILE VAL LYS LYS
SEQRES 28 A 395 ASN PHE ASP LEU ARG PRO GLY VAL ILE VAL ARG ASP LEU
SEQRES 29 A 395 ASP LEU LYS LYS PRO ILE TYR GLN ARG THR ALA ALA TYR
SEQRES 30 A 395 GLY HIS PHE GLY ARG ASP SER PHE PRO TRP GLU VAL PRO
SEQRES 31 A 395 LYS LYS LEU LYS TYR
HET MPD A 400 8
HET MPD A 401 8
HET PPK A 402 13
HET IMD A 403 5
HET S7M A 404 28
HET K A 405 1
HET MG A 406 1
HET MG A 407 1
HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL
HETNAM PPK (DIPHOSPHONO)AMINOPHOSPHONIC ACID
HETNAM IMD IMIDAZOLE
HETNAM S7M [(3S)-3-AMINO-3-CARBOXYPROPYL]{[(2S,3S,4R,5R)-5-(6-
HETNAM 2 S7M AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-
HETNAM 3 S7M YL]METHYL}ETHYLS ULFONIUM
HETNAM K POTASSIUM ION
HETNAM MG MAGNESIUM ION
HETSYN S7M S-ADENOSYL ETHIONINE
FORMUL 2 MPD 2(C6 H14 O2)
FORMUL 4 PPK H6 N O9 P3
FORMUL 5 IMD C3 H5 N2 1+
FORMUL 6 S7M C16 H25 N6 O5 S 1+
FORMUL 7 K K 1+
FORMUL 8 MG 2(MG 2+)
FORMUL 10 HOH *278(H2 O)
HELIX 1 1 HIS A 29 ASP A 49 1 21
HELIX 2 2 ASP A 78 GLY A 91 1 14
HELIX 3 3 SER A 95 GLY A 98 5 4
HELIX 4 4 SER A 114 HIS A 122 1 9
HELIX 5 5 ASN A 126 ILE A 130 5 5
HELIX 6 6 PRO A 151 ASN A 170 1 20
HELIX 7 7 CYS A 214 LYS A 225 1 12
HELIX 8 8 VAL A 226 VAL A 231 1 6
HELIX 9 9 PRO A 232 LEU A 236 5 5
HELIX 10 10 GLY A 253 GLY A 257 5 5
HELIX 11 11 LYS A 289 GLY A 308 1 20
HELIX 12 12 SER A 341 PHE A 353 1 13
HELIX 13 13 ARG A 356 LEU A 364 1 9
HELIX 14 14 TYR A 371 ALA A 375 5 5
HELIX 15 15 PHE A 385 VAL A 389 5 5
SHEET 1 AA 4 THR A 17 VAL A 25 0
SHEET 2 AA 4 LEU A 176 ASP A 191 -1 O THR A 182 N SER A 24
SHEET 3 AA 4 ALA A 194 HIS A 209 -1 O ALA A 194 N ASP A 191
SHEET 4 AA 4 ILE A 241 LEU A 244 1 O ILE A 241 N ILE A 203
SHEET 1 AB 4 ASN A 105 GLU A 111 0
SHEET 2 AB 4 MET A 64 THR A 72 1 O ILE A 65 N LEU A 107
SHEET 3 AB 4 LYS A 53 LYS A 61 -1 O LYS A 53 N THR A 72
SHEET 4 AB 4 GLY A 260 LEU A 261 -1 O GLY A 260 N ALA A 60
SHEET 1 AC 2 ASP A 93 ASP A 94 0
SHEET 2 AC 2 PHE A 99 ASP A 100 -1 O PHE A 99 N ASP A 94
SHEET 1 AD 3 GLY A 136 THR A 143 0
SHEET 2 AD 3 ARG A 313 TYR A 320 -1 O VAL A 314 N ALA A 142
SHEET 3 AD 3 SER A 329 PHE A 333 -1 O SER A 329 N SER A 319
LINK OD2 ASP A 31 MG MG A 406 1555 1555 2.14
LINK OE2 GLU A 57 K K A 405 2555 1555 2.89
LINK OD1 ASP A 258 K K A 405 1555 1555 2.76
LINK O ALA A 259 K K A 405 1555 1555 2.89
LINK O1B PPK A 402 K K A 405 1555 1555 2.73
LINK O2A PPK A 402 MG MG A 406 1555 1555 2.04
LINK O1B PPK A 402 MG MG A 406 1555 1555 2.08
LINK O2G PPK A 402 MG MG A 406 1555 1555 2.01
LINK O4A PPK A 402 MG MG A 407 1555 1555 2.02
LINK O1G PPK A 402 MG MG A 407 1555 1555 2.29
LINK K K A 405 O HOH A2014 1555 1555 3.09
LINK K K A 405 O HOH A2015 1555 1555 3.12
LINK K K A 405 O HOH A2035 1555 2555 2.97
LINK MG MG A 406 O HOH A2014 1555 1555 2.18
LINK MG MG A 406 O HOH A2015 1555 1555 2.13
LINK MG MG A 407 O HOH A2006 1555 1555 2.66
LINK MG MG A 407 O HOH A2008 1555 1555 2.40
LINK MG MG A 407 O HOH A2273 1555 1555 2.00
LINK MG MG A 407 O HOH A2276 1555 1555 1.90
SITE 1 AC1 4 GLY A 273 GLY A 275 ARG A 313 TYR A 335
SITE 1 AC2 21 HIS A 29 ASP A 31 ASP A 134 LYS A 181
SITE 2 AC2 21 ARG A 264 LYS A 265 GLY A 280 ALA A 281
SITE 3 AC2 21 LYS A 285 ASP A 291 S7M A 404 K A 405
SITE 4 AC2 21 MG A 406 MG A 407 HOH A2008 HOH A2015
SITE 5 AC2 21 HOH A2208 HOH A2209 HOH A2273 HOH A2274
SITE 6 AC2 21 HOH A2275
SITE 1 AC3 4 PHE A 18 GLN A 190 GLU A 342 HOH A2154
SITE 1 AC4 24 HIS A 29 PRO A 30 ALA A 55 GLU A 70
SITE 2 AC4 24 GLN A 113 ASP A 116 ILE A 117 GLY A 133
SITE 3 AC4 24 ASP A 134 ASP A 179 LYS A 181 SER A 247
SITE 4 AC4 24 ARG A 249 PHE A 250 ASP A 258 LYS A 289
SITE 5 AC4 24 ILE A 322 PPK A 402 HOH A2040 HOH A2106
SITE 6 AC4 24 HOH A2204 HOH A2206 HOH A2274 HOH A2277
SITE 1 AC5 7 GLU A 57 ASP A 258 ALA A 259 PPK A 402
SITE 2 AC5 7 MG A 406 HOH A2014 HOH A2035
SITE 1 AC6 6 ASP A 31 LYS A 265 PPK A 402 K A 405
SITE 2 AC6 6 HOH A2014 HOH A2015
SITE 1 AC7 6 ASP A 291 PPK A 402 HOH A2006 HOH A2008
SITE 2 AC7 6 HOH A2273 HOH A2276
CRYST1 68.390 94.390 117.390 90.00 90.00 90.00 I 2 2 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 0.014622 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010594 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008519 0.00000