data_3VYK # _model_server_result.job_id OMj66Agd3a3thvF5JQT41A _model_server_result.datetime_utc '2024-12-22 05:59:47' _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 3vyk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1009}' # _entry.id 3VYK # _exptl.entry_id 3VYK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 96.063 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SULFATE ION' _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 90 _cell.angle_gamma 120 _cell.entry_id 3VYK _cell.length_a 76.341 _cell.length_b 76.341 _cell.length_c 50.556 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VYK _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 _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 D N N ? 4 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 MAN MMA C1 O1 . O3 HO3 . sing 2 ? 2 3 2 NAG MAN C1 O1 . O2 HO2 . sing 3 ? 2 4 1 MAN MMA C1 O1 . O6 HO6 . sing 4 ? 2 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 2 6 1 NAG MMA C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B MMA 1 B 1 MMA A 1001 OMM 2 n B MAN 2 B 2 MAN A 1002 MAN 2 n B NAG 3 B 3 NAG A 1003 NAG 2 n B MAN 4 B 4 MAN A 1004 MAN 2 n B NAG 5 B 5 NAG A 1005 NAG 2 n B NAG 6 B 6 NAG A 1006 NAG # 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 disulf ? disulf1 A SG CYS 3 A CYS 107 1_555 A SG CYS 14 A CYS 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 32 A CYS 136 1_555 A SG CYS 125 A CYS 229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf3 A SG CYS 100 A CYS 204 1_555 A SG CYS 117 A CYS 221 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 B O3 MMA . B MMA 1 1_555 B C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B O6 MMA . B MMA 1 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 B O4 MMA . B MMA 1 1_555 B C1 NAG . B NAG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale4 B O2 MAN . B MAN 2 1_555 B C1 NAG . B NAG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale5 B O2 MAN . B MAN 4 1_555 B C1 NAG . B NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? metalc ? metalc1 A OE1 GLU 92 A GLU 196 1_555 C CA CA . A CA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc2 A OD1 ASN 94 A ASN 198 1_555 C CA CA . A CA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? metalc ? metalc3 A OE1 GLU 98 A GLU 202 1_555 C CA CA . A CA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc4 A OD1 ASN 113 A ASN 217 1_555 C CA CA . A CA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc5 A OD1 ASP 114 A ASP 218 1_555 C CA CA . A CA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc6 A O ASP 114 A ASP 218 1_555 C CA CA . A CA 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc7 C CA CA . A CA 1007 1_555 B O3 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc8 C CA CA . A CA 1007 1_555 B O4 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? # _chem_comp.formula 'O4 S -2' _chem_comp.formula_weight 96.063 _chem_comp.id SO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'SULFATE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 S O1 SO4 doub 380 n n S O2 SO4 doub 381 n n S O3 SO4 sing 382 n n S O4 SO4 sing 383 n n # _atom_sites.entry_id 3VYK _atom_sites.fract_transf_matrix[1][1] 0.013099 _atom_sites.fract_transf_matrix[1][2] 0.007563 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015126 _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] 0.01978 _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 3 CA A 1 1007 2001 CA CA . D 4 SO4 A 1 1008 1 SO4 SO4 . E 4 SO4 A 1 1009 2 SO4 SO4 . F 5 EDO A 1 1010 3 EDO EDO . G 6 HOH A 1 1101 1 HOH HOH . G 6 HOH A 2 1102 2 HOH HOH . G 6 HOH A 3 1103 3 HOH HOH . G 6 HOH A 4 1104 4 HOH HOH . G 6 HOH A 5 1105 5 HOH HOH . G 6 HOH A 6 1106 6 HOH HOH . G 6 HOH A 7 1107 7 HOH HOH . G 6 HOH A 8 1108 8 HOH HOH . G 6 HOH A 9 1109 9 HOH HOH . G 6 HOH A 10 1110 10 HOH HOH . G 6 HOH A 11 1111 11 HOH HOH . G 6 HOH A 12 1112 12 HOH HOH . G 6 HOH A 13 1113 13 HOH HOH . G 6 HOH A 14 1114 14 HOH HOH . G 6 HOH A 15 1115 15 HOH HOH . G 6 HOH A 16 1116 16 HOH HOH . G 6 HOH A 17 1117 17 HOH HOH . G 6 HOH A 18 1118 18 HOH HOH . G 6 HOH A 19 1119 19 HOH HOH . G 6 HOH A 20 1120 20 HOH HOH . G 6 HOH A 21 1121 21 HOH HOH . G 6 HOH A 22 1122 22 HOH HOH . G 6 HOH A 23 1123 23 HOH HOH . G 6 HOH A 24 1124 24 HOH HOH . G 6 HOH A 25 1125 25 HOH HOH . G 6 HOH A 26 1126 26 HOH HOH . G 6 HOH A 27 1127 27 HOH HOH . G 6 HOH A 28 1128 28 HOH HOH . G 6 HOH A 29 1129 29 HOH HOH . G 6 HOH A 30 1130 30 HOH HOH . G 6 HOH A 31 1131 31 HOH HOH . G 6 HOH A 32 1132 32 HOH HOH . G 6 HOH A 33 1133 33 HOH HOH . G 6 HOH A 34 1134 34 HOH HOH . G 6 HOH A 35 1135 35 HOH HOH . G 6 HOH A 36 1136 36 HOH HOH . G 6 HOH A 37 1137 37 HOH HOH . G 6 HOH A 38 1138 38 HOH HOH . G 6 HOH A 39 1139 39 HOH HOH . G 6 HOH A 40 1140 40 HOH HOH . G 6 HOH A 41 1141 41 HOH HOH . G 6 HOH A 42 1142 42 HOH HOH . G 6 HOH A 43 1143 43 HOH HOH . G 6 HOH A 44 1144 44 HOH HOH . G 6 HOH A 45 1145 45 HOH HOH . G 6 HOH A 46 1146 46 HOH HOH . G 6 HOH A 47 1147 47 HOH HOH . G 6 HOH A 48 1148 48 HOH HOH . G 6 HOH A 49 1149 49 HOH HOH . G 6 HOH A 50 1150 50 HOH HOH . G 6 HOH A 51 1151 51 HOH HOH . G 6 HOH A 52 1152 52 HOH HOH . G 6 HOH A 53 1153 53 HOH HOH . G 6 HOH A 54 1154 54 HOH HOH . G 6 HOH A 55 1155 55 HOH HOH . G 6 HOH A 56 1156 56 HOH HOH . G 6 HOH A 57 1157 57 HOH HOH . G 6 HOH A 58 1158 58 HOH HOH . G 6 HOH A 59 1159 59 HOH HOH . G 6 HOH A 60 1160 60 HOH HOH . G 6 HOH A 61 1161 61 HOH HOH . G 6 HOH A 62 1162 62 HOH HOH . G 6 HOH A 63 1163 63 HOH HOH . G 6 HOH A 64 1164 64 HOH HOH . G 6 HOH A 65 1165 65 HOH HOH . G 6 HOH A 66 1166 66 HOH HOH . G 6 HOH A 67 1167 67 HOH HOH . G 6 HOH A 68 1168 68 HOH HOH . G 6 HOH A 69 1169 69 HOH HOH . G 6 HOH A 70 1170 70 HOH HOH . G 6 HOH A 71 1171 71 HOH HOH . G 6 HOH A 72 1172 72 HOH HOH . G 6 HOH A 73 1173 73 HOH HOH . G 6 HOH A 74 1174 74 HOH HOH . G 6 HOH A 75 1175 75 HOH HOH . G 6 HOH A 76 1176 76 HOH HOH . G 6 HOH A 77 1177 77 HOH HOH . G 6 HOH A 78 1178 78 HOH HOH . G 6 HOH A 79 1179 79 HOH HOH . G 6 HOH A 80 1180 80 HOH HOH . G 6 HOH A 81 1181 81 HOH HOH . G 6 HOH A 82 1182 82 HOH HOH . G 6 HOH A 83 1183 83 HOH HOH . G 6 HOH A 84 1184 84 HOH HOH . G 6 HOH A 85 1185 85 HOH HOH . G 6 HOH A 86 1186 86 HOH HOH . G 6 HOH A 87 1187 87 HOH HOH . G 6 HOH A 88 1188 88 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 S S SO4 . . . E 4 -21.171 -17.648 7.697 1 42.77 ? S SO4 1009 A 1 HETATM 2 O O1 SO4 . . . E 4 -20.348 -18.342 6.681 1 41.58 ? O1 SO4 1009 A 1 HETATM 3 O O2 SO4 . . . E 4 -21.16 -16.196 7.407 1 41.62 ? O2 SO4 1009 A 1 HETATM 4 O O3 SO4 . . . E 4 -20.615 -17.881 9.051 1 44.27 ? O3 SO4 1009 A 1 HETATM 5 O O4 SO4 . . . E 4 -22.568 -18.136 7.634 1 44.85 ? O4 SO4 1009 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 5 #