data_5EJL # _model_server_result.job_id qXPFrzeKtzGCPlVpzxa5gg _model_server_result.datetime_utc '2024-11-09 02:35:42' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5ejl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 5EJL # _exptl.entry_id 5EJL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5EJL _cell.length_a 68.556 _cell.length_b 68.556 _cell.length_c 179.457 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EJL _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 2 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N # _chem_comp.formula 'C20 H24 N10 O14 P2' _chem_comp.formula_weight 690.411 _chem_comp.id C2E _chem_comp.mon_nstd_flag . _chem_comp.name "9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'c-di-GMP;Cyclic diguanosine monophosphate' # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P1 O2P C2E sing 70 n n O1P P1 C2E doub 71 n n O5' P1 C2E sing 72 n n C5' O5' C2E sing 73 n n C4' O4' C2E sing 74 n n C4' C5' C2E sing 75 n n C3' C4' C2E sing 76 n n O3' P11 C2E sing 77 n n O3' C3' C2E sing 78 n n C2' C3' C2E sing 79 n n C2' C1' C2E sing 80 n n O2' C2' C2E sing 81 n n C1' O4' C2E sing 82 n n C1' N9 C2E sing 83 n n N9 C4 C2E sing 84 n y N9 C8 C2E sing 85 n y C8 N7 C2E doub 86 n y C5 N7 C2E sing 87 n y C5 C6 C2E sing 88 n n C6 O6 C2E doub 89 n n N1 C6 C2E sing 90 n n C2 N1 C2E sing 91 n n N2 C2 C2E sing 92 n n N3 C2 C2E doub 93 n n N3 C4 C2E sing 94 n n C4 C5 C2E doub 95 n y P11 O21 C2E sing 96 n n P11 O5A C2E sing 97 n n O11 P11 C2E doub 98 n n C5A O5A C2E sing 99 n n C5A C4A C2E sing 100 n n C4A O4A C2E sing 101 n n C4A C3A C2E sing 102 n n O4A C1A C2E sing 103 n n C3A C2A C2E sing 104 n n O3A C3A C2E sing 105 n n O3A P1 C2E sing 106 n n C2A O2A C2E sing 107 n n C1A C2A C2E sing 108 n n C1A N91 C2E sing 109 n n N91 C41 C2E sing 110 n y C81 N71 C2E doub 111 n y C81 N91 C2E sing 112 n y N71 C51 C2E sing 113 n y C51 C41 C2E doub 114 n y C51 C61 C2E sing 115 n n C61 O61 C2E doub 116 n n C61 N11 C2E sing 117 n n C21 N11 C2E sing 118 n n C21 N21 C2E sing 119 n n N31 C21 C2E doub 120 n n C41 N31 C2E sing 121 n n O2P HO2P C2E sing 122 n n C5' "H5'1" C2E sing 123 n n C5' "H5'2" C2E sing 124 n n C4' H4' C2E sing 125 n n C3' H3' C2E sing 126 n n C2' H2' C2E sing 127 n n O2' HO2' C2E sing 128 n n C1' H1' C2E sing 129 n n C8 H8 C2E sing 130 n n N1 HN1 C2E sing 131 n n N2 HN21 C2E sing 132 n n N2 HN22 C2E sing 133 n n O21 HO21 C2E sing 134 n n C5A H511 C2E sing 135 n n C5A H512 C2E sing 136 n n C4A H4A C2E sing 137 n n C3A H3A C2E sing 138 n n C2A H2A C2E sing 139 n n O2A HO2A C2E sing 140 n n C1A H1A C2E sing 141 n n C81 H81 C2E sing 142 n n N11 HN11 C2E sing 143 n n N21 HN24 C2E sing 144 n n N21 HN23 C2E sing 145 n n # _atom_sites.entry_id 5EJL _atom_sites.fract_transf_matrix[1][1] 0.014587 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014587 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.005572 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 C2E A 1 301 800 C2E C2E . C 2 C2E A 1 302 801 C2E C2E . D 3 SO4 A 1 303 803 SO4 SO4 . E 3 SO4 A 1 304 804 SO4 SO4 . F 3 SO4 A 1 305 805 SO4 SO4 . G 4 EDO A 1 306 806 EDO EDO . H 4 EDO A 1 307 807 EDO EDO . I 4 EDO A 1 308 808 EDO EDO . J 5 HOH A 1 401 67 HOH HOH . J 5 HOH A 2 402 28 HOH HOH . J 5 HOH A 3 403 16 HOH HOH . J 5 HOH A 4 404 63 HOH HOH . J 5 HOH A 5 405 70 HOH HOH . J 5 HOH A 6 406 86 HOH HOH . J 5 HOH A 7 407 66 HOH HOH . J 5 HOH A 8 408 85 HOH HOH . J 5 HOH A 9 409 58 HOH HOH . J 5 HOH A 10 410 19 HOH HOH . J 5 HOH A 11 411 84 HOH HOH . J 5 HOH A 12 412 68 HOH HOH . J 5 HOH A 13 413 88 HOH HOH . J 5 HOH A 14 414 62 HOH HOH . J 5 HOH A 15 415 2 HOH HOH . J 5 HOH A 16 416 30 HOH HOH . J 5 HOH A 17 417 4 HOH HOH . J 5 HOH A 18 418 81 HOH HOH . J 5 HOH A 19 419 12 HOH HOH . J 5 HOH A 20 420 33 HOH HOH . J 5 HOH A 21 421 36 HOH HOH . J 5 HOH A 22 422 59 HOH HOH . J 5 HOH A 23 423 71 HOH HOH . J 5 HOH A 24 424 53 HOH HOH . J 5 HOH A 25 425 25 HOH HOH . J 5 HOH A 26 426 8 HOH HOH . J 5 HOH A 27 427 1 HOH HOH . J 5 HOH A 28 428 15 HOH HOH . J 5 HOH A 29 429 29 HOH HOH . J 5 HOH A 30 430 41 HOH HOH . J 5 HOH A 31 431 47 HOH HOH . J 5 HOH A 32 432 18 HOH HOH . J 5 HOH A 33 433 3 HOH HOH . J 5 HOH A 34 434 49 HOH HOH . J 5 HOH A 35 435 31 HOH HOH . J 5 HOH A 36 436 6 HOH HOH . J 5 HOH A 37 437 13 HOH HOH . J 5 HOH A 38 438 38 HOH HOH . J 5 HOH A 39 439 21 HOH HOH . J 5 HOH A 40 440 22 HOH HOH . J 5 HOH A 41 441 40 HOH HOH . J 5 HOH A 42 442 23 HOH HOH . J 5 HOH A 43 443 9 HOH HOH . J 5 HOH A 44 444 26 HOH HOH . J 5 HOH A 45 445 44 HOH HOH . J 5 HOH A 46 446 52 HOH HOH . J 5 HOH A 47 447 10 HOH HOH . J 5 HOH A 48 448 51 HOH HOH . J 5 HOH A 49 449 45 HOH HOH . J 5 HOH A 50 450 24 HOH HOH . J 5 HOH A 51 451 54 HOH HOH . J 5 HOH A 52 452 76 HOH HOH . J 5 HOH A 53 453 60 HOH HOH . J 5 HOH A 54 454 46 HOH HOH . J 5 HOH A 55 455 32 HOH HOH . J 5 HOH A 56 456 20 HOH HOH . J 5 HOH A 57 457 75 HOH HOH . J 5 HOH A 58 458 80 HOH HOH . J 5 HOH A 59 459 42 HOH HOH . J 5 HOH A 60 460 7 HOH HOH . J 5 HOH A 61 461 35 HOH HOH . J 5 HOH A 62 462 27 HOH HOH . J 5 HOH A 63 463 48 HOH HOH . J 5 HOH A 64 464 77 HOH HOH . J 5 HOH A 65 465 56 HOH HOH . J 5 HOH A 66 466 55 HOH HOH . J 5 HOH A 67 467 43 HOH HOH . J 5 HOH A 68 468 39 HOH HOH . J 5 HOH A 69 469 57 HOH HOH . J 5 HOH A 70 470 64 HOH HOH . J 5 HOH A 71 471 37 HOH HOH . J 5 HOH A 72 472 69 HOH HOH . J 5 HOH A 73 473 14 HOH HOH . J 5 HOH A 74 474 17 HOH HOH . J 5 HOH A 75 475 78 HOH HOH . J 5 HOH A 76 476 34 HOH HOH . J 5 HOH A 77 477 72 HOH HOH . J 5 HOH A 78 478 65 HOH HOH . J 5 HOH A 79 479 87 HOH HOH . J 5 HOH A 80 480 61 HOH HOH . J 5 HOH A 81 481 79 HOH HOH . J 5 HOH A 82 482 5 HOH HOH . J 5 HOH A 83 483 82 HOH HOH . J 5 HOH A 84 484 74 HOH HOH . J 5 HOH A 85 485 11 HOH HOH . J 5 HOH A 86 486 73 HOH HOH . J 5 HOH A 87 487 50 HOH HOH . J 5 HOH A 88 488 83 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P P1 C2E . . . C 2 -21.878 -7.19 15.789 1 28.68 ? P1 C2E 302 A 1 HETATM 2 O O2P C2E . . . C 2 -21.575 -8.7 15.997 1 32.59 ? O2P C2E 302 A 1 HETATM 3 O O1P C2E . . . C 2 -22.751 -6.687 16.913 1 31.66 ? O1P C2E 302 A 1 HETATM 4 O O5' C2E . . . C 2 -20.581 -6.261 15.831 1 34.49 ? O5' C2E 302 A 1 HETATM 5 C C5' C2E . . . C 2 -20.744 -4.864 15.996 1 29.93 ? C5' C2E 302 A 1 HETATM 6 C C4' C2E . . . C 2 -19.471 -4.097 15.644 1 29.32 ? C4' C2E 302 A 1 HETATM 7 O O4' C2E . . . C 2 -18.483 -4.567 16.522 1 29.37 ? O4' C2E 302 A 1 HETATM 8 C C3' C2E . . . C 2 -18.957 -4.362 14.343 1 27.76 ? C3' C2E 302 A 1 HETATM 9 O O3' C2E . . . C 2 -19.549 -3.578 13.25 1 29.71 ? O3' C2E 302 A 1 HETATM 10 C C2' C2E . . . C 2 -17.613 -4.035 14.498 1 28.66 ? C2' C2E 302 A 1 HETATM 11 O O2' C2E . . . C 2 -17.436 -2.665 14.391 1 33.16 ? O2' C2E 302 A 1 HETATM 12 C C1' C2E . . . C 2 -17.249 -4.466 15.873 1 28.6 ? C1' C2E 302 A 1 HETATM 13 N N9 C2E . . . C 2 -16.654 -5.769 15.847 1 29.14 ? N9 C2E 302 A 1 HETATM 14 C C8 C2E . . . C 2 -17.299 -6.926 16.101 1 23.99 ? C8 C2E 302 A 1 HETATM 15 N N7 C2E . . . C 2 -16.421 -7.938 15.948 1 28.31 ? N7 C2E 302 A 1 HETATM 16 C C5 C2E . . . C 2 -15.214 -7.432 15.619 1 26.18 ? C5 C2E 302 A 1 HETATM 17 C C6 C2E . . . C 2 -13.97 -8.011 15.37 1 24.21 ? C6 C2E 302 A 1 HETATM 18 O O6 C2E . . . C 2 -13.845 -9.37 15.428 1 28.98 ? O6 C2E 302 A 1 HETATM 19 N N1 C2E . . . C 2 -12.922 -7.236 15.046 1 24.99 ? N1 C2E 302 A 1 HETATM 20 C C2 C2E . . . C 2 -13.112 -5.887 14.977 1 28.35 ? C2 C2E 302 A 1 HETATM 21 N N2 C2E . . . C 2 -11.994 -5.017 14.643 1 27.87 ? N2 C2E 302 A 1 HETATM 22 N N3 C2E . . . C 2 -14.294 -5.291 15.228 1 27.02 ? N3 C2E 302 A 1 HETATM 23 C C4 C2E . . . C 2 -15.362 -6.042 15.556 1 24.17 ? C4 C2E 302 A 1 HETATM 24 P P11 C2E . . . C 2 -19.582 -4.127 11.776 1 33.26 ? P11 C2E 302 A 1 HETATM 25 O O21 C2E . . . C 2 -18.281 -4.461 11.133 1 30.23 ? O21 C2E 302 A 1 HETATM 26 O O11 C2E . . . C 2 -20.104 -3.017 10.909 1 30.93 ? O11 C2E 302 A 1 HETATM 27 O O5A C2E . . . C 2 -20.593 -5.322 11.618 1 26.16 ? O5A C2E 302 A 1 HETATM 28 C C5A C2E . . . C 2 -21.921 -5.176 11.882 1 27.84 ? C5A C2E 302 A 1 HETATM 29 C C4A C2E . . . C 2 -22.646 -6.354 12.137 1 32.26 ? C4A C2E 302 A 1 HETATM 30 O O4A C2E . . . C 2 -22.516 -7.298 10.912 1 32.6 ? O4A C2E 302 A 1 HETATM 31 C C3A C2E . . . C 2 -22.058 -7.126 13.251 1 31.34 ? C3A C2E 302 A 1 HETATM 32 O O3A C2E . . . C 2 -22.699 -6.881 14.459 1 33.76 ? O3A C2E 302 A 1 HETATM 33 C C2A C2E . . . C 2 -22.31 -8.519 12.901 1 33.69 ? C2A C2E 302 A 1 HETATM 34 O O2A C2E . . . C 2 -23.609 -8.832 13.124 1 33.95 ? O2A C2E 302 A 1 HETATM 35 C C1A C2E . . . C 2 -22.126 -8.568 11.428 1 31.31 ? C1A C2E 302 A 1 HETATM 36 N N91 C2E . . . C 2 -20.808 -8.999 10.97 1 30.79 ? N91 C2E 302 A 1 HETATM 37 C C81 C2E . . . C 2 -19.895 -8.192 10.386 1 29.56 ? C81 C2E 302 A 1 HETATM 38 N N71 C2E . . . C 2 -18.818 -8.925 10.068 1 27.91 ? N71 C2E 302 A 1 HETATM 39 C C51 C2E . . . C 2 -19.051 -10.211 10.409 1 25.51 ? C51 C2E 302 A 1 HETATM 40 C C61 C2E . . . C 2 -18.319 -11.398 10.298 1 26.06 ? C61 C2E 302 A 1 HETATM 41 O O61 C2E . . . C 2 -17.038 -11.409 9.726 1 27.25 ? O61 C2E 302 A 1 HETATM 42 N N11 C2E . . . C 2 -18.844 -12.525 10.775 1 26.08 ? N11 C2E 302 A 1 HETATM 43 C C21 C2E . . . C 2 -20.065 -12.518 11.335 1 29.1 ? C21 C2E 302 A 1 HETATM 44 N N21 C2E . . . C 2 -20.609 -13.786 11.828 1 30.88 ? N21 C2E 302 A 1 HETATM 45 N N31 C2E . . . C 2 -20.803 -11.406 11.45 1 28.4 ? N31 C2E 302 A 1 HETATM 46 C C41 C2E . . . C 2 -20.317 -10.248 10.994 1 25.76 ? C41 C2E 302 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 46 #