data_8IXZ # _model_server_result.job_id fY9ixWCJ-r6AEKQdQB8vKg _model_server_result.datetime_utc '2024-10-15 00:23:45' _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 8ixz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":101}' # _entry.id 8IXZ # _exptl.entry_id 8IXZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 674.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'2'-cGAMP" _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 8IXZ _cell.length_a 104.045 _cell.length_b 104.045 _cell.length_c 101.141 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8IXZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 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 ? hexameric 6 author_defined_assembly 1 ? hexameric 6 author_defined_assembly 2 ? hexameric 6 author_defined_assembly 3 ? hexameric 6 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,K 1 1 A,G,K 1 2 A,G,K 1 4 A,G,K 1 6 A,G,K 1 8 A,G,K 1 10 B,H,L 2 1 B,H,L 2 2 B,H,L 2 4 B,H,L 2 7 B,H,L 2 9 B,H,L 2 11 C,D,I,M,N 3 1 C,D,I,M,N 3 3 C,D,I,M,N 3 5 E,F,J,O,P 4 1 E,F,J,O,P 4 3 E,F,J,O,P 4 5 # 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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -52.0225 90.105613 0 4 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -104.045 0 0 6 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 101.141 7 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 101.141 9 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 10 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 101.141 11 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 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 G N N ? 2 H N N ? 2 I N N ? 2 J N N # _chem_comp.formula 'C20 H24 N10 O13 P2' _chem_comp.formula_weight 674.411 _chem_comp.id 4UR _chem_comp.mon_nstd_flag . _chem_comp.name "3'2'-cGAMP" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 2-amino-9-[(2S,5R,7R,8R,10R,12aR,14R,15R,15aS,16R)-7-(6-amino-9H-purin-9-yl)-2,10,15,16-tetrahydroxy-2,10-dioxidooctahydro-12H-5,8-methanofuro[3,2-l][1,3,6,9,11,2,10]pentaoxadiphosphacyclotetradecin-14-yl]-1,9-dihydro-6H-purin-6-one # 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 O25 P24 4UR doub 1 n n C22 O23 4UR sing 2 n n C22 C21 4UR sing 3 n n O26 P24 4UR sing 4 n n P24 O23 4UR sing 5 n n P24 O27 4UR sing 6 n n O31 C21 4UR sing 7 n n O31 C32 4UR sing 8 n n C21 C19 4UR sing 9 n n N35 C34 4UR doub 10 n y N35 C36 4UR sing 11 n y C34 N33 4UR sing 12 n y N38 C37 4UR sing 13 n n C36 C37 4UR doub 14 n y C36 C42 4UR sing 15 n y N33 C32 4UR sing 16 n n N33 C42 4UR sing 17 n y C32 C18 4UR sing 18 n n C37 N39 4UR sing 19 n y O27 C28 4UR sing 20 n n C42 N41 4UR doub 21 n y C19 O20 4UR sing 22 n n C19 C18 4UR sing 23 n n N39 C40 4UR doub 24 n y N41 C40 4UR sing 25 n y O30 C29 4UR sing 26 n n C18 O17 4UR sing 27 n n C28 C29 4UR sing 28 n n C28 C11 4UR sing 29 n n C29 C09 4UR sing 30 n n N01 C02 4UR sing 31 n n C02 N45 4UR sing 32 n n C02 N03 4UR doub 33 n n N45 C43 4UR sing 34 n n N03 C04 4UR sing 35 n n C43 O44 4UR doub 36 n n C43 C05 4UR sing 37 n n O17 P14 4UR sing 38 n n C04 C05 4UR doub 39 n y C04 N08 4UR sing 40 n y C05 N06 4UR sing 41 n y C11 C12 4UR sing 42 n n C11 O10 4UR sing 43 n n N08 C09 4UR sing 44 n n N08 C07 4UR sing 45 n y C09 O10 4UR sing 46 n n N06 C07 4UR doub 47 n y C12 O13 4UR sing 48 n n O13 P14 4UR sing 49 n n O15 P14 4UR doub 50 n n P14 O16 4UR sing 51 n n C21 H211 4UR sing 52 n n C22 H221 4UR sing 53 n n C22 H222 4UR sing 54 n n C28 H281 4UR sing 55 n n N01 H012 4UR sing 56 n n N01 H011 4UR sing 57 n n C07 H071 4UR sing 58 n n C09 H091 4UR sing 59 n n C11 H111 4UR sing 60 n n C12 H121 4UR sing 61 n n C12 H122 4UR sing 62 n n O16 H1 4UR sing 63 n n C18 H181 4UR sing 64 n n C19 H191 4UR sing 65 n n O20 H201 4UR sing 66 n n O26 H2 4UR sing 67 n n C29 H291 4UR sing 68 n n O30 H301 4UR sing 69 n n C32 H321 4UR sing 70 n n C34 H341 4UR sing 71 n n N38 H381 4UR sing 72 n n N38 H382 4UR sing 73 n n C40 H401 4UR sing 74 n n N45 H451 4UR sing 75 n n # _atom_sites.entry_id 8IXZ _atom_sites.fract_transf_matrix[1][1] 0.009611 _atom_sites.fract_transf_matrix[1][2] 0.005549 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011098 _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] 0.009887 _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 G 2 4UR A 1 101 101 4UR 4UR . H 2 4UR B 1 101 101 4UR 4UR . I 2 4UR D 1 101 101 4UR 4UR . J 2 4UR E 1 101 101 4UR 4UR . K 3 HOH A 1 201 28 HOH HOH . K 3 HOH A 2 202 69 HOH HOH . K 3 HOH A 3 203 10 HOH HOH . K 3 HOH A 4 204 20 HOH HOH . K 3 HOH A 5 205 6 HOH HOH . K 3 HOH A 6 206 30 HOH HOH . K 3 HOH A 7 207 12 HOH HOH . K 3 HOH A 8 208 1 HOH HOH . K 3 HOH A 9 209 26 HOH HOH . K 3 HOH A 10 210 46 HOH HOH . K 3 HOH A 11 211 61 HOH HOH . K 3 HOH A 12 212 43 HOH HOH . K 3 HOH A 13 213 7 HOH HOH . K 3 HOH A 14 214 42 HOH HOH . K 3 HOH A 15 215 3 HOH HOH . K 3 HOH A 16 216 21 HOH HOH . K 3 HOH A 17 217 51 HOH HOH . K 3 HOH A 18 218 68 HOH HOH . K 3 HOH A 19 219 15 HOH HOH . K 3 HOH A 20 220 40 HOH HOH . K 3 HOH A 21 221 35 HOH HOH . K 3 HOH A 22 222 52 HOH HOH . K 3 HOH A 23 223 16 HOH HOH . K 3 HOH A 24 224 45 HOH HOH . K 3 HOH A 25 225 57 HOH HOH . K 3 HOH A 26 226 33 HOH HOH . K 3 HOH A 27 227 44 HOH HOH . K 3 HOH A 28 228 70 HOH HOH . K 3 HOH A 29 229 32 HOH HOH . L 3 HOH B 1 201 14 HOH HOH . L 3 HOH B 2 202 22 HOH HOH . L 3 HOH B 3 203 38 HOH HOH . L 3 HOH B 4 204 63 HOH HOH . L 3 HOH B 5 205 39 HOH HOH . L 3 HOH B 6 206 19 HOH HOH . L 3 HOH B 7 207 8 HOH HOH . L 3 HOH B 8 208 41 HOH HOH . L 3 HOH B 9 209 55 HOH HOH . L 3 HOH B 10 210 48 HOH HOH . L 3 HOH B 11 211 54 HOH HOH . M 3 HOH C 1 101 4 HOH HOH . M 3 HOH C 2 102 37 HOH HOH . M 3 HOH C 3 103 47 HOH HOH . M 3 HOH C 4 104 11 HOH HOH . M 3 HOH C 5 105 49 HOH HOH . M 3 HOH C 6 106 9 HOH HOH . M 3 HOH C 7 107 13 HOH HOH . M 3 HOH C 8 108 18 HOH HOH . M 3 HOH C 9 109 34 HOH HOH . M 3 HOH C 10 110 62 HOH HOH . N 3 HOH D 1 201 66 HOH HOH . N 3 HOH D 2 202 31 HOH HOH . N 3 HOH D 3 203 71 HOH HOH . N 3 HOH D 4 204 59 HOH HOH . N 3 HOH D 5 205 2 HOH HOH . N 3 HOH D 6 206 72 HOH HOH . N 3 HOH D 7 207 27 HOH HOH . N 3 HOH D 8 208 25 HOH HOH . N 3 HOH D 9 209 23 HOH HOH . N 3 HOH D 10 210 74 HOH HOH . N 3 HOH D 11 211 60 HOH HOH . N 3 HOH D 12 212 65 HOH HOH . N 3 HOH D 13 213 56 HOH HOH . N 3 HOH D 14 214 17 HOH HOH . N 3 HOH D 15 215 29 HOH HOH . N 3 HOH D 16 216 5 HOH HOH . N 3 HOH D 17 217 53 HOH HOH . N 3 HOH D 18 218 24 HOH HOH . N 3 HOH D 19 219 73 HOH HOH . O 3 HOH E 1 201 75 HOH HOH . P 3 HOH F 1 101 50 HOH HOH . P 3 HOH F 2 102 67 HOH HOH . P 3 HOH F 3 103 36 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 C C21 4UR . . . H 2 -9.527 14.081 -2.693 0.48 42.66 ? C21 4UR 101 B 1 HETATM 2 C C22 4UR . . . H 2 -10.462 14.105 -1.513 0.48 43.05 ? C22 4UR 101 B 1 HETATM 3 C C28 4UR . . . H 2 -9.493 14.787 1.924 0.48 42.55 ? C28 4UR 101 B 1 HETATM 4 N N01 4UR . . . H 2 -12.603 18.88 7.026 0.48 48.69 ? N01 4UR 101 B 1 HETATM 5 C C02 4UR . . . H 2 -12.06 19.058 5.813 0.48 50.01 ? C02 4UR 101 B 1 HETATM 6 N N03 4UR . . . H 2 -11.265 18.123 5.303 0.48 48.62 ? N03 4UR 101 B 1 HETATM 7 C C04 4UR . . . H 2 -10.811 18.46 4.085 0.48 49.02 ? C04 4UR 101 B 1 HETATM 8 C C05 4UR . . . H 2 -11.059 19.603 3.349 0.48 51.19 ? C05 4UR 101 B 1 HETATM 9 N N06 4UR . . . H 2 -10.391 19.557 2.146 0.48 49.42 ? N06 4UR 101 B 1 HETATM 10 C C07 4UR . . . H 2 -9.746 18.397 2.16 0.48 47.77 ? C07 4UR 101 B 1 HETATM 11 N N08 4UR . . . H 2 -9.962 17.69 3.325 0.48 45.63 ? N08 4UR 101 B 1 HETATM 12 C C09 4UR . . . H 2 -9.446 16.377 3.688 0.48 43.47 ? C09 4UR 101 B 1 HETATM 13 O O10 4UR . . . H 2 -8.147 16.256 3.131 0.48 40.14 ? O10 4UR 101 B 1 HETATM 14 C C11 4UR . . . H 2 -8.076 14.999 2.439 0.48 42.65 ? C11 4UR 101 B 1 HETATM 15 C C12 4UR . . . H 2 -7.004 15.071 1.381 0.48 41.25 ? C12 4UR 101 B 1 HETATM 16 O O13 4UR . . . H 2 -7.311 16.163 0.477 0.48 40.74 ? O13 4UR 101 B 1 HETATM 17 P P14 4UR . . . H 2 -6.238 16.497 -0.661 0.48 40.96 ? P14 4UR 101 B 1 HETATM 18 O O15 4UR . . . H 2 -5.54 17.776 -0.349 0.48 41.59 ? O15 4UR 101 B 1 HETATM 19 O O16 4UR . . . H 2 -5.415 15.275 -0.894 0.48 39.86 ? O16 4UR 101 B 1 HETATM 20 O O17 4UR . . . H 2 -7.228 16.772 -1.891 0.48 42.98 ? O17 4UR 101 B 1 HETATM 21 C C18 4UR . . . H 2 -8.369 15.96 -2.081 0.48 42.87 ? C18 4UR 101 B 1 HETATM 22 C C19 4UR . . . H 2 -8.099 14.479 -2.321 0.48 42.17 ? C19 4UR 101 B 1 HETATM 23 O O20 4UR . . . H 2 -7.174 14.301 -3.387 0.48 40.12 ? O20 4UR 101 B 1 HETATM 24 O O23 4UR . . . H 2 -10.164 13.005 -0.657 0.48 43.84 ? O23 4UR 101 B 1 HETATM 25 P P24 4UR . . . H 2 -10.961 12.957 0.725 0.48 41.35 ? P24 4UR 101 B 1 HETATM 26 O O25 4UR . . . H 2 -11.362 11.537 0.946 0.48 39.94 ? O25 4UR 101 B 1 HETATM 27 O O26 4UR . . . H 2 -12.022 14.005 0.678 0.48 41.03 ? O26 4UR 101 B 1 HETATM 28 O O27 4UR . . . H 2 -9.746 13.412 1.672 0.48 40.19 ? O27 4UR 101 B 1 HETATM 29 C C29 4UR . . . H 2 -10.298 15.22 3.143 0.48 44.22 ? C29 4UR 101 B 1 HETATM 30 O O30 4UR . . . H 2 -10.306 14.107 4.022 0.48 39.44 ? O30 4UR 101 B 1 HETATM 31 O O31 4UR . . . H 2 -9.956 15.128 -3.59 0.48 40.16 ? O31 4UR 101 B 1 HETATM 32 C C32 4UR . . . H 2 -9.139 16.27 -3.357 0.48 43.15 ? C32 4UR 101 B 1 HETATM 33 N N33 4UR . . . H 2 -9.986 17.455 -3.246 0.48 45.71 ? N33 4UR 101 B 1 HETATM 34 C C34 4UR . . . H 2 -10.672 17.869 -2.136 0.48 47.94 ? C34 4UR 101 B 1 HETATM 35 N N35 4UR . . . H 2 -11.338 18.985 -2.314 0.48 49.19 ? N35 4UR 101 B 1 HETATM 36 C C36 4UR . . . H 2 -11.062 19.335 -3.628 0.48 51.14 ? C36 4UR 101 B 1 HETATM 37 C C37 4UR . . . H 2 -11.473 20.425 -4.421 0.48 54 ? C37 4UR 101 B 1 HETATM 38 N N38 4UR . . . H 2 -12.276 21.398 -3.988 0.48 55.12 ? N38 4UR 101 B 1 HETATM 39 N N39 4UR . . . H 2 -11.017 20.475 -5.696 0.48 51.51 ? N39 4UR 101 B 1 HETATM 40 C C40 4UR . . . H 2 -10.212 19.498 -6.128 0.48 49.16 ? C40 4UR 101 B 1 HETATM 41 N N41 4UR . . . H 2 -9.763 18.431 -5.475 0.48 48.23 ? N41 4UR 101 B 1 HETATM 42 C C42 4UR . . . H 2 -10.225 18.403 -4.213 0.48 48.64 ? C42 4UR 101 B 1 HETATM 43 C C43 4UR . . . H 2 -11.916 20.602 3.903 0.48 54.8 ? C43 4UR 101 B 1 HETATM 44 O O44 4UR . . . H 2 -12.259 21.686 3.414 0.48 56.28 ? O44 4UR 101 B 1 HETATM 45 N N45 4UR . . . H 2 -12.373 20.23 5.167 0.48 52.72 ? N45 4UR 101 B 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 552 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 45 #