data_2WB4 # _model_server_result.job_id SiqQlM2OB10FyOP9H_M68A _model_server_result.datetime_utc '2024-11-22 10:24:32' _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 2wb4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":505}' # _entry.id 2WB4 # _exptl.entry_id 2WB4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 690.411 _entity.id 4 _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 5 _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 2WB4 _cell.length_a 123.56 _cell.length_b 127.43 _cell.length_c 88.13 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2WB4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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,K,L,M,N,O,P,Q _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 ? 4 E N N ? 4 F N N ? 4 K N N ? 4 L N N ? 4 M N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A OD1 ASP 10 A ASP 10 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? metalc ? metalc2 A OD1 ASP 53 A ASP 53 1_555 C BE BEF . A BEF 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.576 ? metalc ? metalc3 A OD2 ASP 53 A ASP 53 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc4 A O MET 55 A MET 55 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc5 C F2 BEF . A BEF 501 1_555 D MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc6 D MG MG . A MG 502 1_555 P O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc7 B OD1 ASP 10 B ASP 10 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc8 B OD1 ASP 53 B ASP 53 1_555 I BE BEF . B BEF 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.575 ? metalc ? metalc9 B OD2 ASP 53 B ASP 53 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc10 B O MET 55 B MET 55 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc11 B OE2 GLU 371 B GLU 371 1_555 N MG MG . B MG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc12 I F2 BEF . B BEF 501 1_555 J MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc13 J MG MG . B MG 502 1_555 Q O HOH . B HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.792 ? metalc ? metalc14 J MG MG . B MG 502 1_555 Q O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc15 M O11 C2E . B C2E 507 1_555 N MG MG . B MG 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? # _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 73 n n O1P P1 C2E doub 74 n n O5' P1 C2E sing 75 n n C5' O5' C2E sing 76 n n C4' O4' C2E sing 77 n n C4' C5' C2E sing 78 n n C3' C4' C2E sing 79 n n O3' P11 C2E sing 80 n n O3' C3' C2E sing 81 n n C2' C3' C2E sing 82 n n C2' C1' C2E sing 83 n n O2' C2' C2E sing 84 n n C1' O4' C2E sing 85 n n C1' N9 C2E sing 86 n n N9 C4 C2E sing 87 n y N9 C8 C2E sing 88 n y C8 N7 C2E doub 89 n y C5 N7 C2E sing 90 n y C5 C6 C2E sing 91 n n C6 O6 C2E doub 92 n n N1 C6 C2E sing 93 n n C2 N1 C2E sing 94 n n N2 C2 C2E sing 95 n n N3 C2 C2E doub 96 n n N3 C4 C2E sing 97 n n C4 C5 C2E doub 98 n y P11 O21 C2E sing 99 n n P11 O5A C2E sing 100 n n O11 P11 C2E doub 101 n n C5A O5A C2E sing 102 n n C5A C4A C2E sing 103 n n C4A O4A C2E sing 104 n n C4A C3A C2E sing 105 n n O4A C1A C2E sing 106 n n C3A C2A C2E sing 107 n n O3A C3A C2E sing 108 n n O3A P1 C2E sing 109 n n C2A O2A C2E sing 110 n n C1A C2A C2E sing 111 n n C1A N91 C2E sing 112 n n N91 C41 C2E sing 113 n y C81 N71 C2E doub 114 n y C81 N91 C2E sing 115 n y N71 C51 C2E sing 116 n y C51 C41 C2E doub 117 n y C51 C61 C2E sing 118 n n C61 O61 C2E doub 119 n n C61 N11 C2E sing 120 n n C21 N11 C2E sing 121 n n C21 N21 C2E sing 122 n n N31 C21 C2E doub 123 n n C41 N31 C2E sing 124 n n O2P HO2P C2E sing 125 n n C5' "H5'1" C2E sing 126 n n C5' "H5'2" C2E sing 127 n n C4' H4' C2E sing 128 n n C3' H3' C2E sing 129 n n C2' H2' C2E sing 130 n n O2' HO2' C2E sing 131 n n C1' H1' C2E sing 132 n n C8 H8 C2E sing 133 n n N1 HN1 C2E sing 134 n n N2 HN21 C2E sing 135 n n N2 HN22 C2E sing 136 n n O21 HO21 C2E sing 137 n n C5A H511 C2E sing 138 n n C5A H512 C2E sing 139 n n C4A H4A C2E sing 140 n n C3A H3A C2E sing 141 n n C2A H2A C2E sing 142 n n O2A HO2A C2E sing 143 n n C1A H1A C2E sing 144 n n C81 H81 C2E sing 145 n n N11 HN11 C2E sing 146 n n N21 HN24 C2E sing 147 n n N21 HN23 C2E sing 148 n n # _atom_sites.entry_id 2WB4 _atom_sites.fract_transf_matrix[1][1] 0.008093 _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] 0.007847 _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] 0.011347 _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 BEF A 1 501 501 BEF BEF . D 3 MG A 1 502 502 MG MG . E 4 C2E A 1 503 503 C2E C2E . F 4 C2E A 1 505 505 C2E C2E . G 5 SO4 A 1 1460 1460 SO4 SO4 . H 5 SO4 A 1 1461 1461 SO4 SO4 . I 2 BEF B 1 501 501 BEF BEF . J 3 MG B 1 502 502 MG MG . K 4 C2E B 1 503 503 C2E C2E . L 4 C2E B 1 505 505 C2E C2E . M 4 C2E B 1 507 507 C2E C2E . N 3 MG B 1 509 509 MG MG . O 5 SO4 B 1 1455 1455 SO4 SO4 . P 6 HOH A 1 2001 2001 HOH HOH . P 6 HOH A 2 2002 2002 HOH HOH . P 6 HOH A 3 2003 2003 HOH HOH . P 6 HOH A 4 2004 2004 HOH HOH . P 6 HOH A 5 2005 2005 HOH HOH . P 6 HOH A 6 2006 2006 HOH HOH . P 6 HOH A 7 2007 2007 HOH HOH . P 6 HOH A 8 2008 2008 HOH HOH . P 6 HOH A 9 2009 2009 HOH HOH . P 6 HOH A 10 2010 2010 HOH HOH . P 6 HOH A 11 2011 2011 HOH HOH . P 6 HOH A 12 2012 2012 HOH HOH . P 6 HOH A 13 2013 2013 HOH HOH . P 6 HOH A 14 2014 2014 HOH HOH . P 6 HOH A 15 2015 2015 HOH HOH . P 6 HOH A 16 2016 2016 HOH HOH . P 6 HOH A 17 2017 2017 HOH HOH . P 6 HOH A 18 2018 2018 HOH HOH . P 6 HOH A 19 2019 2019 HOH HOH . P 6 HOH A 20 2020 2020 HOH HOH . P 6 HOH A 21 2021 2021 HOH HOH . P 6 HOH A 22 2022 2022 HOH HOH . P 6 HOH A 23 2023 2023 HOH HOH . P 6 HOH A 24 2024 2024 HOH HOH . P 6 HOH A 25 2025 2025 HOH HOH . Q 6 HOH B 1 2001 2001 HOH HOH . Q 6 HOH B 2 2002 2002 HOH HOH . Q 6 HOH B 3 2003 2003 HOH HOH . Q 6 HOH B 4 2004 2004 HOH HOH . Q 6 HOH B 5 2005 2005 HOH HOH . Q 6 HOH B 6 2006 2006 HOH HOH . Q 6 HOH B 7 2007 2007 HOH HOH . Q 6 HOH B 8 2008 2008 HOH HOH . Q 6 HOH B 9 2009 2009 HOH HOH . Q 6 HOH B 10 2010 2010 HOH HOH . Q 6 HOH B 11 2011 2011 HOH HOH . Q 6 HOH B 12 2012 2012 HOH HOH . Q 6 HOH B 13 2013 2013 HOH HOH . Q 6 HOH B 14 2014 2014 HOH HOH . Q 6 HOH B 15 2015 2015 HOH HOH . Q 6 HOH B 16 2016 2016 HOH HOH . Q 6 HOH B 17 2017 2017 HOH HOH . Q 6 HOH B 18 2018 2018 HOH HOH . Q 6 HOH B 19 2019 2019 HOH HOH . Q 6 HOH B 20 2020 2020 HOH HOH . Q 6 HOH B 21 2021 2021 HOH HOH . Q 6 HOH B 22 2022 2022 HOH HOH . Q 6 HOH B 23 2023 2023 HOH HOH . Q 6 HOH B 24 2024 2024 HOH HOH . Q 6 HOH B 25 2025 2025 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 . . . F 4 20.742 52.686 22.049 1 14.38 ? P1 C2E 505 A 1 HETATM 2 O O2P C2E . . . F 4 20.539 54.136 21.674 1 15.5 ? O2P C2E 505 A 1 HETATM 3 O O1P C2E . . . F 4 22.105 52.113 21.852 1 18.52 ? O1P C2E 505 A 1 HETATM 4 O O5' C2E . . . F 4 20.552 52.505 23.644 1 4.07 ? O5' C2E 505 A 1 HETATM 5 C C5' C2E . . . F 4 20.849 51.228 24.168 1 2 ? C5' C2E 505 A 1 HETATM 6 C C4' C2E . . . F 4 20.103 51.006 25.475 1 4.91 ? C4' C2E 505 A 1 HETATM 7 O O4' C2E . . . F 4 20.643 51.87 26.455 1 9.33 ? O4' C2E 505 A 1 HETATM 8 C C3' C2E . . . F 4 18.59 51.242 25.484 1 8.2 ? C3' C2E 505 A 1 HETATM 9 O O3' C2E . . . F 4 17.963 49.955 25.407 1 9.37 ? O3' C2E 505 A 1 HETATM 10 C C2' C2E . . . F 4 18.353 51.896 26.823 1 6.85 ? C2' C2E 505 A 1 HETATM 11 O O2' C2E . . . F 4 18.098 50.874 27.779 1 4.82 ? O2' C2E 505 A 1 HETATM 12 C C1' C2E . . . F 4 19.649 52.56 27.207 1 8.25 ? C1' C2E 505 A 1 HETATM 13 N N9 C2E . . . F 4 19.689 54.01 26.886 1 6.4 ? N9 C2E 505 A 1 HETATM 14 C C8 C2E . . . F 4 20.302 54.591 25.839 1 8.08 ? C8 C2E 505 A 1 HETATM 15 N N7 C2E . . . F 4 20.114 55.936 25.891 1 8.83 ? N7 C2E 505 A 1 HETATM 16 C C5 C2E . . . F 4 19.377 56.179 26.986 1 4 ? C5 C2E 505 A 1 HETATM 17 C C6 C2E . . . F 4 18.887 57.346 27.532 1 2.9 ? C6 C2E 505 A 1 HETATM 18 O O6 C2E . . . F 4 19.108 58.445 26.976 1 5.11 ? O6 C2E 505 A 1 HETATM 19 N N1 C2E . . . F 4 18.167 57.279 28.655 1 2 ? N1 C2E 505 A 1 HETATM 20 C C2 C2E . . . F 4 17.912 56.097 29.246 1 2 ? C2 C2E 505 A 1 HETATM 21 N N2 C2E . . . F 4 17.176 56.088 30.38 1 2 ? N2 C2E 505 A 1 HETATM 22 N N3 C2E . . . F 4 18.374 54.933 28.73 1 2 ? N3 C2E 505 A 1 HETATM 23 C C4 C2E . . . F 4 19.121 54.968 27.611 1 2.97 ? C4 C2E 505 A 1 HETATM 24 P P11 C2E . . . F 4 16.467 50.097 24.922 1 6.95 ? P11 C2E 505 A 1 HETATM 25 O O21 C2E . . . F 4 15.715 50.894 25.942 1 7.51 ? O21 C2E 505 A 1 HETATM 26 O O11 C2E . . . F 4 15.958 48.715 24.569 1 15.26 ? O11 C2E 505 A 1 HETATM 27 O O5A C2E . . . F 4 16.419 50.828 23.496 1 2 ? O5A C2E 505 A 1 HETATM 28 C C5A C2E . . . F 4 17.146 50.182 22.467 1 6.72 ? C5A C2E 505 A 1 HETATM 29 C C4A C2E . . . F 4 17.328 51.05 21.242 1 6.59 ? C4A C2E 505 A 1 HETATM 30 O O4A C2E . . . F 4 16.068 51.62 20.837 1 9.79 ? O4A C2E 505 A 1 HETATM 31 C C3A C2E . . . F 4 18.315 52.188 21.463 1 5.96 ? C3A C2E 505 A 1 HETATM 32 O O3A C2E . . . F 4 19.668 51.745 21.236 1 11.44 ? O3A C2E 505 A 1 HETATM 33 C C2A C2E . . . F 4 17.798 53.13 20.402 1 8.82 ? C2A C2E 505 A 1 HETATM 34 O O2A C2E . . . F 4 18.411 52.734 19.172 1 5.09 ? O2A C2E 505 A 1 HETATM 35 C C1A C2E . . . F 4 16.271 52.947 20.343 1 7.08 ? C1A C2E 505 A 1 HETATM 36 N N91 C2E . . . F 4 15.576 53.937 21.217 1 7.51 ? N91 C2E 505 A 1 HETATM 37 C C81 C2E . . . F 4 14.877 53.683 22.362 1 3.46 ? C81 C2E 505 A 1 HETATM 38 N N71 C2E . . . F 4 14.426 54.86 22.872 1 2 ? N71 C2E 505 A 1 HETATM 39 C C51 C2E . . . F 4 14.856 55.841 22.03 1 2 ? C51 C2E 505 A 1 HETATM 40 C C61 C2E . . . F 4 14.716 57.217 22.01 1 2 ? C61 C2E 505 A 1 HETATM 41 O O61 C2E . . . F 4 14.078 57.833 22.875 1 3.66 ? O61 C2E 505 A 1 HETATM 42 N N11 C2E . . . F 4 15.244 57.937 21.049 1 2 ? N11 C2E 505 A 1 HETATM 43 C C21 C2E . . . F 4 15.924 57.347 20.069 1 4.18 ? C21 C2E 505 A 1 HETATM 44 N N21 C2E . . . F 4 16.441 58.141 19.106 1 2.48 ? N21 C2E 505 A 1 HETATM 45 N N31 C2E . . . F 4 16.094 55.995 20.032 1 2 ? N31 C2E 505 A 1 HETATM 46 C C41 C2E . . . F 4 15.56 55.248 21.004 1 2 ? C41 C2E 505 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 558 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 46 #