data_6QRL # _model_server_result.job_id Uw4qLcpW3JxEBOl_pZyL_A _model_server_result.datetime_utc '2024-11-05 04:50:50' _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 6qrl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6QRL # _exptl.entry_id 6QRL _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 4 _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 120 _cell.entry_id 6QRL _cell.length_a 55.11 _cell.length_b 55.11 _cell.length_c 179.661 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QRL _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # 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 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,I 1 1 B,G,H,J 2 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 C N N ? 2 E N N ? 2 F N N ? 2 G 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 6QRL _atom_sites.fract_transf_matrix[1][1] 0.018146 _atom_sites.fract_transf_matrix[1][2] 0.010476 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020953 _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] 0.005566 _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 C 2 C2E A 1 401 600 C2E C2E . D 3 SO4 A 1 402 602 SO4 SO4 . E 2 C2E A 1 403 600 C2E C2E . F 2 C2E A 1 404 601 C2E C2E . G 2 C2E B 1 401 600 C2E C2E . H 3 SO4 B 1 402 602 SO4 SO4 . I 4 HOH A 1 501 171 HOH HOH . I 4 HOH A 2 502 114 HOH HOH . I 4 HOH A 3 503 261 HOH HOH . I 4 HOH A 4 504 209 HOH HOH . I 4 HOH A 5 505 61 HOH HOH . I 4 HOH A 6 506 35 HOH HOH . I 4 HOH A 7 507 109 HOH HOH . I 4 HOH A 8 508 71 HOH HOH . I 4 HOH A 9 509 140 HOH HOH . I 4 HOH A 10 510 137 HOH HOH . I 4 HOH A 11 511 95 HOH HOH . I 4 HOH A 12 512 85 HOH HOH . I 4 HOH A 13 513 32 HOH HOH . I 4 HOH A 14 514 118 HOH HOH . I 4 HOH A 15 515 115 HOH HOH . I 4 HOH A 16 516 189 HOH HOH . I 4 HOH A 17 517 31 HOH HOH . I 4 HOH A 18 518 100 HOH HOH . I 4 HOH A 19 519 150 HOH HOH . I 4 HOH A 20 520 13 HOH HOH . I 4 HOH A 21 521 16 HOH HOH . I 4 HOH A 22 522 80 HOH HOH . I 4 HOH A 23 523 82 HOH HOH . I 4 HOH A 24 524 104 HOH HOH . I 4 HOH A 25 525 214 HOH HOH . I 4 HOH A 26 526 45 HOH HOH . I 4 HOH A 27 527 78 HOH HOH . I 4 HOH A 28 528 86 HOH HOH . I 4 HOH A 29 529 24 HOH HOH . I 4 HOH A 30 530 133 HOH HOH . I 4 HOH A 31 531 2 HOH HOH . I 4 HOH A 32 532 33 HOH HOH . I 4 HOH A 33 533 47 HOH HOH . I 4 HOH A 34 534 41 HOH HOH . I 4 HOH A 35 535 11 HOH HOH . I 4 HOH A 36 536 57 HOH HOH . I 4 HOH A 37 537 81 HOH HOH . I 4 HOH A 38 538 34 HOH HOH . I 4 HOH A 39 539 97 HOH HOH . I 4 HOH A 40 540 302 HOH HOH . I 4 HOH A 41 541 38 HOH HOH . I 4 HOH A 42 542 21 HOH HOH . I 4 HOH A 43 543 296 HOH HOH . I 4 HOH A 44 544 269 HOH HOH . I 4 HOH A 45 545 64 HOH HOH . I 4 HOH A 46 546 67 HOH HOH . I 4 HOH A 47 547 198 HOH HOH . I 4 HOH A 48 548 173 HOH HOH . I 4 HOH A 49 549 254 HOH HOH . I 4 HOH A 50 550 51 HOH HOH . I 4 HOH A 51 551 253 HOH HOH . I 4 HOH A 52 552 164 HOH HOH . I 4 HOH A 53 553 46 HOH HOH . I 4 HOH A 54 554 20 HOH HOH . I 4 HOH A 55 555 9 HOH HOH . I 4 HOH A 56 556 255 HOH HOH . I 4 HOH A 57 557 181 HOH HOH . I 4 HOH A 58 558 182 HOH HOH . I 4 HOH A 59 559 239 HOH HOH . I 4 HOH A 60 560 30 HOH HOH . I 4 HOH A 61 561 251 HOH HOH . I 4 HOH A 62 562 89 HOH HOH . I 4 HOH A 63 563 229 HOH HOH . I 4 HOH A 64 564 124 HOH HOH . I 4 HOH A 65 565 183 HOH HOH . I 4 HOH A 66 566 278 HOH HOH . I 4 HOH A 67 567 297 HOH HOH . I 4 HOH A 68 568 59 HOH HOH . I 4 HOH A 69 569 76 HOH HOH . I 4 HOH A 70 570 148 HOH HOH . I 4 HOH A 71 571 1 HOH HOH . I 4 HOH A 72 572 49 HOH HOH . I 4 HOH A 73 573 63 HOH HOH . I 4 HOH A 74 574 196 HOH HOH . I 4 HOH A 75 575 177 HOH HOH . I 4 HOH A 76 576 262 HOH HOH . I 4 HOH A 77 577 26 HOH HOH . I 4 HOH A 78 578 131 HOH HOH . I 4 HOH A 79 579 87 HOH HOH . I 4 HOH A 80 580 134 HOH HOH . I 4 HOH A 81 581 135 HOH HOH . I 4 HOH A 82 582 39 HOH HOH . I 4 HOH A 83 583 172 HOH HOH . I 4 HOH A 84 584 301 HOH HOH . J 4 HOH B 1 501 279 HOH HOH . J 4 HOH B 2 502 74 HOH HOH . J 4 HOH B 3 503 29 HOH HOH . J 4 HOH B 4 504 7 HOH HOH . J 4 HOH B 5 505 4 HOH HOH . J 4 HOH B 6 506 139 HOH HOH . J 4 HOH B 7 507 199 HOH HOH . J 4 HOH B 8 508 3 HOH HOH . J 4 HOH B 9 509 273 HOH HOH . J 4 HOH B 10 510 50 HOH HOH . J 4 HOH B 11 511 187 HOH HOH . J 4 HOH B 12 512 15 HOH HOH . J 4 HOH B 13 513 96 HOH HOH . J 4 HOH B 14 514 52 HOH HOH . J 4 HOH B 15 515 23 HOH HOH . J 4 HOH B 16 516 250 HOH HOH . J 4 HOH B 17 517 125 HOH HOH . J 4 HOH B 18 518 121 HOH HOH . J 4 HOH B 19 519 17 HOH HOH . J 4 HOH B 20 520 28 HOH HOH . J 4 HOH B 21 521 73 HOH HOH . J 4 HOH B 22 522 18 HOH HOH . J 4 HOH B 23 523 48 HOH HOH . J 4 HOH B 24 524 22 HOH HOH . J 4 HOH B 25 525 180 HOH HOH . J 4 HOH B 26 526 195 HOH HOH . J 4 HOH B 27 527 98 HOH HOH . J 4 HOH B 28 528 120 HOH HOH . J 4 HOH B 29 529 68 HOH HOH . J 4 HOH B 30 530 44 HOH HOH . J 4 HOH B 31 531 79 HOH HOH . J 4 HOH B 32 532 208 HOH HOH . J 4 HOH B 33 533 8 HOH HOH . J 4 HOH B 34 534 62 HOH HOH . J 4 HOH B 35 535 25 HOH HOH . J 4 HOH B 36 536 53 HOH HOH . J 4 HOH B 37 537 88 HOH HOH . J 4 HOH B 38 538 132 HOH HOH . J 4 HOH B 39 539 10 HOH HOH . J 4 HOH B 40 540 123 HOH HOH . J 4 HOH B 41 541 6 HOH HOH . J 4 HOH B 42 542 117 HOH HOH . J 4 HOH B 43 543 14 HOH HOH . J 4 HOH B 44 544 12 HOH HOH . J 4 HOH B 45 545 5 HOH HOH . J 4 HOH B 46 546 66 HOH HOH . J 4 HOH B 47 547 260 HOH HOH . J 4 HOH B 48 548 268 HOH HOH . J 4 HOH B 49 549 136 HOH HOH . J 4 HOH B 50 550 94 HOH HOH . J 4 HOH B 51 551 293 HOH HOH . J 4 HOH B 52 552 69 HOH HOH . J 4 HOH B 53 553 36 HOH HOH . J 4 HOH B 54 554 216 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 -5.476 21.282 61.282 1 45.6 ? P1 C2E 401 A 1 HETATM 2 O O2P C2E . . . C 2 -4.625 22.516 61.477 1 42.35 ? O2P C2E 401 A 1 HETATM 3 O O1P C2E . . . C 2 -6.083 21.004 59.94 1 46.55 ? O1P C2E 401 A 1 HETATM 4 O O5' C2E . . . C 2 -4.492 20.05 61.565 1 46.13 ? O5' C2E 401 A 1 HETATM 5 C C5' C2E . . . C 2 -4.929 18.736 61.213 1 48.76 ? C5' C2E 401 A 1 HETATM 6 C C4' C2E . . . C 2 -3.825 17.788 61.573 1 49.19 ? C4' C2E 401 A 1 HETATM 7 O O4' C2E . . . C 2 -2.692 18.018 60.714 1 49.6 ? O4' C2E 401 A 1 HETATM 8 C C3' C2E . . . C 2 -3.265 17.965 62.975 1 50.63 ? C3' C2E 401 A 1 HETATM 9 O O3' C2E . . . C 2 -4.161 17.265 63.856 1 51.01 ? O3' C2E 401 A 1 HETATM 10 C C2' C2E . . . C 2 -1.841 17.381 62.84 1 50.82 ? C2' C2E 401 A 1 HETATM 11 O O2' C2E . . . C 2 -1.758 16.065 63.345 1 51.47 ? O2' C2E 401 A 1 HETATM 12 C C1' C2E . . . C 2 -1.563 17.441 61.332 1 51.24 ? C1' C2E 401 A 1 HETATM 13 N N9 C2E . . . C 2 -0.426 18.265 60.921 1 51.45 ? N9 C2E 401 A 1 HETATM 14 C C8 C2E . . . C 2 0.385 18.017 59.839 1 50.17 ? C8 C2E 401 A 1 HETATM 15 N N7 C2E . . . C 2 1.28 18.956 59.643 1 49.44 ? N7 C2E 401 A 1 HETATM 16 C C5 C2E . . . C 2 1.032 19.891 60.638 1 45.29 ? C5 C2E 401 A 1 HETATM 17 C C6 C2E . . . C 2 1.683 21.114 60.921 1 42.72 ? C6 C2E 401 A 1 HETATM 18 O O6 C2E . . . C 2 2.606 21.653 60.308 1 41.11 ? O6 C2E 401 A 1 HETATM 19 N N1 C2E . . . C 2 1.108 21.763 62.013 1 42.09 ? N1 C2E 401 A 1 HETATM 20 C C2 C2E . . . C 2 0.054 21.291 62.759 1 42.64 ? C2 C2E 401 A 1 HETATM 21 N N2 C2E . . . C 2 -0.356 22.07 63.773 1 42.44 ? N2 C2E 401 A 1 HETATM 22 N N3 C2E . . . C 2 -0.564 20.136 62.499 1 45.19 ? N3 C2E 401 A 1 HETATM 23 C C4 C2E . . . C 2 -0.025 19.487 61.431 1 47.55 ? C4 C2E 401 A 1 HETATM 24 P P11 C2E . . . C 2 -4.362 17.903 65.314 1 47.66 ? P11 C2E 401 A 1 HETATM 25 O O21 C2E . . . C 2 -2.987 18.277 65.781 1 48.11 ? O21 C2E 401 A 1 HETATM 26 O O11 C2E . . . C 2 -5.186 16.949 66.129 1 50.94 ? O11 C2E 401 A 1 HETATM 27 O O5A C2E . . . C 2 -5.257 19.21 65.073 1 45.68 ? O5A C2E 401 A 1 HETATM 28 C C5A C2E . . . C 2 -6.687 19.112 64.801 1 45.6 ? C5A C2E 401 A 1 HETATM 29 C C4A C2E . . . C 2 -7.248 20.5 64.613 1 44.32 ? C4A C2E 401 A 1 HETATM 30 O O4A C2E . . . C 2 -7.297 21.177 65.893 1 43.63 ? O4A C2E 401 A 1 HETATM 31 C C3A C2E . . . C 2 -6.435 21.44 63.728 1 42.98 ? C3A C2E 401 A 1 HETATM 32 O O3A C2E . . . C 2 -6.691 21.15 62.346 1 46.44 ? O3A C2E 401 A 1 HETATM 33 C C2A C2E . . . C 2 -6.926 22.803 64.208 1 42.6 ? C2A C2E 401 A 1 HETATM 34 O O2A C2E . . . C 2 -8.18 23.25 63.758 1 47.39 ? O2A C2E 401 A 1 HETATM 35 C C1A C2E . . . C 2 -7.064 22.564 65.712 1 42.47 ? C1A C2E 401 A 1 HETATM 36 N N91 C2E . . . C 2 -5.845 22.934 66.407 1 37.04 ? N91 C2E 401 A 1 HETATM 37 C C81 C2E . . . C 2 -4.743 22.129 66.544 1 36.15 ? C81 C2E 401 A 1 HETATM 38 N N71 C2E . . . C 2 -3.743 22.718 67.156 1 35.73 ? N71 C2E 401 A 1 HETATM 39 C C51 C2E . . . C 2 -4.224 23.991 67.427 1 35.41 ? C51 C2E 401 A 1 HETATM 40 C C61 C2E . . . C 2 -3.585 25.064 68.086 1 35.99 ? C61 C2E 401 A 1 HETATM 41 O O61 C2E . . . C 2 -2.416 25.116 68.494 1 36.49 ? O61 C2E 401 A 1 HETATM 42 N N11 C2E . . . C 2 -4.432 26.173 68.173 1 36.74 ? N11 C2E 401 A 1 HETATM 43 C C21 C2E . . . C 2 -5.723 26.235 67.702 1 35.67 ? C21 C2E 401 A 1 HETATM 44 N N21 C2E . . . C 2 -6.366 27.394 67.919 1 35.57 ? N21 C2E 401 A 1 HETATM 45 N N31 C2E . . . C 2 -6.32 25.236 67.057 1 34.9 ? N31 C2E 401 A 1 HETATM 46 C C41 C2E . . . C 2 -5.523 24.143 66.972 1 36.18 ? C41 C2E 401 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 46 #