data_1VFU # _model_server_result.job_id Y5Kqd6zNMUgL-LBUbmi5PQ _model_server_result.datetime_utc '2024-10-16 10:29:17' _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 1vfu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1001}' # _entry.id 1VFU # _exptl.entry_id 1VFU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM 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 90 _cell.entry_id 1VFU _cell.length_a 113.454 _cell.length_b 118.496 _cell.length_c 114.08 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VFU _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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,E,G 1 1 B,D,F,H 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 ? 3 E N N ? 3 F 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 1 8 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 2 1 GLC GLC C1 O1 . O4 HO4 . sing 3 ? 2 3 2 GLC GLC C1 O1 . O4 HO4 . sing 4 ? 2 4 3 GLC GLC C1 O1 . O4 HO4 . sing 5 ? 2 5 4 GLC GLC C1 O1 . O4 HO4 . sing 6 ? 2 6 5 GLC GLC C1 O1 . O4 HO4 . sing 7 ? 2 7 6 GLC GLC C1 O1 . O4 HO4 . sing 8 ? 2 8 7 GLC GLC 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 C GLC 1 C 1 GLC ? 801 GLC 2 n C GLC 2 C 2 GLC ? 808 GLC 2 n C GLC 3 C 3 GLC ? 807 GLC 2 n C GLC 4 C 4 GLC ? 806 GLC 2 n C GLC 5 C 5 GLC ? 805 GLC 2 n C GLC 6 C 6 GLC ? 804 GLC 2 n C GLC 7 C 7 GLC ? 803 GLC 2 n C GLC 8 C 8 GLC ? 802 GLC 2 n D GLC 1 D 1 GLC ? 901 GLC 2 n D GLC 2 D 2 GLC ? 908 GLC 2 n D GLC 3 D 3 GLC ? 907 GLC 2 n D GLC 4 D 4 GLC ? 906 GLC 2 n D GLC 5 D 5 GLC ? 905 GLC 2 n D GLC 6 D 6 GLC ? 904 GLC 2 n D GLC 7 D 7 GLC ? 903 GLC 2 n D GLC 8 D 8 GLC ? 902 GLC # 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 covale ? covale1 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale2 C C1 GLC . C GLC 1 1_555 C O4 GLC . C GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale3 C O4 GLC . C GLC 2 1_555 C C1 GLC . C GLC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale4 C O4 GLC . C GLC 3 1_555 C C1 GLC . C GLC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale5 C O4 GLC . C GLC 4 1_555 C C1 GLC . C GLC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale6 C O4 GLC . C GLC 5 1_555 C C1 GLC . C GLC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale7 C O4 GLC . C GLC 6 1_555 C C1 GLC . C GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale8 C O4 GLC . C GLC 7 1_555 C C1 GLC . C GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.395 ? covale ? covale9 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? covale ? covale10 D C1 GLC . D GLC 1 1_555 D O4 GLC . D GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? covale ? covale11 D O4 GLC . D GLC 2 1_555 D C1 GLC . D GLC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale12 D O4 GLC . D GLC 3 1_555 D C1 GLC . D GLC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale13 D O4 GLC . D GLC 4 1_555 D C1 GLC . D GLC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale14 D O4 GLC . D GLC 5 1_555 D C1 GLC . D GLC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.406 ? covale ? covale15 D O4 GLC . D GLC 6 1_555 D C1 GLC . D GLC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale16 D O4 GLC . D GLC 7 1_555 D C1 GLC . D GLC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? metalc ? metalc1 A OD1 ASN 143 A ASN 143 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? metalc ? metalc2 A ND2 ASN 143 A ASN 143 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.154 ? metalc ? metalc3 A O ASP 145 A ASP 145 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.83 ? metalc ? metalc4 A OD1 ASN 148 A ASN 148 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc5 A ND2 ASN 148 A ASN 148 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.283 ? metalc ? metalc6 A OD2 ASP 149 A ASP 149 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc7 A O GLY 169 A GLY 169 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc8 A OD2 ASP 171 A ASP 171 1_555 E CA CA . A CA 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc9 B OD1 ASN 143 B ASN 143 1_555 F CA CA . B CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.545 ? metalc ? metalc10 B ND2 ASN 143 B ASN 143 1_555 F CA CA . B CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc11 B O ASP 145 B ASP 145 1_555 F CA CA . B CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.204 ? metalc ? metalc12 B OD1 ASN 148 B ASN 148 1_555 F CA CA . B CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc13 B OD1 ASP 149 B ASP 149 1_555 F CA CA . B CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.104 ? metalc ? metalc14 B O GLY 169 B GLY 169 1_555 F CA CA . B CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc15 B OD1 ASP 171 B ASP 171 1_555 F CA CA . B CA 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.214 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1VFU _atom_sites.fract_transf_matrix[1][1] 0.008814 _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] 0.008439 _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] 0.008766 _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 E 3 CA A 1 1001 1 CA CA2 . F 3 CA B 1 1002 2 CA CA2 . G 4 HOH A 1 1002 1 HOH HOH . G 4 HOH A 2 1003 2 HOH HOH . G 4 HOH A 3 1004 3 HOH HOH . G 4 HOH A 4 1005 5 HOH HOH . G 4 HOH A 5 1006 6 HOH HOH . G 4 HOH A 6 1007 7 HOH HOH . G 4 HOH A 7 1008 10 HOH HOH . G 4 HOH A 8 1009 11 HOH HOH . G 4 HOH A 9 1010 13 HOH HOH . G 4 HOH A 10 1011 14 HOH HOH . G 4 HOH A 11 1012 16 HOH HOH . G 4 HOH A 12 1013 18 HOH HOH . G 4 HOH A 13 1014 19 HOH HOH . G 4 HOH A 14 1015 20 HOH HOH . G 4 HOH A 15 1016 21 HOH HOH . G 4 HOH A 16 1017 22 HOH HOH . G 4 HOH A 17 1018 25 HOH HOH . G 4 HOH A 18 1019 26 HOH HOH . G 4 HOH A 19 1020 28 HOH HOH . G 4 HOH A 20 1021 35 HOH HOH . G 4 HOH A 21 1022 36 HOH HOH . G 4 HOH A 22 1023 38 HOH HOH . G 4 HOH A 23 1024 40 HOH HOH . G 4 HOH A 24 1025 42 HOH HOH . G 4 HOH A 25 1026 46 HOH HOH . G 4 HOH A 26 1027 47 HOH HOH . G 4 HOH A 27 1028 48 HOH HOH . G 4 HOH A 28 1029 49 HOH HOH . G 4 HOH A 29 1030 53 HOH HOH . G 4 HOH A 30 1031 57 HOH HOH . G 4 HOH A 31 1032 65 HOH HOH . G 4 HOH A 32 1033 66 HOH HOH . G 4 HOH A 33 1034 69 HOH HOH . G 4 HOH A 34 1035 70 HOH HOH . G 4 HOH A 35 1036 77 HOH HOH . G 4 HOH A 36 1037 78 HOH HOH . G 4 HOH A 37 1038 79 HOH HOH . G 4 HOH A 38 1039 84 HOH HOH . G 4 HOH A 39 1040 85 HOH HOH . G 4 HOH A 40 1041 89 HOH HOH . G 4 HOH A 41 1042 93 HOH HOH . G 4 HOH A 42 1043 94 HOH HOH . G 4 HOH A 43 1044 95 HOH HOH . G 4 HOH A 44 1045 98 HOH HOH . G 4 HOH A 45 1046 102 HOH HOH . G 4 HOH A 46 1047 103 HOH HOH . G 4 HOH A 47 1048 105 HOH HOH . G 4 HOH A 48 1049 110 HOH HOH . G 4 HOH A 49 1050 111 HOH HOH . G 4 HOH A 50 1051 113 HOH HOH . G 4 HOH A 51 1052 114 HOH HOH . G 4 HOH A 52 1053 116 HOH HOH . G 4 HOH A 53 1054 117 HOH HOH . G 4 HOH A 54 1055 119 HOH HOH . G 4 HOH A 55 1056 122 HOH HOH . G 4 HOH A 56 1057 126 HOH HOH . G 4 HOH A 57 1058 127 HOH HOH . G 4 HOH A 58 1059 128 HOH HOH . G 4 HOH A 59 1060 129 HOH HOH . G 4 HOH A 60 1061 131 HOH HOH . H 4 HOH B 1 1003 4 HOH HOH . H 4 HOH B 2 1004 8 HOH HOH . H 4 HOH B 3 1005 9 HOH HOH . H 4 HOH B 4 1006 12 HOH HOH . H 4 HOH B 5 1007 15 HOH HOH . H 4 HOH B 6 1008 17 HOH HOH . H 4 HOH B 7 1009 23 HOH HOH . H 4 HOH B 8 1010 24 HOH HOH . H 4 HOH B 9 1011 27 HOH HOH . H 4 HOH B 10 1012 29 HOH HOH . H 4 HOH B 11 1013 30 HOH HOH . H 4 HOH B 12 1014 31 HOH HOH . H 4 HOH B 13 1015 32 HOH HOH . H 4 HOH B 14 1016 33 HOH HOH . H 4 HOH B 15 1017 34 HOH HOH . H 4 HOH B 16 1018 37 HOH HOH . H 4 HOH B 17 1019 39 HOH HOH . H 4 HOH B 18 1020 41 HOH HOH . H 4 HOH B 19 1021 43 HOH HOH . H 4 HOH B 20 1022 44 HOH HOH . H 4 HOH B 21 1023 45 HOH HOH . H 4 HOH B 22 1024 50 HOH HOH . H 4 HOH B 23 1025 51 HOH HOH . H 4 HOH B 24 1026 52 HOH HOH . H 4 HOH B 25 1027 54 HOH HOH . H 4 HOH B 26 1028 55 HOH HOH . H 4 HOH B 27 1029 56 HOH HOH . H 4 HOH B 28 1030 58 HOH HOH . H 4 HOH B 29 1031 59 HOH HOH . H 4 HOH B 30 1032 60 HOH HOH . H 4 HOH B 31 1033 61 HOH HOH . H 4 HOH B 32 1034 62 HOH HOH . H 4 HOH B 33 1035 63 HOH HOH . H 4 HOH B 34 1036 64 HOH HOH . H 4 HOH B 35 1037 67 HOH HOH . H 4 HOH B 36 1038 68 HOH HOH . H 4 HOH B 37 1039 71 HOH HOH . H 4 HOH B 38 1040 72 HOH HOH . H 4 HOH B 39 1041 73 HOH HOH . H 4 HOH B 40 1042 74 HOH HOH . H 4 HOH B 41 1043 75 HOH HOH . H 4 HOH B 42 1044 76 HOH HOH . H 4 HOH B 43 1045 80 HOH HOH . H 4 HOH B 44 1046 81 HOH HOH . H 4 HOH B 45 1047 82 HOH HOH . H 4 HOH B 46 1048 83 HOH HOH . H 4 HOH B 47 1049 86 HOH HOH . H 4 HOH B 48 1050 87 HOH HOH . H 4 HOH B 49 1051 88 HOH HOH . H 4 HOH B 50 1052 90 HOH HOH . H 4 HOH B 51 1053 91 HOH HOH . H 4 HOH B 52 1054 92 HOH HOH . H 4 HOH B 53 1055 96 HOH HOH . H 4 HOH B 54 1056 97 HOH HOH . H 4 HOH B 55 1057 99 HOH HOH . H 4 HOH B 56 1058 100 HOH HOH . H 4 HOH B 57 1059 101 HOH HOH . H 4 HOH B 58 1060 104 HOH HOH . H 4 HOH B 59 1061 106 HOH HOH . H 4 HOH B 60 1062 107 HOH HOH . H 4 HOH B 61 1063 108 HOH HOH . H 4 HOH B 62 1064 109 HOH HOH . H 4 HOH B 63 1065 112 HOH HOH . H 4 HOH B 64 1066 115 HOH HOH . H 4 HOH B 65 1067 118 HOH HOH . H 4 HOH B 66 1068 120 HOH HOH . H 4 HOH B 67 1069 121 HOH HOH . H 4 HOH B 68 1070 123 HOH HOH . H 4 HOH B 69 1071 124 HOH HOH . H 4 HOH B 70 1072 125 HOH HOH . H 4 HOH B 71 1073 130 HOH HOH . H 4 HOH B 72 1074 132 HOH HOH . H 4 HOH B 73 1075 133 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 3 _atom_site.Cartn_x 24.063 _atom_site.Cartn_y 67.188 _atom_site.Cartn_z 79.483 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 32 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 1001 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 26 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #