HEADER GENE REGULATION 04-DEC-20 7KXT
TITLE CRYSTAL STRUCTURE OF HUMAN EED
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 BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28GST-LIC
KEYWDS EED, WD40, STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC,
KEYWDS 2 GENE REGULATION
EXPDTA X-RAY DIFFRACTION
AUTHOR L.ZHU,A.DONG,D.DU,Y.LIU,C.LUO,C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,
AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (SGC)
REVDAT 3 18-OCT-23 7KXT 1 REMARK
REVDAT 2 04-AUG-21 7KXT 1 JRNL
REVDAT 1 24-FEB-21 7KXT 0
JRNL AUTH D.DU,D.XU,L.ZHU,G.STAZI,C.ZWERGEL,Y.LIU,Z.LUO,Y.LI,Y.ZHANG,
JRNL AUTH 2 K.ZHU,Y.DING,J.LIU,S.FAN,K.ZHAO,N.ZHANG,X.KONG,H.JIANG,
JRNL AUTH 3 K.CHEN,K.ZHAO,S.VALENTE,J.MIN,W.DUAN,C.LUO
JRNL TITL STRUCTURE-GUIDED DEVELOPMENT OF SMALL-MOLECULE PRC2
JRNL TITL 2 INHIBITORS TARGETING EZH2-EED INTERACTION.
JRNL REF J.MED.CHEM. V. 64 8194 2021
JRNL REFN ISSN 0022-2623
JRNL PMID 34077206
JRNL DOI 10.1021/ACS.JMEDCHEM.0C02261
REMARK 2
REMARK 2 RESOLUTION. 2.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX 1.11.1_2575
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.39
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6
REMARK 3 NUMBER OF REFLECTIONS : 44334
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : 0.215
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880
REMARK 3 FREE R VALUE TEST SET COUNT : 2165
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 40.3900 - 5.2987 0.99 2946 142 0.1900 0.2129
REMARK 3 2 5.2987 - 4.2072 0.99 2891 137 0.1324 0.1480
REMARK 3 3 4.2072 - 3.6757 0.99 2834 139 0.1429 0.1775
REMARK 3 4 3.6757 - 3.3398 0.99 2861 134 0.1594 0.1877
REMARK 3 5 3.3398 - 3.1006 0.98 2765 157 0.1652 0.2168
REMARK 3 6 3.1006 - 2.9178 0.98 2812 127 0.1796 0.2217
REMARK 3 7 2.9178 - 2.7717 0.99 2819 147 0.1840 0.2187
REMARK 3 8 2.7717 - 2.6511 0.99 2842 128 0.2115 0.2813
REMARK 3 9 2.6511 - 2.5490 0.99 2828 152 0.2071 0.2654
REMARK 3 10 2.5490 - 2.4611 0.97 2717 161 0.2138 0.2762
REMARK 3 11 2.4611 - 2.3842 0.99 2779 148 0.2249 0.2789
REMARK 3 12 2.3842 - 2.3160 0.99 2854 136 0.2345 0.2649
REMARK 3 13 2.3160 - 2.2550 1.00 2776 163 0.2386 0.2734
REMARK 3 14 2.2550 - 2.2000 0.99 2806 148 0.2452 0.2978
REMARK 3 15 2.2000 - 2.1500 0.94 2639 146 0.2797 0.3236
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.910
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 34.97
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.76
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.008 6029
REMARK 3 ANGLE : 0.932 8212
REMARK 3 CHIRALITY : 0.060 890
REMARK 3 PLANARITY : 0.006 1052
REMARK 3 DIHEDRAL : 13.791 3571
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 2
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ( CHAIN A AND RESID 77:441 )
REMARK 3 ORIGIN FOR THE GROUP (A): -9.414 -5.764 -44.189
REMARK 3 T TENSOR
REMARK 3 T11: 0.1815 T22: 0.2531
REMARK 3 T33: 0.2285 T12: -0.0257
REMARK 3 T13: -0.0096 T23: 0.0344
REMARK 3 L TENSOR
REMARK 3 L11: 0.9789 L22: 1.4364
REMARK 3 L33: 1.4181 L12: 0.0125
REMARK 3 L13: 0.3985 L23: 0.2737
REMARK 3 S TENSOR
REMARK 3 S11: -0.0116 S12: 0.1377 S13: 0.0719
REMARK 3 S21: 0.0341 S22: -0.0074 S23: -0.2835
REMARK 3 S31: -0.0493 S32: 0.3708 S33: 0.0037
REMARK 3 TLS GROUP : 2
REMARK 3 SELECTION: ( CHAIN B AND RESID 80:440 )
REMARK 3 ORIGIN FOR THE GROUP (A): -22.332 -15.429 2.952
REMARK 3 T TENSOR
REMARK 3 T11: 0.1942 T22: 0.2046
REMARK 3 T33: 0.2024 T12: -0.0112
REMARK 3 T13: -0.0102 T23: 0.0190
REMARK 3 L TENSOR
REMARK 3 L11: 1.3465 L22: 1.4050
REMARK 3 L33: 0.9438 L12: -0.5190
REMARK 3 L13: -0.2658 L23: 0.0414
REMARK 3 S TENSOR
REMARK 3 S11: -0.0072 S12: -0.1810 S13: 0.0346
REMARK 3 S21: 0.0783 S22: -0.0090 S23: -0.2256
REMARK 3 S31: -0.0078 S32: 0.2050 S33: 0.0192
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : 1
REMARK 3 NCS GROUP : 1
REMARK 3 NCS OPERATOR : 1
REMARK 3 REFERENCE SELECTION: (CHAIN A AND ((RESID 80 THROUGH 81 AND
REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR
REMARK 3 NAME CB )) OR RESID 82 OR (RESID 83 AND
REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR
REMARK 3 NAME CB OR NAME CG )) OR RESID 84 THROUGH
REMARK 3 105 OR RESID 108 THROUGH 274 OR (RESID
REMARK 3 275 AND (NAME N OR NAME CA OR NAME C OR
REMARK 3 NAME O OR NAME CB )) OR RESID 276 THROUGH
REMARK 3 282 OR (RESID 283 THROUGH 287 AND (NAME N
REMARK 3 OR NAME CA OR NAME C OR NAME O OR NAME CB
REMARK 3 )) OR RESID 288 THROUGH 305 OR (RESID 306
REMARK 3 AND (NAME N OR NAME CA OR NAME C OR NAME
REMARK 3 O OR NAME CB OR NAME CG OR NAME CD )) OR
REMARK 3 RESID 307 THROUGH 324 OR (RESID 325 AND
REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR
REMARK 3 NAME CB OR NAME CG OR NAME CD )) OR RESID
REMARK 3 326 THROUGH 341 OR (RESID 342 AND (NAME N
REMARK 3 OR NAME CA OR NAME C OR NAME O OR NAME CB
REMARK 3 OR NAME CG OR NAME CD )) OR RESID 343
REMARK 3 THROUGH 354 OR RESID 356 THROUGH 368 OR
REMARK 3 RESID 370 THROUGH 391 OR RESID 402
REMARK 3 THROUGH 438 OR (RESID 439 AND (NAME N OR
REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB OR
REMARK 3 NAME CG OR NAME CD )) OR (RESID 440 AND
REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR
REMARK 3 NAME CB ))))
REMARK 3 SELECTION : (CHAIN B AND ((RESID 80 THROUGH 81 AND
REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR
REMARK 3 NAME CB )) OR RESID 82 THROUGH 158 OR
REMARK 3 (RESID 159 AND (NAME N OR NAME CA OR NAME
REMARK 3 C OR NAME O OR NAME CB )) OR RESID 160
REMARK 3 THROUGH 177 OR (RESID 178 AND (NAME N OR
REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB ))
REMARK 3 OR RESID 179 THROUGH 200 OR (RESID 201
REMARK 3 AND (NAME N OR NAME CA OR NAME C OR NAME
REMARK 3 O OR NAME CB OR NAME CG OR NAME CD )) OR
REMARK 3 RESID 202 THROUGH 334 OR (RESID 335 AND
REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR
REMARK 3 NAME CB OR NAME CG OR NAME CD OR NAME CE )
REMARK 3 ) OR RESID 336 THROUGH 343 OR (RESID 344
REMARK 3 AND (NAME N OR NAME CA OR NAME C OR NAME
REMARK 3 O OR NAME CB )) OR RESID 345 THROUGH 354
REMARK 3 OR RESID 356 THROUGH 368 OR RESID 370
REMARK 3 THROUGH 374 OR (RESID 375 AND (NAME N OR
REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB OR
REMARK 3 NAME CG OR NAME CD )) OR RESID 376
REMARK 3 THROUGH 391 OR RESID 402 THROUGH 440))
REMARK 3 ATOM PAIRS NUMBER : 3222
REMARK 3 RMSD : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 7KXT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-DEC-20.
REMARK 100 THE DEPOSITION ID IS D_1000253335.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-AUG-16
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 8.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 19-ID
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97934
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : PIXEL
REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.27
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44346
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150
REMARK 200 RESOLUTION RANGE LOW (A) : 40.392
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7
REMARK 200 DATA REDUNDANCY : 3.400
REMARK 200 R MERGE (I) : 0.10400
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21
REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6
REMARK 200 DATA REDUNDANCY IN SHELL : 3.10
REMARK 200 R MERGE FOR SHELL (I) : 0.81300
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: NULL
REMARK 200 STARTING MODEL: 3JZN
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.10
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5M SODIUM FORMATE, 0.1M TRISCL
REMARK 280 PH8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,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 0.00000
REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.97000
REMARK 290 SMTRY3 2 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 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 350
REMARK 350 BIOMOLECULE: 2
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: 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 ASP A 40
REMARK 465 ALA A 41
REMARK 465 VAL A 42
REMARK 465 SER A 43
REMARK 465 ILE A 44
REMARK 465 GLU A 45
REMARK 465 SER A 46
REMARK 465 GLY A 47
REMARK 465 THR A 48
REMARK 465 ASN A 49
REMARK 465 THR A 50
REMARK 465 GLU A 51
REMARK 465 ARG A 52
REMARK 465 PRO A 53
REMARK 465 ASP A 54
REMARK 465 THR A 55
REMARK 465 PRO A 56
REMARK 465 THR A 57
REMARK 465 ASN A 58
REMARK 465 THR A 59
REMARK 465 PRO A 60
REMARK 465 ASN A 61
REMARK 465 ALA A 62
REMARK 465 PRO A 63
REMARK 465 GLY A 64
REMARK 465 ARG A 65
REMARK 465 LYS A 66
REMARK 465 SER A 67
REMARK 465 TRP A 68
REMARK 465 GLY A 69
REMARK 465 LYS A 70
REMARK 465 GLY A 71
REMARK 465 LYS A 72
REMARK 465 TRP A 73
REMARK 465 LYS A 74
REMARK 465 SER A 75
REMARK 465 LYS A 76
REMARK 465 ASP B 40
REMARK 465 ALA B 41
REMARK 465 VAL B 42
REMARK 465 SER B 43
REMARK 465 ILE B 44
REMARK 465 GLU B 45
REMARK 465 SER B 46
REMARK 465 GLY B 47
REMARK 465 THR B 48
REMARK 465 ASN B 49
REMARK 465 THR B 50
REMARK 465 GLU B 51
REMARK 465 ARG B 52
REMARK 465 PRO B 53
REMARK 465 ASP B 54
REMARK 465 THR B 55
REMARK 465 PRO B 56
REMARK 465 THR B 57
REMARK 465 ASN B 58
REMARK 465 THR B 59
REMARK 465 PRO B 60
REMARK 465 ASN B 61
REMARK 465 ALA B 62
REMARK 465 PRO B 63
REMARK 465 GLY B 64
REMARK 465 ARG B 65
REMARK 465 LYS B 66
REMARK 465 SER B 67
REMARK 465 TRP B 68
REMARK 465 GLY B 69
REMARK 465 LYS B 70
REMARK 465 GLY B 71
REMARK 465 LYS B 72
REMARK 465 TRP B 73
REMARK 465 LYS B 74
REMARK 465 SER B 75
REMARK 465 LYS B 76
REMARK 465 LYS B 77
REMARK 465 CYS B 78
REMARK 465 LYS B 79
REMARK 465 LYS B 106
REMARK 465 GLU B 107
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 77 CG CD CE NZ
REMARK 470 SER A 81 OG
REMARK 470 LYS A 83 NZ
REMARK 470 LYS A 89 NZ
REMARK 470 ASP A 91 OD1 OD2
REMARK 470 LYS A 106 CG CD CE NZ
REMARK 470 GLU A 107 CG CD OE1 OE2
REMARK 470 ASP A 109 CG OD1 OD2
REMARK 470 SER A 128 OG
REMARK 470 GLN A 129 CG CD OE1 NE2
REMARK 470 ASN A 157 CG OD1 ND2
REMARK 470 SER A 159 OG
REMARK 470 ILE A 178 CG1 CG2 CD1
REMARK 470 ARG A 201 NE CZ NH1 NH2
REMARK 470 LYS A 268 CG CD CE NZ
REMARK 470 LYS A 275 CE NZ
REMARK 470 ASN A 281 CG OD1 ND2
REMARK 470 ASN A 283 OD1 ND2
REMARK 470 LYS A 284 CG CD CE NZ
REMARK 470 ARG A 287 CG CD NE CZ NH1 NH2
REMARK 470 LYS A 335 NZ
REMARK 470 LYS A 344 CG CD CE NZ
REMARK 470 LYS A 375 CE NZ
REMARK 470 LYS A 385 CD CE NZ
REMARK 470 VAL A 393 CG1 CG2
REMARK 470 GLU A 394 CG CD OE1 OE2
REMARK 470 ASP A 395 CG OD1 OD2
REMARK 470 LYS A 398 CG CD CE NZ
REMARK 470 LYS A 400 CG CD CE NZ
REMARK 470 LYS A 408 CG CD CE NZ
REMARK 470 ARG A 441 CG CD NE CZ NH1 NH2
REMARK 470 TYR B 80 CG CD1 CD2 CE1 CE2 CZ OH
REMARK 470 LYS B 83 CD CE NZ
REMARK 470 LYS B 89 NZ
REMARK 470 ASP B 91 OD1 OD2
REMARK 470 ASP B 109 CG OD1 OD2
REMARK 470 SER B 128 OG
REMARK 470 GLN B 129 CG CD OE1 NE2
REMARK 470 ASN B 157 CG OD1 ND2
REMARK 470 LYS B 268 CG CD CE NZ
REMARK 470 LYS B 275 CG CD CE NZ
REMARK 470 ASN B 281 CG OD1 ND2
REMARK 470 ASN B 283 CG OD1 ND2
REMARK 470 LYS B 284 CG CD CE NZ
REMARK 470 THR B 285 OG1 CG2
REMARK 470 ASN B 286 CG OD1 ND2
REMARK 470 ARG B 287 CG CD NE CZ NH1 NH2
REMARK 470 ARG B 306 NE CZ NH1 NH2
REMARK 470 GLU B 325 OE1 OE2
REMARK 470 LYS B 342 CE NZ
REMARK 470 LYS B 344 CD CE NZ
REMARK 470 LYS B 385 CD CE NZ
REMARK 470 GLU B 394 CG CD OE1 OE2
REMARK 470 LYS B 398 CG CD CE NZ
REMARK 470 LYS B 400 CG CD CE NZ
REMARK 470 LYS B 408 CG CD CE NZ
REMARK 470 ARG B 439 NE CZ NH1 NH2
REMARK 470 LEU B 440 CG CD1 CD2
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 93 17.63 59.87
REMARK 500 GLU A 107 73.80 -66.45
REMARK 500 SER A 118 -141.69 52.72
REMARK 500 ASN A 119 32.93 -97.92
REMARK 500 LEU A 135 -63.13 -96.46
REMARK 500 HIS A 213 10.22 84.29
REMARK 500 ASN A 283 30.87 -75.77
REMARK 500 PHE A 299 145.22 -171.29
REMARK 500 SER A 323 -153.60 -112.88
REMARK 500 TYR A 365 60.31 74.04
REMARK 500 SER B 118 -140.65 51.75
REMARK 500 ASN B 119 32.77 -97.28
REMARK 500 LEU B 135 -60.44 -96.40
REMARK 500 HIS B 213 8.53 84.25
REMARK 500 HIS B 258 -0.94 73.95
REMARK 500 ASN B 283 30.49 -74.90
REMARK 500 PHE B 299 145.06 -171.20
REMARK 500 SER B 323 -154.91 -111.58
REMARK 500 TYR B 365 61.71 71.98
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue XB7 A 501
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: binding site for residue XB7 B 501
DBREF 7KXT A 40 441 UNP O75530 EED_HUMAN 40 441
DBREF 7KXT B 40 441 UNP O75530 EED_HUMAN 40 441
SEQRES 1 A 402 ASP ALA VAL SER ILE GLU SER GLY THR ASN THR GLU ARG
SEQRES 2 A 402 PRO ASP THR PRO THR ASN THR PRO ASN ALA PRO GLY ARG
SEQRES 3 A 402 LYS SER TRP GLY LYS GLY LYS TRP LYS SER LYS LYS CYS
SEQRES 4 A 402 LYS TYR SER PHE LYS CYS VAL ASN SER LEU LYS GLU ASP
SEQRES 5 A 402 HIS ASN GLN PRO LEU PHE GLY VAL GLN PHE ASN TRP HIS
SEQRES 6 A 402 SER LYS GLU GLY ASP PRO LEU VAL PHE ALA THR VAL GLY
SEQRES 7 A 402 SER ASN ARG VAL THR LEU TYR GLU CYS HIS SER GLN GLY
SEQRES 8 A 402 GLU ILE ARG LEU LEU GLN SER TYR VAL ASP ALA ASP ALA
SEQRES 9 A 402 ASP GLU ASN PHE TYR THR CYS ALA TRP THR TYR ASP SER
SEQRES 10 A 402 ASN THR SER HIS PRO LEU LEU ALA VAL ALA GLY SER ARG
SEQRES 11 A 402 GLY ILE ILE ARG ILE ILE ASN PRO ILE THR MET GLN CYS
SEQRES 12 A 402 ILE LYS HIS TYR VAL GLY HIS GLY ASN ALA ILE ASN GLU
SEQRES 13 A 402 LEU LYS PHE HIS PRO ARG ASP PRO ASN LEU LEU LEU SER
SEQRES 14 A 402 VAL SER LYS ASP HIS ALA LEU ARG LEU TRP ASN ILE GLN
SEQRES 15 A 402 THR ASP THR LEU VAL ALA ILE PHE GLY GLY VAL GLU GLY
SEQRES 16 A 402 HIS ARG ASP GLU VAL LEU SER ALA ASP TYR ASP LEU LEU
SEQRES 17 A 402 GLY GLU LYS ILE MET SER CYS GLY MET ASP HIS SER LEU
SEQRES 18 A 402 LYS LEU TRP ARG ILE ASN SER LYS ARG MET MET ASN ALA
SEQRES 19 A 402 ILE LYS GLU SER TYR ASP TYR ASN PRO ASN LYS THR ASN
SEQRES 20 A 402 ARG PRO PHE ILE SER GLN LYS ILE HIS PHE PRO ASP PHE
SEQRES 21 A 402 SER THR ARG ASP ILE HIS ARG ASN TYR VAL ASP CYS VAL
SEQRES 22 A 402 ARG TRP LEU GLY ASP LEU ILE LEU SER LYS SER CYS GLU
SEQRES 23 A 402 ASN ALA ILE VAL CYS TRP LYS PRO GLY LYS MET GLU ASP
SEQRES 24 A 402 ASP ILE ASP LYS ILE LYS PRO SER GLU SER ASN VAL THR
SEQRES 25 A 402 ILE LEU GLY ARG PHE ASP TYR SER GLN CYS ASP ILE TRP
SEQRES 26 A 402 TYR MET ARG PHE SER MET ASP PHE TRP GLN LYS MET LEU
SEQRES 27 A 402 ALA LEU GLY ASN GLN VAL GLY LYS LEU TYR VAL TRP ASP
SEQRES 28 A 402 LEU GLU VAL GLU ASP PRO HIS LYS ALA LYS CYS THR THR
SEQRES 29 A 402 LEU THR HIS HIS LYS CYS GLY ALA ALA ILE ARG GLN THR
SEQRES 30 A 402 SER PHE SER ARG ASP SER SER ILE LEU ILE ALA VAL CYS
SEQRES 31 A 402 ASP ASP ALA SER ILE TRP ARG TRP ASP ARG LEU ARG
SEQRES 1 B 402 ASP ALA VAL SER ILE GLU SER GLY THR ASN THR GLU ARG
SEQRES 2 B 402 PRO ASP THR PRO THR ASN THR PRO ASN ALA PRO GLY ARG
SEQRES 3 B 402 LYS SER TRP GLY LYS GLY LYS TRP LYS SER LYS LYS CYS
SEQRES 4 B 402 LYS TYR SER PHE LYS CYS VAL ASN SER LEU LYS GLU ASP
SEQRES 5 B 402 HIS ASN GLN PRO LEU PHE GLY VAL GLN PHE ASN TRP HIS
SEQRES 6 B 402 SER LYS GLU GLY ASP PRO LEU VAL PHE ALA THR VAL GLY
SEQRES 7 B 402 SER ASN ARG VAL THR LEU TYR GLU CYS HIS SER GLN GLY
SEQRES 8 B 402 GLU ILE ARG LEU LEU GLN SER TYR VAL ASP ALA ASP ALA
SEQRES 9 B 402 ASP GLU ASN PHE TYR THR CYS ALA TRP THR TYR ASP SER
SEQRES 10 B 402 ASN THR SER HIS PRO LEU LEU ALA VAL ALA GLY SER ARG
SEQRES 11 B 402 GLY ILE ILE ARG ILE ILE ASN PRO ILE THR MET GLN CYS
SEQRES 12 B 402 ILE LYS HIS TYR VAL GLY HIS GLY ASN ALA ILE ASN GLU
SEQRES 13 B 402 LEU LYS PHE HIS PRO ARG ASP PRO ASN LEU LEU LEU SER
SEQRES 14 B 402 VAL SER LYS ASP HIS ALA LEU ARG LEU TRP ASN ILE GLN
SEQRES 15 B 402 THR ASP THR LEU VAL ALA ILE PHE GLY GLY VAL GLU GLY
SEQRES 16 B 402 HIS ARG ASP GLU VAL LEU SER ALA ASP TYR ASP LEU LEU
SEQRES 17 B 402 GLY GLU LYS ILE MET SER CYS GLY MET ASP HIS SER LEU
SEQRES 18 B 402 LYS LEU TRP ARG ILE ASN SER LYS ARG MET MET ASN ALA
SEQRES 19 B 402 ILE LYS GLU SER TYR ASP TYR ASN PRO ASN LYS THR ASN
SEQRES 20 B 402 ARG PRO PHE ILE SER GLN LYS ILE HIS PHE PRO ASP PHE
SEQRES 21 B 402 SER THR ARG ASP ILE HIS ARG ASN TYR VAL ASP CYS VAL
SEQRES 22 B 402 ARG TRP LEU GLY ASP LEU ILE LEU SER LYS SER CYS GLU
SEQRES 23 B 402 ASN ALA ILE VAL CYS TRP LYS PRO GLY LYS MET GLU ASP
SEQRES 24 B 402 ASP ILE ASP LYS ILE LYS PRO SER GLU SER ASN VAL THR
SEQRES 25 B 402 ILE LEU GLY ARG PHE ASP TYR SER GLN CYS ASP ILE TRP
SEQRES 26 B 402 TYR MET ARG PHE SER MET ASP PHE TRP GLN LYS MET LEU
SEQRES 27 B 402 ALA LEU GLY ASN GLN VAL GLY LYS LEU TYR VAL TRP ASP
SEQRES 28 B 402 LEU GLU VAL GLU ASP PRO HIS LYS ALA LYS CYS THR THR
SEQRES 29 B 402 LEU THR HIS HIS LYS CYS GLY ALA ALA ILE ARG GLN THR
SEQRES 30 B 402 SER PHE SER ARG ASP SER SER ILE LEU ILE ALA VAL CYS
SEQRES 31 B 402 ASP ASP ALA SER ILE TRP ARG TRP ASP ARG LEU ARG
HET XB7 A 501 34
HET UNX A 502 1
HET UNX A 503 1
HET UNX A 504 1
HET UNX A 505 1
HET UNX A 506 1
HET UNX A 507 1
HET UNX A 508 1
HET UNX A 509 1
HET UNX A 510 1
HET UNX A 511 1
HET UNX A 512 1
HET UNX A 513 1
HET UNX A 514 1
HET UNX A 515 1
HET UNX A 516 1
HET UNX A 517 1
HET UNX A 518 1
HET UNX A 519 1
HET UNX A 520 1
HET UNX A 521 1
HET UNX A 522 1
HET UNX A 523 1
HET UNX A 524 1
HET UNX A 525 1
HET UNX A 526 1
HET UNX A 527 1
HET UNX A 528 1
HET XB7 B 501 34
HET UNX B 502 1
HET UNX B 503 1
HET UNX B 504 1
HET UNX B 505 1
HET UNX B 506 1
HET UNX B 507 1
HET UNX B 508 1
HET UNX B 509 1
HET UNX B 510 1
HET UNX B 511 1
HET UNX B 512 1
HET UNX B 513 1
HET UNX B 514 1
HET UNX B 515 1
HET UNX B 516 1
HET UNX B 517 1
HET UNX B 518 1
HET UNX B 519 1
HET UNX B 520 1
HET UNX B 521 1
HET UNX B 522 1
HET UNX B 523 1
HET UNX B 524 1
HET UNX B 525 1
HET UNX B 526 1
HETNAM XB7 1-[(4-FLUOROPHENYL)METHYL]-N-{1-[2-(4-METHOXYPHENYL)
HETNAM 2 XB7 ETHYL]PIPERIDIN-4-YL}-1H-BENZIMIDAZOL-2-AMINE
HETNAM UNX UNKNOWN ATOM OR ION
FORMUL 3 XB7 2(C28 H31 F N4 O)
FORMUL 4 UNX 52(X)
FORMUL 57 HOH *98(H2 O)
HELIX 1 AA1 SER A 128 GLY A 130 5 3
HELIX 2 AA2 SER A 267 TYR A 280 1 14
HELIX 3 AA3 ASN A 281 THR A 285 5 5
HELIX 4 AA4 ASP A 339 ILE A 343 5 5
HELIX 5 AA5 ASP A 395 ALA A 399 5 5
HELIX 6 AA6 SER B 128 GLY B 130 5 3
HELIX 7 AA7 SER B 267 TYR B 280 1 14
HELIX 8 AA8 ASN B 281 THR B 285 5 5
HELIX 9 AA9 ASP B 339 ILE B 343 5 5
HELIX 10 AB1 ASP B 395 ALA B 399 5 5
SHEET 1 AA1 4 PHE A 82 LYS A 89 0
SHEET 2 AA1 4 SER A 433 ARG A 439 -1 O ILE A 434 N LEU A 88
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 TYR A 124 N PHE A 113
SHEET 4 AA2 4 ILE A 132 VAL A 139 -1 O ARG A 133 N GLU A 125
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 ILE A 183 N ILE A 174
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 ILE A 294 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 318 N LEU A 315
SHEET 3 AA6 4 ALA A 327 PRO A 333 -1 O VAL A 329 N SER A 321
SHEET 4 AA6 4 VAL A 350 ASP A 357 -1 O THR A 351 N LYS A 332
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 THR A 402 N VAL A 388
SHEET 1 AA8 4 PHE B 82 LYS B 89 0
SHEET 2 AA8 4 SER B 433 ARG B 439 -1 O ILE B 434 N LEU B 88
SHEET 3 AA8 4 ILE B 424 CYS B 429 -1 N ALA B 427 O TRP B 435
SHEET 4 AA8 4 ILE B 413 PHE B 418 -1 N SER B 417 O ILE B 426
SHEET 1 AA9 4 GLY B 98 PHE B 101 0
SHEET 2 AA9 4 VAL B 112 GLY B 117 -1 O ALA B 114 N GLN B 100
SHEET 3 AA9 4 ARG B 120 CYS B 126 -1 O TYR B 124 N PHE B 113
SHEET 4 AA9 4 ILE B 132 VAL B 139 -1 O ARG B 133 N GLU B 125
SHEET 1 AB1 4 PHE B 147 TYR B 154 0
SHEET 2 AB1 4 PRO B 161 GLY B 167 -1 O LEU B 162 N THR B 153
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 ILE B 183 N ILE B 174
SHEET 1 AB2 5 ILE B 193 PHE B 198 0
SHEET 2 AB2 5 LEU B 205 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 PHE B 229 N LEU B 215
SHEET 5 AB2 5 GLN B 292 ILE B 294 1 O ILE B 294 N ILE B 228
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 318 N LEU B 315
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 GLY B 354 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 CYS B 401 LEU B 404 -1 O THR B 402 N VAL B 388
SITE 1 AC1 15 LEU A 246 LEU A 315 GLY A 316 LEU A 318
SITE 2 AC1 15 MET A 336 PHE A 356 PHE A 372 TRP A 373
SITE 3 AC1 15 LEU A 391 VAL A 393 GLU A 394 PRO A 396
SITE 4 AC1 15 HIS A 397 GLU B 394 ASP B 395
SITE 1 AC2 14 LEU B 246 LEU B 315 GLY B 316 MET B 336
SITE 2 AC2 14 PHE B 356 PHE B 372 TRP B 373 GLN B 374
SITE 3 AC2 14 LEU B 391 VAL B 393 GLU B 394 PRO B 396
SITE 4 AC2 14 HIS B 397 HOH B 631
CRYST1 81.470 49.940 105.320 90.00 105.11 90.00 P 1 21 1 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 0.012274 0.000000 0.003314 0.00000
SCALE2 0.000000 0.020024 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009835 0.00000