data_7MIE # _model_server_result.job_id 7SbYxq7vwj_MLy7zRaO3pA _model_server_result.datetime_utc '2024-11-14 07:12:21' _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 7mie # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7MIE # _exptl.entry_id 7MIE _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 113.9 _cell.angle_gamma 90 _cell.entry_id 7MIE _cell.length_a 63.699 _cell.length_b 36.861 _cell.length_c 64.905 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MIE _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 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 7MIE _atom_sites.fract_transf_matrix[1][1] 0.015699 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006957 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.027129 _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] 0.016852 _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 1 301 300 C2E C2E . C 2 C2E A 1 302 301 C2E C2E . D 3 CL A 1 303 400 CL CL . E 4 PEG A 1 304 500 PEG PEG . F 5 EDO A 1 305 600 EDO EDO . G 5 EDO A 1 306 601 EDO EDO . H 6 HOH A 1 401 117 HOH HOH . H 6 HOH A 2 402 102 HOH HOH . H 6 HOH A 3 403 104 HOH HOH . H 6 HOH A 4 404 68 HOH HOH . H 6 HOH A 5 405 105 HOH HOH . H 6 HOH A 6 406 30 HOH HOH . H 6 HOH A 7 407 116 HOH HOH . H 6 HOH A 8 408 40 HOH HOH . H 6 HOH A 9 409 74 HOH HOH . H 6 HOH A 10 410 77 HOH HOH . H 6 HOH A 11 411 65 HOH HOH . H 6 HOH A 12 412 66 HOH HOH . H 6 HOH A 13 413 56 HOH HOH . H 6 HOH A 14 414 59 HOH HOH . H 6 HOH A 15 415 45 HOH HOH . H 6 HOH A 16 416 79 HOH HOH . H 6 HOH A 17 417 39 HOH HOH . H 6 HOH A 18 418 35 HOH HOH . H 6 HOH A 19 419 14 HOH HOH . H 6 HOH A 20 420 51 HOH HOH . H 6 HOH A 21 421 95 HOH HOH . H 6 HOH A 22 422 37 HOH HOH . H 6 HOH A 23 423 60 HOH HOH . H 6 HOH A 24 424 90 HOH HOH . H 6 HOH A 25 425 13 HOH HOH . H 6 HOH A 26 426 41 HOH HOH . H 6 HOH A 27 427 57 HOH HOH . H 6 HOH A 28 428 78 HOH HOH . H 6 HOH A 29 429 108 HOH HOH . H 6 HOH A 30 430 47 HOH HOH . H 6 HOH A 31 431 16 HOH HOH . H 6 HOH A 32 432 25 HOH HOH . H 6 HOH A 33 433 84 HOH HOH . H 6 HOH A 34 434 111 HOH HOH . H 6 HOH A 35 435 86 HOH HOH . H 6 HOH A 36 436 87 HOH HOH . H 6 HOH A 37 437 97 HOH HOH . H 6 HOH A 38 438 28 HOH HOH . H 6 HOH A 39 439 80 HOH HOH . H 6 HOH A 40 440 63 HOH HOH . H 6 HOH A 41 441 98 HOH HOH . H 6 HOH A 42 442 112 HOH HOH . H 6 HOH A 43 443 24 HOH HOH . H 6 HOH A 44 444 49 HOH HOH . H 6 HOH A 45 445 120 HOH HOH . H 6 HOH A 46 446 46 HOH HOH . H 6 HOH A 47 447 36 HOH HOH . H 6 HOH A 48 448 15 HOH HOH . H 6 HOH A 49 449 52 HOH HOH . H 6 HOH A 50 450 27 HOH HOH . H 6 HOH A 51 451 1 HOH HOH . H 6 HOH A 52 452 122 HOH HOH . H 6 HOH A 53 453 12 HOH HOH . H 6 HOH A 54 454 91 HOH HOH . H 6 HOH A 55 455 5 HOH HOH . H 6 HOH A 56 456 83 HOH HOH . H 6 HOH A 57 457 17 HOH HOH . H 6 HOH A 58 458 82 HOH HOH . H 6 HOH A 59 459 33 HOH HOH . H 6 HOH A 60 460 103 HOH HOH . H 6 HOH A 61 461 76 HOH HOH . H 6 HOH A 62 462 9 HOH HOH . H 6 HOH A 63 463 11 HOH HOH . H 6 HOH A 64 464 4 HOH HOH . H 6 HOH A 65 465 23 HOH HOH . H 6 HOH A 66 466 8 HOH HOH . H 6 HOH A 67 467 10 HOH HOH . H 6 HOH A 68 468 113 HOH HOH . H 6 HOH A 69 469 19 HOH HOH . H 6 HOH A 70 470 18 HOH HOH . H 6 HOH A 71 471 31 HOH HOH . H 6 HOH A 72 472 6 HOH HOH . H 6 HOH A 73 473 110 HOH HOH . H 6 HOH A 74 474 109 HOH HOH . H 6 HOH A 75 475 100 HOH HOH . H 6 HOH A 76 476 26 HOH HOH . H 6 HOH A 77 477 106 HOH HOH . H 6 HOH A 78 478 55 HOH HOH . H 6 HOH A 79 479 32 HOH HOH . H 6 HOH A 80 480 92 HOH HOH . H 6 HOH A 81 481 71 HOH HOH . H 6 HOH A 82 482 7 HOH HOH . H 6 HOH A 83 483 119 HOH HOH . H 6 HOH A 84 484 67 HOH HOH . H 6 HOH A 85 485 64 HOH HOH . H 6 HOH A 86 486 89 HOH HOH . H 6 HOH A 87 487 121 HOH HOH . H 6 HOH A 88 488 70 HOH HOH . H 6 HOH A 89 489 62 HOH HOH . H 6 HOH A 90 490 42 HOH HOH . H 6 HOH A 91 491 3 HOH HOH . H 6 HOH A 92 492 20 HOH HOH . H 6 HOH A 93 493 54 HOH HOH . H 6 HOH A 94 494 69 HOH HOH . H 6 HOH A 95 495 2 HOH HOH . H 6 HOH A 96 496 21 HOH HOH . H 6 HOH A 97 497 114 HOH HOH . H 6 HOH A 98 498 22 HOH HOH . H 6 HOH A 99 499 34 HOH HOH . H 6 HOH A 100 500 99 HOH HOH . H 6 HOH A 101 501 107 HOH HOH . H 6 HOH A 102 502 53 HOH HOH . H 6 HOH A 103 503 29 HOH HOH . H 6 HOH A 104 504 88 HOH HOH . H 6 HOH A 105 505 44 HOH HOH . H 6 HOH A 106 506 73 HOH HOH . H 6 HOH A 107 507 48 HOH HOH . H 6 HOH A 108 508 85 HOH HOH . H 6 HOH A 109 509 118 HOH HOH . H 6 HOH A 110 510 50 HOH HOH . H 6 HOH A 111 511 61 HOH HOH . H 6 HOH A 112 512 72 HOH HOH . H 6 HOH A 113 513 38 HOH HOH . H 6 HOH A 114 514 43 HOH HOH . H 6 HOH A 115 515 58 HOH HOH . H 6 HOH A 116 516 93 HOH HOH . H 6 HOH A 117 517 75 HOH HOH . H 6 HOH A 118 518 81 HOH HOH . H 6 HOH A 119 519 94 HOH HOH . H 6 HOH A 120 520 96 HOH HOH . H 6 HOH A 121 521 101 HOH HOH . H 6 HOH A 122 522 115 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 . . . B 2 23.359 -6.045 11.767 1 42.31 ? P1 C2E 301 A 1 HETATM 2 O O2P C2E . . . B 2 22.077 -5.997 12.548 1 35.64 ? O2P C2E 301 A 1 HETATM 3 O O1P C2E . . . B 2 23.353 -6.827 10.491 1 44.85 ? O1P C2E 301 A 1 HETATM 4 O O5' C2E . . . B 2 23.86 -4.549 11.466 1 42.38 ? O5' C2E 301 A 1 HETATM 5 C C5' C2E . . . B 2 24.628 -4.341 10.264 1 42.93 ? C5' C2E 301 A 1 HETATM 6 C C4' C2E . . . B 2 25.174 -2.937 10.258 1 41.34 ? C4' C2E 301 A 1 HETATM 7 O O4' C2E . . . B 2 24.109 -2.006 9.927 1 40.64 ? O4' C2E 301 A 1 HETATM 8 C C3' C2E . . . B 2 25.701 -2.446 11.595 1 41.95 ? C3' C2E 301 A 1 HETATM 9 O O3' C2E . . . B 2 27.048 -2.858 11.684 1 43.65 ? O3' C2E 301 A 1 HETATM 10 C C2' C2E . . . B 2 25.587 -0.932 11.426 1 42.01 ? C2' C2E 301 A 1 HETATM 11 O O2' C2E . . . B 2 26.593 -0.322 10.636 1 45.99 ? O2' C2E 301 A 1 HETATM 12 C C1' C2E . . . B 2 24.253 -0.836 10.705 1 36.54 ? C1' C2E 301 A 1 HETATM 13 N N9 C2E . . . B 2 23.097 -0.674 11.592 1 35.29 ? N9 C2E 301 A 1 HETATM 14 C C8 C2E . . . B 2 22.178 -1.631 11.96 1 32.57 ? C8 C2E 301 A 1 HETATM 15 N N7 C2E . . . B 2 21.26 -1.167 12.773 1 32.22 ? N7 C2E 301 A 1 HETATM 16 C C5 C2E . . . B 2 21.583 0.169 12.955 1 32.24 ? C5 C2E 301 A 1 HETATM 17 C C6 C2E . . . B 2 20.95 1.183 13.719 1 31.23 ? C6 C2E 301 A 1 HETATM 18 O O6 C2E . . . B 2 19.937 1.14 14.431 1 29.28 ? O6 C2E 301 A 1 HETATM 19 N N1 C2E . . . B 2 21.618 2.406 13.593 1 33.83 ? N1 C2E 301 A 1 HETATM 20 C C2 C2E . . . B 2 22.736 2.628 12.834 1 34.32 ? C2 C2E 301 A 1 HETATM 21 N N2 C2E . . . B 2 23.209 3.881 12.847 1 36.06 ? N2 C2E 301 A 1 HETATM 22 N N3 C2E . . . B 2 23.347 1.681 12.129 1 35.72 ? N3 C2E 301 A 1 HETATM 23 C C4 C2E . . . B 2 22.719 0.482 12.231 1 34.4 ? C4 C2E 301 A 1 HETATM 24 P P11 C2E . . . B 2 27.795 -2.818 13.096 1 44.25 ? P11 C2E 301 A 1 HETATM 25 O O21 C2E . . . B 2 27.644 -1.577 13.922 1 40.91 ? O21 C2E 301 A 1 HETATM 26 O O11 C2E . . . B 2 29.205 -3.275 12.831 1 46.31 ? O11 C2E 301 A 1 HETATM 27 O O5A C2E . . . B 2 27.149 -3.998 13.977 1 41.96 ? O5A C2E 301 A 1 HETATM 28 C C5A C2E . . . B 2 27.377 -5.358 13.528 1 40.29 ? C5A C2E 301 A 1 HETATM 29 C C4A C2E . . . B 2 26.413 -6.271 14.237 1 38.38 ? C4A C2E 301 A 1 HETATM 30 O O4A C2E . . . B 2 26.476 -6.037 15.668 1 36.09 ? O4A C2E 301 A 1 HETATM 31 C C3A C2E . . . B 2 24.955 -5.989 13.887 1 36.29 ? C3A C2E 301 A 1 HETATM 32 O O3A C2E . . . B 2 24.61 -6.579 12.635 1 39.48 ? O3A C2E 301 A 1 HETATM 33 C C2A C2E . . . B 2 24.255 -6.658 15.073 1 34.14 ? C2A C2E 301 A 1 HETATM 34 O O2A C2E . . . B 2 24.207 -8.066 14.95 1 33.32 ? O2A C2E 301 A 1 HETATM 35 C C1A C2E . . . B 2 25.18 -6.248 16.217 1 34.65 ? C1A C2E 301 A 1 HETATM 36 N N91 C2E . . . B 2 24.763 -5.068 16.975 1 30.3 ? N91 C2E 301 A 1 HETATM 37 C C81 C2E . . . B 2 25.344 -3.817 16.985 1 30.85 ? C81 C2E 301 A 1 HETATM 38 N N71 C2E . . . B 2 24.772 -2.988 17.822 1 30.94 ? N71 C2E 301 A 1 HETATM 39 C C51 C2E . . . B 2 23.773 -3.735 18.435 1 28.96 ? C51 C2E 301 A 1 HETATM 40 C C61 C2E . . . B 2 22.866 -3.395 19.462 1 28.68 ? C61 C2E 301 A 1 HETATM 41 O O61 C2E . . . B 2 22.75 -2.314 20.065 1 32.84 ? O61 C2E 301 A 1 HETATM 42 N N11 C2E . . . B 2 22.066 -4.476 19.838 1 27.95 ? N11 C2E 301 A 1 HETATM 43 C C21 C2E . . . B 2 22.12 -5.725 19.241 1 29.98 ? C21 C2E 301 A 1 HETATM 44 N N21 C2E . . . B 2 21.282 -6.669 19.7 1 32.68 ? N21 C2E 301 A 1 HETATM 45 N N31 C2E . . . B 2 22.957 -6.032 18.256 1 28.65 ? N31 C2E 301 A 1 HETATM 46 C C41 C2E . . . B 2 23.773 -5.014 17.926 1 30.11 ? C41 C2E 301 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #