HEADER PROTEIN BINDING 28-APR-20 6YVI TITLE EED IN COMPLEX WITH A CYANO-BENZOFURAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLYCOMB PROTEIN EED; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HEED,EMBRYONIC ECTODERM DEVELOPMENT PROTEIN,WD PROTEIN COMPND 5 ASSOCIATING WITH INTEGRIN CYTOPLASMIC TAILS 1,WAIT-1; COMPND 6 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: EED; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS METHYL TRANSFERASE EED PRC2 EPIGENETIC H3K27 WD40 INHIBITOR, PROTEIN KEYWDS 2 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.A.READ REVDAT 3 24-JAN-24 6YVI 1 REMARK REVDAT 2 14-JUL-21 6YVI 1 COMPND JRNL REMARK HETNAM REVDAT 2 2 1 FORMUL REVDAT 1 12-MAY-21 6YVI 0 JRNL AUTH D.H.O' DONOVAN,C.GREGSON,M.J.PACKER,R.GREENWOOD,K.G.PIKE, JRNL AUTH 2 S.KAWATKAR,A.BLOECHER,J.ROBINSON,J.READ,E.CODE,J.H.HSU, JRNL AUTH 3 M.SHEN,H.WOODS,P.BARTON,S.FILLERY,B.WILLIAMSON,P.B.RAWLINS, JRNL AUTH 4 S.K.BAGAL JRNL TITL FREE ENERGY PERTURBATION IN THE DESIGN OF EED LIGANDS AS JRNL TITL 2 INHIBITORS OF POLYCOMB REPRESSIVE COMPLEX 2 (PRC2) JRNL TITL 3 METHYLTRANSFERASE. JRNL REF BIOORG.MED.CHEM.LETT. V. 39 27904 2021 JRNL REFN ESSN 1464-3405 JRNL PMID 33684441 JRNL DOI 10.1016/J.BMCL.2021.127904 REMARK 2 REMARK 2 RESOLUTION. 2.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 67.2 REMARK 3 NUMBER OF REFLECTIONS : 23221 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.241 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 1194 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.26 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.36 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : NULL REMARK 3 BIN R VALUE (WORKING + TEST SET) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 96 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 4 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5513 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 61 REMARK 3 SOLVENT ATOMS : 291 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.58180 REMARK 3 B22 (A**2) : 4.53560 REMARK 3 B33 (A**2) : -1.95380 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.290 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : NULL REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.314 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : NULL REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : NULL REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 5719 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 7771 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 1933 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 135 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 831 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 5719 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : 0 ; 5.000 ; SEMIHARMONIC REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 737 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 6584 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.13 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.45 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 18.92 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|82 - A|439 } REMARK 3 ORIGIN FOR THE GROUP (A): 25.6552 33.6499 6.0252 REMARK 3 T TENSOR REMARK 3 T11: -0.0919 T22: -0.0026 REMARK 3 T33: -0.1108 T12: -0.0196 REMARK 3 T13: -0.0263 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 1.5738 L22: 1.1334 REMARK 3 L33: 1.1167 L12: -0.1352 REMARK 3 L13: -0.0548 L23: -0.1780 REMARK 3 S TENSOR REMARK 3 S11: -0.0287 S12: 0.0850 S13: 0.1470 REMARK 3 S21: -0.0494 S22: 0.0294 S23: 0.0730 REMARK 3 S31: 0.0171 S32: -0.0545 S33: -0.0006 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|81 - B|439 } REMARK 3 ORIGIN FOR THE GROUP (A): -23.6277 42.8503 16.7174 REMARK 3 T TENSOR REMARK 3 T11: -0.1308 T22: -0.0578 REMARK 3 T33: -0.1012 T12: -0.0589 REMARK 3 T13: 0.0170 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 2.8658 L22: 1.2201 REMARK 3 L33: 2.0534 L12: 0.0121 REMARK 3 L13: 0.0831 L23: -0.4955 REMARK 3 S TENSOR REMARK 3 S11: 0.0037 S12: -0.2323 S13: -0.1051 REMARK 3 S21: 0.0602 S22: -0.1562 S23: -0.0518 REMARK 3 S31: -0.0827 S32: 0.3089 S33: 0.1525 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YVI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108341. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAY-18 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 : 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) : 0.91587 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23221 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.260 REMARK 200 RESOLUTION RANGE LOW (A) : 64.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.3 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 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 FOR SHELL : 1.400 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: 6SFB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15M CACL2, 18% PEG 3350, 0.1M PCPT REMARK 280 PH 8.3, VAPOR DIFFUSION, SITTING DROP, 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 42.94400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.59300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.26400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.59300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 42.94400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.26400 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 LYS A 76 REMARK 465 LYS A 77 REMARK 465 CYS A 78 REMARK 465 LYS A 79 REMARK 465 TYR A 80 REMARK 465 SER A 81 REMARK 465 VAL A 393 REMARK 465 GLU A 394 REMARK 465 ASP A 395 REMARK 465 PRO A 396 REMARK 465 HIS A 397 REMARK 465 LYS A 398 REMARK 465 ALA A 399 REMARK 465 LYS A 400 REMARK 465 LEU A 440 REMARK 465 ARG A 441 REMARK 465 LYS B 76 REMARK 465 LYS B 77 REMARK 465 CYS B 78 REMARK 465 LYS B 79 REMARK 465 TYR B 80 REMARK 465 TYR B 280 REMARK 465 ASN B 281 REMARK 465 PRO B 282 REMARK 465 ASN B 283 REMARK 465 LYS B 284 REMARK 465 THR B 285 REMARK 465 ASN B 286 REMARK 465 VAL B 393 REMARK 465 GLU B 394 REMARK 465 ASP B 395 REMARK 465 PRO B 396 REMARK 465 HIS B 397 REMARK 465 LYS B 398 REMARK 465 ALA B 399 REMARK 465 LYS B 400 REMARK 465 LEU B 440 REMARK 465 ARG B 441 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 LYS A 83 CG CD CE NZ REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 SER A 128 OG REMARK 470 GLN A 129 CG CD OE1 NE2 REMARK 470 GLN A 181 CG CD OE1 NE2 REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 LYS A 268 CG CD CE NZ REMARK 470 LYS A 275 CD CE NZ REMARK 470 GLU A 276 CD OE1 OE2 REMARK 470 LYS A 342 CD CE NZ REMARK 470 GLU A 392 CG CD OE1 OE2 REMARK 470 LYS A 408 CD CE NZ REMARK 470 LYS B 83 CG CD CE NZ REMARK 470 LYS B 106 CG CD CE NZ REMARK 470 GLU B 107 CG CD OE1 OE2 REMARK 470 SER B 137 OG REMARK 470 HIS B 160 CG ND1 CD2 CE1 NE2 REMARK 470 GLN B 181 CG CD OE1 NE2 REMARK 470 LYS B 268 CG CD CE NZ REMARK 470 LYS B 275 CG CD CE NZ REMARK 470 ARG B 306 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 325 CD OE1 OE2 REMARK 470 LYS B 335 CD CE NZ REMARK 470 LYS B 342 CD CE NZ REMARK 470 LYS B 344 CD CE NZ REMARK 470 LYS B 375 CG CD CE NZ REMARK 470 GLU B 392 CG CD OE1 OE2 REMARK 470 LYS B 408 CE NZ REMARK 470 ARG B 439 CZ NH1 NH2 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 SER A 118 -135.06 51.32 REMARK 500 ASN A 191 179.44 178.76 REMARK 500 HIS A 213 -5.62 88.01 REMARK 500 HIS A 258 -12.66 75.82 REMARK 500 SER A 323 -149.10 -117.33 REMARK 500 CYS A 361 47.02 -148.20 REMARK 500 TYR A 365 62.15 73.53 REMARK 500 SER B 118 -134.27 51.95 REMARK 500 GLN B 129 5.43 139.79 REMARK 500 VAL B 187 84.70 -61.65 REMARK 500 HIS B 213 -4.59 87.73 REMARK 500 HIS B 258 -11.44 75.24 REMARK 500 SER B 323 -149.35 -116.08 REMARK 500 CYS B 361 48.01 -148.87 REMARK 500 TYR B 365 60.60 74.79 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 ARG B 313 0.07 SIDE CHAIN 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 B 715 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH B 716 DISTANCE = 6.01 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 CA A 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 341 OD2 REMARK 620 2 HOH A 704 O 84.2 REMARK 620 3 HOH A 746 O 85.8 162.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue L9W A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PV5 B 501 DBREF 6YVI A 76 441 UNP O75530 EED_HUMAN 76 441 DBREF 6YVI B 76 441 UNP O75530 EED_HUMAN 76 441 SEQRES 1 A 366 LYS LYS CYS LYS TYR SER PHE LYS CYS VAL ASN SER LEU SEQRES 2 A 366 LYS GLU ASP HIS ASN GLN PRO LEU PHE GLY VAL GLN PHE SEQRES 3 A 366 ASN TRP HIS SER LYS GLU GLY ASP PRO LEU VAL PHE ALA SEQRES 4 A 366 THR VAL GLY SER ASN ARG VAL THR LEU TYR GLU CYS HIS SEQRES 5 A 366 SER GLN GLY GLU ILE ARG LEU LEU GLN SER TYR VAL ASP SEQRES 6 A 366 ALA ASP ALA ASP GLU ASN PHE TYR THR CYS ALA TRP THR SEQRES 7 A 366 TYR ASP SER ASN THR SER HIS PRO LEU LEU ALA VAL ALA SEQRES 8 A 366 GLY SER ARG GLY ILE ILE ARG ILE ILE ASN PRO ILE THR SEQRES 9 A 366 MET GLN CYS ILE LYS HIS TYR VAL GLY HIS GLY ASN ALA SEQRES 10 A 366 ILE ASN GLU LEU LYS PHE HIS PRO ARG ASP PRO ASN LEU SEQRES 11 A 366 LEU LEU SER VAL SER LYS ASP HIS ALA LEU ARG LEU TRP SEQRES 12 A 366 ASN ILE GLN THR ASP THR LEU VAL ALA ILE PHE GLY GLY SEQRES 13 A 366 VAL GLU GLY HIS ARG ASP GLU VAL LEU SER ALA ASP TYR SEQRES 14 A 366 ASP LEU LEU GLY GLU LYS ILE MET SER CYS GLY MET ASP SEQRES 15 A 366 HIS SER LEU LYS LEU TRP ARG ILE ASN SER LYS ARG MET SEQRES 16 A 366 MET ASN ALA ILE LYS GLU SER TYR ASP TYR ASN PRO ASN SEQRES 17 A 366 LYS THR ASN ARG PRO PHE ILE SER GLN LYS ILE HIS PHE SEQRES 18 A 366 PRO ASP PHE SER THR ARG ASP ILE HIS ARG ASN TYR VAL SEQRES 19 A 366 ASP CYS VAL ARG TRP LEU GLY ASP LEU ILE LEU SER LYS SEQRES 20 A 366 SER CYS GLU ASN ALA ILE VAL CYS TRP LYS PRO GLY LYS SEQRES 21 A 366 MET GLU ASP ASP ILE ASP LYS ILE LYS PRO SER GLU SER SEQRES 22 A 366 ASN VAL THR ILE LEU GLY ARG PHE ASP TYR SER GLN CYS SEQRES 23 A 366 ASP ILE TRP TYR MET ARG PHE SER MET ASP PHE TRP GLN SEQRES 24 A 366 LYS MET LEU ALA LEU GLY ASN GLN VAL GLY LYS LEU TYR SEQRES 25 A 366 VAL TRP ASP LEU GLU VAL GLU ASP PRO HIS LYS ALA LYS SEQRES 26 A 366 CYS THR THR LEU THR HIS HIS LYS CYS GLY ALA ALA ILE SEQRES 27 A 366 ARG GLN THR SER PHE SER ARG ASP SER SER ILE LEU ILE SEQRES 28 A 366 ALA VAL CYS ASP ASP ALA SER ILE TRP ARG TRP ASP ARG SEQRES 29 A 366 LEU ARG SEQRES 1 B 366 LYS LYS CYS LYS TYR SER PHE LYS CYS VAL ASN SER LEU SEQRES 2 B 366 LYS GLU ASP HIS ASN GLN PRO LEU PHE GLY VAL GLN PHE SEQRES 3 B 366 ASN TRP HIS SER LYS GLU GLY ASP PRO LEU VAL PHE ALA SEQRES 4 B 366 THR VAL GLY SER ASN ARG VAL THR LEU TYR GLU CYS HIS SEQRES 5 B 366 SER GLN GLY GLU ILE ARG LEU LEU GLN SER TYR VAL ASP SEQRES 6 B 366 ALA ASP ALA ASP GLU ASN PHE TYR THR CYS ALA TRP THR SEQRES 7 B 366 TYR ASP SER ASN THR SER HIS PRO LEU LEU ALA VAL ALA SEQRES 8 B 366 GLY SER ARG GLY ILE ILE ARG ILE ILE ASN PRO ILE THR SEQRES 9 B 366 MET GLN CYS ILE LYS HIS TYR VAL GLY HIS GLY ASN ALA SEQRES 10 B 366 ILE ASN GLU LEU LYS PHE HIS PRO ARG ASP PRO ASN LEU SEQRES 11 B 366 LEU LEU SER VAL SER LYS ASP HIS ALA LEU ARG LEU TRP SEQRES 12 B 366 ASN ILE GLN THR ASP THR LEU VAL ALA ILE PHE GLY GLY SEQRES 13 B 366 VAL GLU GLY HIS ARG ASP GLU VAL LEU SER ALA ASP TYR SEQRES 14 B 366 ASP LEU LEU GLY GLU LYS ILE MET SER CYS GLY MET ASP SEQRES 15 B 366 HIS SER LEU LYS LEU TRP ARG ILE ASN SER LYS ARG MET SEQRES 16 B 366 MET ASN ALA ILE LYS GLU SER TYR ASP TYR ASN PRO ASN SEQRES 17 B 366 LYS THR ASN ARG PRO PHE ILE SER GLN LYS ILE HIS PHE SEQRES 18 B 366 PRO ASP PHE SER THR ARG ASP ILE HIS ARG ASN TYR VAL SEQRES 19 B 366 ASP CYS VAL ARG TRP LEU GLY ASP LEU ILE LEU SER LYS SEQRES 20 B 366 SER CYS GLU ASN ALA ILE VAL CYS TRP LYS PRO GLY LYS SEQRES 21 B 366 MET GLU ASP ASP ILE ASP LYS ILE LYS PRO SER GLU SER SEQRES 22 B 366 ASN VAL THR ILE LEU GLY ARG PHE ASP TYR SER GLN CYS SEQRES 23 B 366 ASP ILE TRP TYR MET ARG PHE SER MET ASP PHE TRP GLN SEQRES 24 B 366 LYS MET LEU ALA LEU GLY ASN GLN VAL GLY LYS LEU TYR SEQRES 25 B 366 VAL TRP ASP LEU GLU VAL GLU ASP PRO HIS LYS ALA LYS SEQRES 26 B 366 CYS THR THR LEU THR HIS HIS LYS CYS GLY ALA ALA ILE SEQRES 27 B 366 ARG GLN THR SER PHE SER ARG ASP SER SER ILE LEU ILE SEQRES 28 B 366 ALA VAL CYS ASP ASP ALA SER ILE TRP ARG TRP ASP ARG SEQRES 29 B 366 LEU ARG HET CA A 501 1 HET L9W A 502 30 HET PV5 B 501 30 HETNAM CA CALCIUM ION HETNAM L9W N-(2,3-DIHYDRO-1-BENZOFURAN-4-YLMETHYL)-8-(4- HETNAM 2 L9W METHYLSULFONYLPHENYL)-[1,2,4]TRIAZOLO[4,3-C]PYRIMIDIN- HETNAM 3 L9W 5-AMINE HETNAM PV5 5-FLUORANYL-4-[[[8-(2-METHYLPYRIDIN-3-YL)-[1,2, HETNAM 2 PV5 4]TRIAZOLO[4,3-C]PYRIMIDIN-5-YL]AMINO]METHYL]-2,3- HETNAM 3 PV5 DIHYDRO-1-BENZOFURAN-7-CARBONITRILE FORMUL 3 CA CA 2+ FORMUL 4 L9W C21 H19 N5 O3 S FORMUL 5 PV5 C21 H16 F N7 O FORMUL 6 HOH *291(H2 O) HELIX 1 AA1 SER A 128 GLY A 130 5 3 HELIX 2 AA2 SER A 267 ASP A 279 1 13 HELIX 3 AA3 SER B 267 ASP B 279 1 13 SHEET 1 AA1 4 LYS A 83 LYS A 89 0 SHEET 2 AA1 4 SER A 433 ASP A 438 -1 O ASP A 438 N LYS A 83 SHEET 3 AA1 4 ILE A 424 CYS A 429 -1 N LEU A 425 O TRP A 437 SHEET 4 AA1 4 ILE A 413 PHE A 418 -1 N SER A 417 O ILE A 426 SHEET 1 AA2 4 LEU A 96 PHE A 101 0 SHEET 2 AA2 4 LEU A 111 GLY A 117 -1 O ALA A 114 N GLN A 100 SHEET 3 AA2 4 ARG A 120 CYS A 126 -1 O CYS A 126 N LEU A 111 SHEET 4 AA2 4 ILE A 132 VAL A 139 -1 O GLN A 136 N LEU A 123 SHEET 1 AA3 4 PHE A 147 TYR A 154 0 SHEET 2 AA3 4 PRO A 161 GLY A 167 -1 O ALA A 164 N ALA A 151 SHEET 3 AA3 4 ILE A 172 ASN A 176 -1 O ILE A 175 N LEU A 163 SHEET 4 AA3 4 GLN A 181 TYR A 186 -1 O GLN A 181 N ASN A 176 SHEET 1 AA4 5 ILE A 193 PHE A 198 0 SHEET 2 AA4 5 LEU A 205 SER A 210 -1 O LEU A 207 N LYS A 197 SHEET 3 AA4 5 LEU A 215 ASN A 219 -1 O TRP A 218 N LEU A 206 SHEET 4 AA4 5 THR A 224 PHE A 229 -1 O THR A 224 N ASN A 219 SHEET 5 AA4 5 GLN A 292 ILE A 294 1 O GLN A 292 N ILE A 228 SHEET 1 AA5 4 VAL A 239 TYR A 244 0 SHEET 2 AA5 4 LYS A 250 GLY A 255 -1 O CYS A 254 N SER A 241 SHEET 3 AA5 4 LEU A 260 ARG A 264 -1 O TRP A 263 N ILE A 251 SHEET 4 AA5 4 PHE A 299 THR A 301 -1 O PHE A 299 N LEU A 262 SHEET 1 AA6 4 CYS A 311 LEU A 315 0 SHEET 2 AA6 4 LEU A 318 LYS A 322 -1 O LEU A 320 N ARG A 313 SHEET 3 AA6 4 ALA A 327 PRO A 333 -1 O TRP A 331 N ILE A 319 SHEET 4 AA6 4 VAL A 350 ASP A 357 -1 O LEU A 353 N CYS A 330 SHEET 1 AA7 4 PHE A 368 MET A 370 0 SHEET 2 AA7 4 MET A 376 GLY A 380 -1 O ALA A 378 N SER A 369 SHEET 3 AA7 4 LEU A 386 ASP A 390 -1 O TYR A 387 N LEU A 379 SHEET 4 AA7 4 THR A 402 LEU A 404 -1 O LEU A 404 N LEU A 386 SHEET 1 AA8 4 LYS B 83 LYS B 89 0 SHEET 2 AA8 4 SER B 433 ASP B 438 -1 O ASP B 438 N LYS B 83 SHEET 3 AA8 4 ILE B 424 CYS B 429 -1 N LEU B 425 O TRP B 437 SHEET 4 AA8 4 ILE B 413 PHE B 418 -1 N SER B 417 O ILE B 426 SHEET 1 AA9 4 LEU B 96 PHE B 101 0 SHEET 2 AA9 4 LEU B 111 GLY B 117 -1 O VAL B 116 N PHE B 97 SHEET 3 AA9 4 ARG B 120 HIS B 127 -1 O CYS B 126 N LEU B 111 SHEET 4 AA9 4 GLU B 131 VAL B 139 -1 O GLN B 136 N LEU B 123 SHEET 1 AB1 4 PHE B 147 TYR B 154 0 SHEET 2 AB1 4 PRO B 161 GLY B 167 -1 O ALA B 164 N ALA B 151 SHEET 3 AB1 4 ILE B 172 ASN B 176 -1 O ILE B 175 N LEU B 163 SHEET 4 AB1 4 GLN B 181 TYR B 186 -1 O LYS B 184 N ILE B 174 SHEET 1 AB2 5 ILE B 193 HIS B 199 0 SHEET 2 AB2 5 ASP B 202 SER B 210 -1 O LEU B 207 N LYS B 197 SHEET 3 AB2 5 LEU B 215 ASN B 219 -1 O TRP B 218 N LEU B 206 SHEET 4 AB2 5 THR B 224 PHE B 229 -1 O THR B 224 N ASN B 219 SHEET 5 AB2 5 GLN B 292 ILE B 294 1 O GLN B 292 N VAL B 226 SHEET 1 AB3 4 VAL B 239 TYR B 244 0 SHEET 2 AB3 4 LYS B 250 GLY B 255 -1 O CYS B 254 N SER B 241 SHEET 3 AB3 4 LEU B 260 ARG B 264 -1 O TRP B 263 N ILE B 251 SHEET 4 AB3 4 PHE B 299 THR B 301 -1 O PHE B 299 N LEU B 262 SHEET 1 AB4 4 CYS B 311 LEU B 315 0 SHEET 2 AB4 4 LEU B 318 LYS B 322 -1 O LEU B 320 N ARG B 313 SHEET 3 AB4 4 ALA B 327 PRO B 333 -1 O VAL B 329 N SER B 321 SHEET 4 AB4 4 VAL B 350 ASP B 357 -1 O LEU B 353 N CYS B 330 SHEET 1 AB5 4 PHE B 368 MET B 370 0 SHEET 2 AB5 4 MET B 376 GLY B 380 -1 O ALA B 378 N SER B 369 SHEET 3 AB5 4 LEU B 386 ASP B 390 -1 O TYR B 387 N LEU B 379 SHEET 4 AB5 4 THR B 402 LEU B 404 -1 O LEU B 404 N LEU B 386 LINK OD2 ASP A 341 CA CA A 501 1555 1555 2.22 LINK CA CA A 501 O HOH A 704 1555 1555 2.59 LINK CA CA A 501 O HOH A 746 1555 1555 3.17 SITE 1 AC1 2 ASP A 341 HOH A 704 SITE 1 AC2 13 PHE A 97 TYR A 148 ASN A 194 LYS A 211 SITE 2 AC2 13 LEU A 240 LYS A 284 THR A 285 ASP A 310 SITE 3 AC2 13 TYR A 365 MET A 366 ARG A 367 ARG A 414 SITE 4 AC2 13 HOH A 645 SITE 1 AC3 13 ARG A 169 PHE B 97 TYR B 148 ASN B 194 SITE 2 AC3 13 LYS B 211 LEU B 240 ASP B 310 CYS B 311 SITE 3 AC3 13 TYR B 365 MET B 366 ARG B 367 ARG B 414 SITE 4 AC3 13 HOH B 659 CRYST1 85.888 86.528 97.186 90.00 90.00 90.00 P 21 21 21 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 0.011643 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010290 0.00000