HEADER TRANSFERASE/TRANSFERASE INHIBITOR 06-MAR-17 5V37
TITLE CRYSTAL STRUCTURE OF SMYD3 WITH SAM AND EPZ028862
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: SET AND MYND DOMAIN-CONTAINING PROTEIN 3,ZINC FINGER MYND
COMPND 5 DOMAIN-CONTAINING PROTEIN 1;
COMPND 6 EC: 2.1.1.43;
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: SMYD3, ZMYND1, ZNFN3A1;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21W7-SUMO
KEYWDS PROTEIN-INHIBITOR COMPLEX, PROTEIN LYSINE METHYLTRANSFERASE,
KEYWDS 2 TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR P.A.BORIACK-SJODIN
REVDAT 3 06-MAR-24 5V37 1 REMARK
REVDAT 2 08-MAY-19 5V37 1 JRNL
REVDAT 1 07-MAR-18 5V37 0
JRNL AUTH M.J.THOMENIUS,J.TOTMAN,D.HARVEY,L.H.MITCHELL,T.V.RIERA,
JRNL AUTH 2 K.COSMOPOULOS,A.R.GRASSIAN,C.KLAUS,M.FOLEY,E.A.ADMIRAND,
JRNL AUTH 3 H.JAHIC,C.MAJER,T.WIGLE,S.L.JACQUES,J.GUREASKO,D.BRACH,
JRNL AUTH 4 T.LINGARAJ,K.WEST,S.SMITH,N.RIOUX,N.J.WATERS,C.TANG,
JRNL AUTH 5 A.RAIMONDI,M.MUNCHHOF,J.E.MILLS,S.RIBICH,M.PORTER SCOTT,
JRNL AUTH 6 K.W.KUNTZ,W.P.JANZEN,M.MOYER,J.J.SMITH,R.CHESWORTH,
JRNL AUTH 7 R.A.COPELAND,P.A.BORIACK-SJODIN
JRNL TITL SMALL MOLECULE INHIBITORS AND CRISPR/CAS9 MUTAGENESIS
JRNL TITL 2 DEMONSTRATE THAT SMYD2 AND SMYD3 ACTIVITY ARE DISPENSABLE
JRNL TITL 3 FOR AUTONOMOUS CANCER CELL PROLIFERATION.
JRNL REF PLOS ONE V. 13 97372 2018
JRNL REFN ESSN 1932-6203
JRNL PMID 29856759
JRNL DOI 10.1371/JOURNAL.PONE.0197372
REMARK 2
REMARK 2 RESOLUTION. 1.42 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.8.0155
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) : 1.42
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.26
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6
REMARK 3 NUMBER OF REFLECTIONS : 75322
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) : 0.230
REMARK 3 R VALUE (WORKING SET) : 0.228
REMARK 3 FREE R VALUE : 0.279
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800
REMARK 3 FREE R VALUE TEST SET COUNT : 3831
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) : 1.42
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.46
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4956
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.90
REMARK 3 BIN R VALUE (WORKING SET) : 0.4780
REMARK 3 BIN FREE R VALUE SET COUNT : 230
REMARK 3 BIN FREE R VALUE : 0.4640
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3395
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 86
REMARK 3 SOLVENT ATOMS : 498
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.09
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : -1.59000
REMARK 3 B22 (A**2) : 1.11000
REMARK 3 B33 (A**2) : 0.48000
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): 0.113
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.125
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3875 ; 0.008 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 3775 ; 0.002 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5236 ; 1.359 ; 2.003
REMARK 3 BOND ANGLES OTHERS (DEGREES): 8721 ; 0.934 ; 3.003
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 482 ; 5.722 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;33.522 ;23.771
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 735 ;14.958 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;14.943 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 567 ; 0.077 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4341 ; 0.005 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 871 ; 0.003 ; 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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
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): 7650 ; 4.713 ; 3.000
REMARK 3 SPHERICITY; FREE ATOMS (A**2): 207 ;26.830 ; 5.000
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7843 ; 9.867 ; 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 : NULL
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 5V37 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAR-17.
REMARK 100 THE DEPOSITION ID IS D_1000226810.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 19-NOV-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-D
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 : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : KYLIN
REMARK 200 DATA SCALING SOFTWARE : KYLIN
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75322
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.410
REMARK 200 RESOLUTION RANGE LOW (A) : 17.260
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7
REMARK 200 DATA REDUNDANCY : 5.800
REMARK 200 R MERGE (I) : 0.07400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45
REMARK 200 COMPLETENESS FOR SHELL (%) : 85.9
REMARK 200 DATA REDUNDANCY IN SHELL : 4.10
REMARK 200 R MERGE FOR SHELL (I) : 0.34600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: NULL
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.07
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.10 M MAGNESIUM FORMATE, 0.1M TRIS
REMARK 280 8.0, 14% W/V PEG 3350, PH 8.0, VAPOR DIFFUSION, HANGING DROP,
REMARK 280 TEMPERATURE 293K
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 30.40900
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.50750
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.93400
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.50750
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.40900
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.93400
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 MET A 1
REMARK 465 GLU A 2
REMARK 465 ALA A 427
REMARK 465 SER A 428
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 NZ LYS A 375 O HOH A 601 2.08
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 ASN A 13 24.74 -144.48
REMARK 500 ARG A 14 36.09 -143.24
REMARK 500 ARG A 14 39.98 -145.22
REMARK 500 CYS A 65 -35.12 -138.33
REMARK 500 VAL A 67 -50.99 -137.74
REMARK 500 LYS A 94 121.21 -30.38
REMARK 500 LYS A 271 -5.67 81.29
REMARK 500 ILE A 425 -69.06 -102.32
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 A1096 DISTANCE = 6.31 ANGSTROMS
REMARK 525 HOH A1097 DISTANCE = 7.89 ANGSTROMS
REMARK 525 HOH A1098 DISTANCE = 12.36 ANGSTROMS
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 ZN A 501 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 49 SG
REMARK 620 2 CYS A 52 SG 104.0
REMARK 620 3 CYS A 71 SG 114.0 106.4
REMARK 620 4 CYS A 75 SG 109.3 115.3 107.8
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 503 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 62 SG
REMARK 620 2 CYS A 65 SG 99.8
REMARK 620 3 HIS A 83 NE2 114.1 105.1
REMARK 620 4 CYS A 87 SG 115.0 104.8 115.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 503 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 62 SG
REMARK 620 2 CYS A 65 SG 108.7
REMARK 620 3 HIS A 83 NE2 109.5 110.9
REMARK 620 4 CYS A 87 SG 109.5 111.2 107.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 502 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 208 SG
REMARK 620 2 CYS A 261 SG 114.5
REMARK 620 3 CYS A 263 SG 104.7 110.1
REMARK 620 4 CYS A 266 SG 100.1 114.4 112.5
REMARK 620 N 1 2 3
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 502
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue SAM A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue 8WD A 505
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 506
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 507
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 508
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 509
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 510
REMARK 800
REMARK 800 SITE_IDENTIFIER: AD2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 511
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5V3H RELATED DB: PDB
DBREF 5V37 A 1 428 UNP Q9H7B4 SMYD3_HUMAN 1 428
SEQADV 5V37 ASN A 13 UNP Q9H7B4 LYS 13 CONFLICT
SEQRES 1 A 428 MET GLU PRO LEU LYS VAL GLU LYS PHE ALA THR ALA ASN
SEQRES 2 A 428 ARG GLY ASN GLY LEU ARG ALA VAL THR PRO LEU ARG PRO
SEQRES 3 A 428 GLY GLU LEU LEU PHE ARG SER ASP PRO LEU ALA TYR THR
SEQRES 4 A 428 VAL CYS LYS GLY SER ARG GLY VAL VAL CYS ASP ARG CYS
SEQRES 5 A 428 LEU LEU GLY LYS GLU LYS LEU MET ARG CYS SER GLN CYS
SEQRES 6 A 428 ARG VAL ALA LYS TYR CYS SER ALA LYS CYS GLN LYS LYS
SEQRES 7 A 428 ALA TRP PRO ASP HIS LYS ARG GLU CYS LYS CYS LEU LYS
SEQRES 8 A 428 SER CYS LYS PRO ARG TYR PRO PRO ASP SER VAL ARG LEU
SEQRES 9 A 428 LEU GLY ARG VAL VAL PHE LYS LEU MET ASP GLY ALA PRO
SEQRES 10 A 428 SER GLU SER GLU LYS LEU TYR SER PHE TYR ASP LEU GLU
SEQRES 11 A 428 SER ASN ILE ASN LYS LEU THR GLU ASP LYS LYS GLU GLY
SEQRES 12 A 428 LEU ARG GLN LEU VAL MET THR PHE GLN HIS PHE MET ARG
SEQRES 13 A 428 GLU GLU ILE GLN ASP ALA SER GLN LEU PRO PRO ALA PHE
SEQRES 14 A 428 ASP LEU PHE GLU ALA PHE ALA LYS VAL ILE CYS ASN SER
SEQRES 15 A 428 PHE THR ILE CYS ASN ALA GLU MET GLN GLU VAL GLY VAL
SEQRES 16 A 428 GLY LEU TYR PRO SER ILE SER LEU LEU ASN HIS SER CYS
SEQRES 17 A 428 ASP PRO ASN CYS SER ILE VAL PHE ASN GLY PRO HIS LEU
SEQRES 18 A 428 LEU LEU ARG ALA VAL ARG ASP ILE GLU VAL GLY GLU GLU
SEQRES 19 A 428 LEU THR ILE CYS TYR LEU ASP MET LEU MET THR SER GLU
SEQRES 20 A 428 GLU ARG ARG LYS GLN LEU ARG ASP GLN TYR CYS PHE GLU
SEQRES 21 A 428 CYS ASP CYS PHE ARG CYS GLN THR GLN ASP LYS ASP ALA
SEQRES 22 A 428 ASP MET LEU THR GLY ASP GLU GLN VAL TRP LYS GLU VAL
SEQRES 23 A 428 GLN GLU SER LEU LYS LYS ILE GLU GLU LEU LYS ALA HIS
SEQRES 24 A 428 TRP LYS TRP GLU GLN VAL LEU ALA MET CYS GLN ALA ILE
SEQRES 25 A 428 ILE SER SER ASN SER GLU ARG LEU PRO ASP ILE ASN ILE
SEQRES 26 A 428 TYR GLN LEU LYS VAL LEU ASP CYS ALA MET ASP ALA CYS
SEQRES 27 A 428 ILE ASN LEU GLY LEU LEU GLU GLU ALA LEU PHE TYR GLY
SEQRES 28 A 428 THR ARG THR MET GLU PRO TYR ARG ILE PHE PHE PRO GLY
SEQRES 29 A 428 SER HIS PRO VAL ARG GLY VAL GLN VAL MET LYS VAL GLY
SEQRES 30 A 428 LYS LEU GLN LEU HIS GLN GLY MET PHE PRO GLN ALA MET
SEQRES 31 A 428 LYS ASN LEU ARG LEU ALA PHE ASP ILE MET ARG VAL THR
SEQRES 32 A 428 HIS GLY ARG GLU HIS SER LEU ILE GLU ASP LEU ILE LEU
SEQRES 33 A 428 LEU LEU GLU GLU CYS ASP ALA ASN ILE ARG ALA SER
HET ZN A 501 1
HET ZN A 502 1
HET ZN A 503 2
HET SAM A 504 27
HET 8WD A 505 29
HET PEG A 506 7
HET DMS A 507 4
HET DMS A 508 4
HET EDO A 509 4
HET EDO A 510 4
HET EDO A 511 4
HETNAM ZN ZINC ION
HETNAM SAM S-ADENOSYLMETHIONINE
HETNAM 8WD N-{(3-ENDO)-8-[(TRANS-4-AMINOCYCLOHEXYL)SULFONYL]-8-
HETNAM 2 8WD AZABICYCLO[3.2.1]OCTAN-3-YL}-5-CYCLOPROPYL-1,2-
HETNAM 3 8WD OXAZOLE-3-CARBOXAMIDE
HETNAM PEG DI(HYDROXYETHYL)ETHER
HETNAM DMS DIMETHYL SULFOXIDE
HETNAM EDO 1,2-ETHANEDIOL
HETSYN EDO ETHYLENE GLYCOL
FORMUL 2 ZN 3(ZN 2+)
FORMUL 5 SAM C15 H22 N6 O5 S
FORMUL 6 8WD C20 H30 N4 O4 S
FORMUL 7 PEG C4 H10 O3
FORMUL 8 DMS 2(C2 H6 O S)
FORMUL 10 EDO 3(C2 H6 O2)
FORMUL 13 HOH *498(H2 O)
HELIX 1 AA1 LYS A 42 ARG A 45 5 4
HELIX 2 AA2 SER A 72 ALA A 79 1 8
HELIX 3 AA3 ALA A 79 LYS A 94 1 16
HELIX 4 AA4 PRO A 99 GLY A 115 1 17
HELIX 5 AA5 SER A 118 LYS A 122 5 5
HELIX 6 AA6 SER A 125 LEU A 129 5 5
HELIX 7 AA7 ASN A 132 LEU A 136 5 5
HELIX 8 AA8 THR A 137 MET A 155 1 19
HELIX 9 AA9 ASP A 161 LEU A 165 5 5
HELIX 10 AB1 ASP A 170 SER A 182 1 13
HELIX 11 AB2 SER A 200 LEU A 204 5 5
HELIX 12 AB3 THR A 245 GLN A 256 1 12
HELIX 13 AB4 CYS A 263 GLN A 269 1 7
HELIX 14 AB5 LYS A 271 LEU A 276 1 6
HELIX 15 AB6 ASP A 279 HIS A 299 1 21
HELIX 16 AB7 LYS A 301 SER A 314 1 14
HELIX 17 AB8 ASN A 324 LEU A 341 1 18
HELIX 18 AB9 LEU A 343 PHE A 362 1 20
HELIX 19 AC1 HIS A 366 GLN A 383 1 18
HELIX 20 AC2 MET A 385 HIS A 404 1 20
HELIX 21 AC3 HIS A 408 ILE A 425 1 18
SHEET 1 AA1 4 VAL A 6 ALA A 10 0
SHEET 2 AA1 4 ASN A 16 ALA A 20 -1 O GLY A 17 N PHE A 9
SHEET 3 AA1 4 GLU A 234 ILE A 237 -1 O LEU A 235 N LEU A 18
SHEET 4 AA1 4 ASN A 205 HIS A 206 1 N ASN A 205 O ILE A 237
SHEET 1 AA2 3 LEU A 29 SER A 33 0
SHEET 2 AA2 3 HIS A 220 ALA A 225 -1 O LEU A 223 N PHE A 31
SHEET 3 AA2 3 CYS A 212 ASN A 217 -1 N ASN A 217 O HIS A 220
SHEET 1 AA3 3 ALA A 37 VAL A 40 0
SHEET 2 AA3 3 GLU A 192 LEU A 197 -1 O VAL A 195 N THR A 39
SHEET 3 AA3 3 PHE A 183 CYS A 186 -1 N PHE A 183 O GLY A 196
SHEET 1 AA4 2 MET A 60 ARG A 61 0
SHEET 2 AA4 2 LYS A 69 TYR A 70 -1 O TYR A 70 N MET A 60
LINK SG CYS A 49 ZN ZN A 501 1555 1555 2.33
LINK SG CYS A 52 ZN ZN A 501 1555 1555 2.33
LINK SG ACYS A 62 ZN A ZN A 503 1555 1555 2.34
LINK SG BCYS A 62 ZN B ZN A 503 1555 1555 2.33
LINK SG ACYS A 65 ZN A ZN A 503 1555 1555 2.31
LINK SG BCYS A 65 ZN B ZN A 503 1555 1555 2.34
LINK SG CYS A 71 ZN ZN A 501 1555 1555 2.34
LINK SG CYS A 75 ZN ZN A 501 1555 1555 2.33
LINK NE2 HIS A 83 ZN A ZN A 503 1555 1555 1.90
LINK NE2 HIS A 83 ZN B ZN A 503 1555 1555 2.29
LINK SG ACYS A 87 ZN A ZN A 503 1555 1555 2.33
LINK SG BCYS A 87 ZN B ZN A 503 1555 1555 2.32
LINK SG CYS A 208 ZN ZN A 502 1555 1555 2.33
LINK SG CYS A 261 ZN ZN A 502 1555 1555 2.31
LINK SG CYS A 263 ZN ZN A 502 1555 1555 2.33
LINK SG CYS A 266 ZN ZN A 502 1555 1555 2.32
CISPEP 1 LYS A 94 PRO A 95 0 12.49
CISPEP 2 LYS A 94 PRO A 95 0 2.12
SITE 1 AC1 5 CYS A 49 CYS A 52 CYS A 71 CYS A 75
SITE 2 AC1 5 HOH A 658
SITE 1 AC2 4 CYS A 208 CYS A 261 CYS A 263 CYS A 266
SITE 1 AC3 4 CYS A 62 CYS A 65 HIS A 83 CYS A 87
SITE 1 AC4 23 ARG A 14 GLY A 15 ASN A 16 TYR A 124
SITE 2 AC4 23 GLU A 130 ASN A 132 CYS A 180 ASN A 181
SITE 3 AC4 23 SER A 202 LEU A 203 LEU A 204 ASN A 205
SITE 4 AC4 23 HIS A 206 TYR A 239 TYR A 257 PHE A 259
SITE 5 AC4 23 HOH A 666 HOH A 669 HOH A 679 HOH A 753
SITE 6 AC4 23 HOH A 810 HOH A 814 HOH A 879
SITE 1 AC5 19 CYS A 180 ASN A 181 SER A 182 PHE A 183
SITE 2 AC5 19 THR A 184 MET A 190 GLU A 192 ILE A 237
SITE 3 AC5 19 TYR A 239 ASP A 241 TYR A 257 VAL A 368
SITE 4 AC5 19 DMS A 507 HOH A 627 HOH A 651 HOH A 681
SITE 5 AC5 19 HOH A 795 HOH A 928 HOH A 942
SITE 1 AC6 8 ALA A 10 THR A 11 ASN A 13 ARG A 14
SITE 2 AC6 8 GLY A 15 GLU A 318 HOH A 663 HOH A 821
SITE 1 AC7 4 SER A 182 THR A 184 GLN A 256 8WD A 505
SITE 1 AC8 5 PRO A 99 MET A 113 ASP A 114 GLY A 115
SITE 2 AC8 5 THR A 150
SITE 1 AC9 7 ALA A 188 GLU A 189 VAL A 371 LYS A 375
SITE 2 AC9 7 LEU A 410 HOH A 624 HOH A 944
SITE 1 AD1 4 ASP A 139 LYS A 140 HOH A 665 HOH A 891
SITE 1 AD2 4 ARG A 359 ARG A 369 HOH A 737 HOH A 842
CRYST1 60.818 65.868 107.015 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 0.016443 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015182 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009344 0.00000