data_6A04 # _model_server_result.job_id DOraaDgM_rYDKVO27gRjLg _model_server_result.datetime_utc '2024-11-25 12:42:10' _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 6a04 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":402}' # _entry.id 6A04 # _exptl.entry_id 6A04 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 3 _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 1 _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 6A04 _cell.length_a 49.692 _cell.length_b 63.95 _cell.length_c 101.591 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6A04 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I,J _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 6A04 _atom_sites.fract_transf_matrix[1][1] 0.020124 _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] 0.015637 _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] 0.009843 _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 SO4 A 1 401 1 SO4 SO4 . D 2 SO4 A 1 402 2 SO4 SO4 . E 2 SO4 A 1 403 4 SO4 SO4 . F 2 SO4 A 1 404 5 SO4 SO4 . G 2 SO4 B 1 401 3 SO4 SO4 . H 3 C2E B 1 402 401 C2E C2E . I 4 HOH A 1 501 3 HOH HOH . I 4 HOH A 2 502 76 HOH HOH . I 4 HOH A 3 503 32 HOH HOH . I 4 HOH A 4 504 12 HOH HOH . I 4 HOH A 5 505 67 HOH HOH . I 4 HOH A 6 506 25 HOH HOH . I 4 HOH A 7 507 48 HOH HOH . I 4 HOH A 8 508 15 HOH HOH . I 4 HOH A 9 509 75 HOH HOH . I 4 HOH A 10 510 102 HOH HOH . I 4 HOH A 11 511 92 HOH HOH . I 4 HOH A 12 512 19 HOH HOH . I 4 HOH A 13 513 123 HOH HOH . I 4 HOH A 14 514 72 HOH HOH . I 4 HOH A 15 515 1 HOH HOH . I 4 HOH A 16 516 50 HOH HOH . I 4 HOH A 17 517 23 HOH HOH . I 4 HOH A 18 518 119 HOH HOH . I 4 HOH A 19 519 60 HOH HOH . I 4 HOH A 20 520 43 HOH HOH . I 4 HOH A 21 521 44 HOH HOH . I 4 HOH A 22 522 37 HOH HOH . I 4 HOH A 23 523 81 HOH HOH . I 4 HOH A 24 524 33 HOH HOH . I 4 HOH A 25 525 59 HOH HOH . I 4 HOH A 26 526 49 HOH HOH . I 4 HOH A 27 527 96 HOH HOH . I 4 HOH A 28 528 127 HOH HOH . I 4 HOH A 29 529 129 HOH HOH . I 4 HOH A 30 530 122 HOH HOH . I 4 HOH A 31 531 125 HOH HOH . I 4 HOH A 32 532 46 HOH HOH . I 4 HOH A 33 533 41 HOH HOH . I 4 HOH A 34 534 39 HOH HOH . I 4 HOH A 35 535 24 HOH HOH . I 4 HOH A 36 536 74 HOH HOH . I 4 HOH A 37 537 117 HOH HOH . I 4 HOH A 38 538 36 HOH HOH . I 4 HOH A 39 539 11 HOH HOH . I 4 HOH A 40 540 106 HOH HOH . I 4 HOH A 41 541 107 HOH HOH . I 4 HOH A 42 542 63 HOH HOH . I 4 HOH A 43 543 38 HOH HOH . I 4 HOH A 44 544 115 HOH HOH . I 4 HOH A 45 545 29 HOH HOH . I 4 HOH A 46 546 55 HOH HOH . I 4 HOH A 47 547 10 HOH HOH . I 4 HOH A 48 548 64 HOH HOH . I 4 HOH A 49 549 79 HOH HOH . I 4 HOH A 50 550 58 HOH HOH . I 4 HOH A 51 551 82 HOH HOH . I 4 HOH A 52 552 78 HOH HOH . I 4 HOH A 53 553 89 HOH HOH . I 4 HOH A 54 554 95 HOH HOH . I 4 HOH A 55 555 87 HOH HOH . I 4 HOH A 56 556 121 HOH HOH . I 4 HOH A 57 557 108 HOH HOH . J 4 HOH B 1 501 93 HOH HOH . J 4 HOH B 2 502 97 HOH HOH . J 4 HOH B 3 503 84 HOH HOH . J 4 HOH B 4 504 18 HOH HOH . J 4 HOH B 5 505 109 HOH HOH . J 4 HOH B 6 506 116 HOH HOH . J 4 HOH B 7 507 21 HOH HOH . J 4 HOH B 8 508 17 HOH HOH . J 4 HOH B 9 509 103 HOH HOH . J 4 HOH B 10 510 27 HOH HOH . J 4 HOH B 11 511 51 HOH HOH . J 4 HOH B 12 512 30 HOH HOH . J 4 HOH B 13 513 124 HOH HOH . J 4 HOH B 14 514 86 HOH HOH . J 4 HOH B 15 515 61 HOH HOH . J 4 HOH B 16 516 128 HOH HOH . J 4 HOH B 17 517 66 HOH HOH . J 4 HOH B 18 518 28 HOH HOH . J 4 HOH B 19 519 62 HOH HOH . J 4 HOH B 20 520 114 HOH HOH . J 4 HOH B 21 521 5 HOH HOH . J 4 HOH B 22 522 2 HOH HOH . J 4 HOH B 23 523 16 HOH HOH . J 4 HOH B 24 524 31 HOH HOH . J 4 HOH B 25 525 83 HOH HOH . J 4 HOH B 26 526 88 HOH HOH . J 4 HOH B 27 527 6 HOH HOH . J 4 HOH B 28 528 22 HOH HOH . J 4 HOH B 29 529 90 HOH HOH . J 4 HOH B 30 530 68 HOH HOH . J 4 HOH B 31 531 91 HOH HOH . J 4 HOH B 32 532 47 HOH HOH . J 4 HOH B 33 533 34 HOH HOH . J 4 HOH B 34 534 4 HOH HOH . J 4 HOH B 35 535 20 HOH HOH . J 4 HOH B 36 536 118 HOH HOH . J 4 HOH B 37 537 14 HOH HOH . J 4 HOH B 38 538 77 HOH HOH . J 4 HOH B 39 539 40 HOH HOH . J 4 HOH B 40 540 57 HOH HOH . J 4 HOH B 41 541 7 HOH HOH . J 4 HOH B 42 542 9 HOH HOH . J 4 HOH B 43 543 26 HOH HOH . J 4 HOH B 44 544 111 HOH HOH . J 4 HOH B 45 545 80 HOH HOH . J 4 HOH B 46 546 8 HOH HOH . J 4 HOH B 47 547 98 HOH HOH . J 4 HOH B 48 548 53 HOH HOH . J 4 HOH B 49 549 101 HOH HOH . J 4 HOH B 50 550 54 HOH HOH . J 4 HOH B 51 551 13 HOH HOH . J 4 HOH B 52 552 69 HOH HOH . J 4 HOH B 53 553 56 HOH HOH . J 4 HOH B 54 554 112 HOH HOH . J 4 HOH B 55 555 99 HOH HOH . J 4 HOH B 56 556 130 HOH HOH . J 4 HOH B 57 557 42 HOH HOH . J 4 HOH B 58 558 35 HOH HOH . J 4 HOH B 59 559 110 HOH HOH . J 4 HOH B 60 560 94 HOH HOH . J 4 HOH B 61 561 126 HOH HOH . J 4 HOH B 62 562 104 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 . . . H 3 6.033 -3.161 -18.481 1 32.8 ? P1 C2E 402 B 1 HETATM 2 O O2P C2E . . . H 3 4.866 -3.645 -17.663 1 34 ? O2P C2E 402 B 1 HETATM 3 O O1P C2E . . . H 3 6.965 -4.295 -18.589 1 36.69 ? O1P C2E 402 B 1 HETATM 4 O O5' C2E . . . H 3 5.469 -2.753 -19.87 1 35.43 ? O5' C2E 402 B 1 HETATM 5 C C5' C2E . . . H 3 6.429 -2.345 -20.79 1 29.6 ? C5' C2E 402 B 1 HETATM 6 C C4' C2E . . . H 3 5.86 -1.605 -21.975 1 31.85 ? C4' C2E 402 B 1 HETATM 7 O O4' C2E . . . H 3 4.96 -2.461 -22.619 1 35.78 ? O4' C2E 402 B 1 HETATM 8 C C3' C2E . . . H 3 5.06 -0.379 -21.66 1 31.09 ? C3' C2E 402 B 1 HETATM 9 O O3' C2E . . . H 3 5.806 0.793 -21.61 1 30.73 ? O3' C2E 402 B 1 HETATM 10 C C2' C2E . . . H 3 4.207 -0.306 -22.779 1 38.92 ? C2' C2E 402 B 1 HETATM 11 O O2' C2E . . . H 3 4.884 0.168 -23.929 1 36.02 ? O2' C2E 402 B 1 HETATM 12 C C1' C2E . . . H 3 3.845 -1.724 -23.016 1 39.5 ? C1' C2E 402 B 1 HETATM 13 N N9 C2E . . . H 3 2.58 -1.97 -22.278 1 46.64 ? N9 C2E 402 B 1 HETATM 14 C C8 C2E . . . H 3 2.447 -2.427 -21.068 1 47.61 ? C8 C2E 402 B 1 HETATM 15 N N7 C2E . . . H 3 1.262 -2.505 -20.693 1 48.47 ? N7 C2E 402 B 1 HETATM 16 C C5 C2E . . . H 3 0.385 -2.103 -21.597 1 48.74 ? C5 C2E 402 B 1 HETATM 17 C C6 C2E . . . H 3 -1.007 -1.98 -21.714 1 49.22 ? C6 C2E 402 B 1 HETATM 18 O O6 C2E . . . H 3 -1.804 -2.334 -20.698 1 52.61 ? O6 C2E 402 B 1 HETATM 19 N N1 C2E . . . H 3 -1.531 -1.499 -22.87 1 50.55 ? N1 C2E 402 B 1 HETATM 20 C C2 C2E . . . H 3 -0.704 -1.143 -23.901 1 57.58 ? C2 C2E 402 B 1 HETATM 21 N N2 C2E . . . H 3 -1.302 -0.616 -25.184 1 61.96 ? N2 C2E 402 B 1 HETATM 22 N N3 C2E . . . H 3 0.652 -1.241 -23.831 1 56.5 ? N3 C2E 402 B 1 HETATM 23 C C4 C2E . . . H 3 1.234 -1.708 -22.716 1 49.71 ? C4 C2E 402 B 1 HETATM 24 P P11 C2E . . . H 3 5.336 1.865 -20.545 1 28.63 ? P11 C2E 402 B 1 HETATM 25 O O21 C2E . . . H 3 3.906 2.274 -20.895 1 27.37 ? O21 C2E 402 B 1 HETATM 26 O O11 C2E . . . H 3 6.272 3.055 -20.635 1 27.69 ? O11 C2E 402 B 1 HETATM 27 O O5A C2E . . . H 3 5.294 1.312 -19.076 1 27.09 ? O5A C2E 402 B 1 HETATM 28 C C5A C2E . . . H 3 6.554 1.104 -18.551 1 27.5 ? C5A C2E 402 B 1 HETATM 29 C C4A C2E . . . H 3 6.496 0.359 -17.251 1 31.61 ? C4A C2E 402 B 1 HETATM 30 O O4A C2E . . . H 3 5.707 1.159 -16.334 1 25.9 ? O4A C2E 402 B 1 HETATM 31 C C3A C2E . . . H 3 5.83 -0.936 -17.362 1 30.69 ? C3A C2E 402 B 1 HETATM 32 O O3A C2E . . . H 3 6.691 -1.977 -17.691 1 28.83 ? O3A C2E 402 B 1 HETATM 33 C C2A C2E . . . H 3 5.355 -1.112 -15.992 1 33.63 ? C2A C2E 402 B 1 HETATM 34 O O2A C2E . . . H 3 6.408 -1.598 -15.216 1 31.09 ? O2A C2E 402 B 1 HETATM 35 C C1A C2E . . . H 3 4.933 0.267 -15.565 1 27.15 ? C1A C2E 402 B 1 HETATM 36 N N91 C2E . . . H 3 3.596 0.373 -15.854 1 29.3 ? N91 C2E 402 B 1 HETATM 37 C C81 C2E . . . H 3 2.99 0.773 -16.951 1 32.28 ? C81 C2E 402 B 1 HETATM 38 N N71 C2E . . . H 3 1.733 0.733 -16.891 1 29.59 ? N71 C2E 402 B 1 HETATM 39 C C51 C2E . . . H 3 1.301 0.291 -15.733 1 28.94 ? C51 C2E 402 B 1 HETATM 40 C C61 C2E . . . H 3 0.107 0.035 -15.059 1 31.93 ? C61 C2E 402 B 1 HETATM 41 O O61 C2E . . . H 3 -1.147 0.234 -15.653 1 30.84 ? O61 C2E 402 B 1 HETATM 42 N N11 C2E . . . H 3 0.148 -0.443 -13.785 1 29.5 ? N11 C2E 402 B 1 HETATM 43 C C21 C2E . . . H 3 1.327 -0.671 -13.128 1 29.43 ? C21 C2E 402 B 1 HETATM 44 N N21 C2E . . . H 3 1.314 -1.165 -11.746 1 28.38 ? N21 C2E 402 B 1 HETATM 45 N N31 C2E . . . H 3 2.506 -0.432 -13.724 1 27.87 ? N31 C2E 402 B 1 HETATM 46 C C41 C2E . . . H 3 2.537 0.038 -14.982 1 25.82 ? C41 C2E 402 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #