data_1YR5
#
_model_server_result.job_id            CBVqn3MAwUQVehEJ_lJRPQ 
_model_server_result.datetime_utc      '2024-12-26 10:03:50' 
_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          1yr5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":154}' 
#
_entry.id    1YR5 
#
_exptl.entry_id    1YR5 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          111.16 
_cell.angle_gamma         90 
_cell.entry_id            1YR5 
_cell.length_a            66.07 
_cell.length_b            33.71 
_cell.length_c            75.89 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YR5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_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 
_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
? 3 C N N 
? 3 D N N 
? 3 E N N 
? 3 F 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 OD2 ASP 20 A ASP 20 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc2 A OD2 ASP 22 A ASP 22 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? 
metalc ? metalc3 A OD1 ASP 24 A ASP 24 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc4 A O THR 26 A THR 26 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc5 A OE1 GLU 31 A GLU 31 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc6 A OE2 GLU 31 A GLU 31 1_555 C CA CA . A CA 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
metalc ? metalc7 A OD1 ASP 56 A ASP 56 1_555 D CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc8 A OD1 ASP 58 A ASP 58 1_555 D CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? 
metalc ? metalc9 A OD1 ASN 60 A ASN 60 1_555 D CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc10 A O THR 62 A THR 62 1_555 D CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc11 A OE1 GLU 67 A GLU 67 1_555 D CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? 
metalc ? metalc12 A OE2 GLU 67 A GLU 67 1_555 D CA CA . A CA 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc13 A OD2 ASP 93 A ASP 93 1_555 E CA CA . A CA 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc14 A OD1 ASP 95 A ASP 95 1_555 E CA CA . A CA 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc15 A OD1 ASN 97 A ASN 97 1_555 E CA CA . A CA 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc16 A O TYR 99 A TYR 99 1_555 E CA CA . A CA 153 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc17 A O TYR 99 A TYR 99 1_555 E CA CA . A CA 153 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc18 A OE1 GLU 104 A GLU 104 1_555 E CA CA . A CA 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? 
metalc ? metalc19 A OE2 GLU 104 A GLU 104 1_555 E CA CA . A CA 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? 
metalc ? metalc20 A OD1 ASP 129 A ASP 129 1_555 F CA CA . A CA 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? 
metalc ? metalc21 A OD2 ASP 131 A ASP 131 1_555 F CA CA . A CA 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc22 A OD2 ASP 133 A ASP 133 1_555 F CA CA . A CA 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc23 A O GLN 135 A GLN 135 1_555 F CA CA . A CA 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
metalc ? metalc24 A OE1 GLU 140 A GLU 140 1_555 F CA CA . A CA 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? 
metalc ? metalc25 A OE2 GLU 140 A GLU 140 1_555 F CA CA . A CA 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc26 C CA CA . A CA 151 1_555 G O HOH . A HOH 5011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc27 D CA CA . A CA 152 1_555 G O HOH . A HOH 5012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc28 E CA CA . A CA 153 1_555 G O HOH . A HOH 5013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc29 F CA CA . A CA 154 1_555 G O HOH . A HOH 5014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
#
_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                     1YR5 
_atom_sites.fract_transf_matrix[1][1]    0.015135 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005859 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.029665 
_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]    0.01413 
_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 1 151 151 CA OC1 . 
D 3 CA A 1 152 152 CA OC1 . 
E 3 CA A 1 153 153 CA OC1 . 
F 3 CA A 1 154 154 CA OC1 . 
G 4 HOH A 1 5011 151 HOH OC1 . 
G 4 HOH A 2 5012 152 HOH OC1 . 
G 4 HOH A 3 5013 153 HOH OC1 . 
G 4 HOH A 4 5014 154 HOH OC1 . 
G 4 HOH A 5 5015 1 HOH HOH . 
G 4 HOH A 6 5016 2 HOH HOH . 
G 4 HOH A 7 5017 3 HOH HOH . 
G 4 HOH A 8 5018 4 HOH HOH . 
G 4 HOH A 9 5019 5 HOH HOH . 
G 4 HOH A 10 5020 6 HOH HOH . 
G 4 HOH A 11 5021 7 HOH HOH . 
G 4 HOH A 12 5022 8 HOH HOH . 
G 4 HOH A 13 5023 9 HOH HOH . 
G 4 HOH A 14 5024 10 HOH HOH . 
G 4 HOH A 15 5025 11 HOH HOH . 
G 4 HOH A 16 5026 12 HOH HOH . 
G 4 HOH A 17 5027 13 HOH HOH . 
G 4 HOH A 18 5028 14 HOH HOH . 
G 4 HOH A 19 5029 15 HOH HOH . 
G 4 HOH A 20 5030 16 HOH HOH . 
G 4 HOH A 21 5031 18 HOH HOH . 
G 4 HOH A 22 5032 19 HOH HOH . 
G 4 HOH A 23 5033 20 HOH HOH . 
G 4 HOH A 24 5034 21 HOH HOH . 
G 4 HOH A 25 5035 22 HOH HOH . 
G 4 HOH A 26 5036 23 HOH HOH . 
G 4 HOH A 27 5037 24 HOH HOH . 
G 4 HOH A 28 5038 25 HOH HOH . 
G 4 HOH A 29 5039 26 HOH HOH . 
G 4 HOH A 30 5040 27 HOH HOH . 
G 4 HOH A 31 5041 28 HOH HOH . 
G 4 HOH A 32 5042 29 HOH HOH . 
G 4 HOH A 33 5043 30 HOH HOH . 
G 4 HOH A 34 5044 31 HOH HOH . 
G 4 HOH A 35 5045 32 HOH HOH . 
G 4 HOH A 36 5046 34 HOH HOH . 
G 4 HOH A 37 5047 36 HOH HOH . 
G 4 HOH A 38 5048 37 HOH HOH . 
G 4 HOH A 39 5049 39 HOH HOH . 
G 4 HOH A 40 5050 40 HOH HOH . 
G 4 HOH A 41 5051 41 HOH HOH . 
G 4 HOH A 42 5052 42 HOH HOH . 
G 4 HOH A 43 5053 43 HOH HOH . 
G 4 HOH A 44 5054 44 HOH HOH . 
G 4 HOH A 45 5055 45 HOH HOH . 
G 4 HOH A 46 5056 46 HOH HOH . 
G 4 HOH A 47 5057 48 HOH HOH . 
G 4 HOH A 48 5058 49 HOH HOH . 
G 4 HOH A 49 5059 50 HOH HOH . 
G 4 HOH A 50 5060 51 HOH HOH . 
G 4 HOH A 51 5061 52 HOH HOH . 
G 4 HOH A 52 5062 53 HOH HOH . 
G 4 HOH A 53 5063 54 HOH HOH . 
G 4 HOH A 54 5064 55 HOH HOH . 
G 4 HOH A 55 5065 57 HOH HOH . 
G 4 HOH A 56 5066 59 HOH HOH . 
G 4 HOH A 57 5067 61 HOH HOH . 
G 4 HOH A 58 5068 62 HOH HOH . 
G 4 HOH A 59 5069 63 HOH HOH . 
G 4 HOH A 60 5070 64 HOH HOH . 
G 4 HOH A 61 5071 65 HOH HOH . 
G 4 HOH A 62 5072 66 HOH HOH . 
G 4 HOH A 63 5073 68 HOH HOH . 
G 4 HOH A 64 5074 69 HOH HOH . 
G 4 HOH A 65 5075 70 HOH HOH . 
G 4 HOH A 66 5076 72 HOH HOH . 
G 4 HOH A 67 5077 73 HOH HOH . 
G 4 HOH A 68 5078 74 HOH HOH . 
G 4 HOH A 69 5079 76 HOH HOH . 
G 4 HOH A 70 5080 77 HOH HOH . 
G 4 HOH A 71 5081 78 HOH HOH . 
G 4 HOH A 72 5082 79 HOH HOH . 
G 4 HOH A 73 5083 80 HOH HOH . 
G 4 HOH A 74 5084 81 HOH HOH . 
G 4 HOH A 75 5085 82 HOH HOH . 
G 4 HOH A 76 5086 83 HOH HOH . 
G 4 HOH A 77 5087 84 HOH HOH . 
G 4 HOH A 78 5088 86 HOH HOH . 
G 4 HOH A 79 5089 88 HOH HOH . 
G 4 HOH A 80 5090 89 HOH HOH . 
G 4 HOH A 81 5091 90 HOH HOH . 
G 4 HOH A 82 5092 91 HOH HOH . 
G 4 HOH A 83 5093 92 HOH HOH . 
G 4 HOH A 84 5094 93 HOH HOH . 
G 4 HOH A 85 5095 94 HOH HOH . 
G 4 HOH A 86 5096 95 HOH HOH . 
G 4 HOH A 87 5097 96 HOH HOH . 
G 4 HOH A 88 5098 98 HOH HOH . 
G 4 HOH A 89 5099 99 HOH HOH . 
G 4 HOH A 90 5100 100 HOH HOH . 
G 4 HOH A 91 5101 101 HOH HOH . 
G 4 HOH A 92 5102 103 HOH HOH . 
G 4 HOH A 93 5103 104 HOH HOH . 
G 4 HOH A 94 5104 105 HOH HOH . 
G 4 HOH A 95 5105 107 HOH HOH . 
G 4 HOH A 96 5106 108 HOH HOH . 
G 4 HOH A 97 5107 109 HOH HOH . 
G 4 HOH A 98 5108 110 HOH HOH . 
G 4 HOH A 99 5109 113 HOH HOH . 
G 4 HOH A 100 5110 114 HOH HOH . 
G 4 HOH A 101 5111 115 HOH HOH . 
G 4 HOH A 102 5112 116 HOH HOH . 
G 4 HOH A 103 5113 117 HOH HOH . 
G 4 HOH A 104 5114 119 HOH HOH . 
G 4 HOH A 105 5115 120 HOH HOH . 
G 4 HOH A 106 5116 121 HOH HOH . 
G 4 HOH A 107 5117 122 HOH HOH . 
G 4 HOH A 108 5118 123 HOH HOH . 
G 4 HOH A 109 5119 124 HOH HOH . 
G 4 HOH A 110 5120 125 HOH HOH . 
G 4 HOH A 111 5121 128 HOH HOH . 
G 4 HOH A 112 5122 129 HOH HOH . 
G 4 HOH A 113 5123 130 HOH HOH . 
G 4 HOH A 114 5124 131 HOH HOH . 
G 4 HOH A 115 5125 132 HOH HOH . 
G 4 HOH A 116 5126 134 HOH HOH . 
G 4 HOH A 117 5127 136 HOH HOH . 
G 4 HOH A 118 5128 137 HOH HOH . 
G 4 HOH A 119 5129 138 HOH HOH . 
G 4 HOH A 120 5130 139 HOH HOH . 
G 4 HOH A 121 5131 140 HOH HOH . 
G 4 HOH A 122 5132 141 HOH HOH . 
G 4 HOH A 123 5133 142 HOH HOH . 
G 4 HOH A 124 5134 143 HOH HOH . 
G 4 HOH A 125 5135 144 HOH HOH . 
G 4 HOH A 126 5136 145 HOH HOH . 
G 4 HOH A 127 5137 146 HOH HOH . 
G 4 HOH A 128 5138 147 HOH HOH . 
G 4 HOH A 129 5139 148 HOH HOH . 
G 4 HOH A 130 5140 149 HOH HOH . 
G 4 HOH A 131 5141 150 HOH HOH . 
H 4 HOH B 1 33 33 HOH HOH . 
H 4 HOH B 2 38 38 HOH HOH . 
H 4 HOH B 3 58 58 HOH HOH . 
H 4 HOH B 4 67 67 HOH HOH . 
H 4 HOH B 5 71 71 HOH HOH . 
H 4 HOH B 6 85 85 HOH HOH . 
H 4 HOH B 7 87 87 HOH HOH . 
H 4 HOH B 8 102 102 HOH HOH . 
H 4 HOH B 9 106 106 HOH HOH . 
H 4 HOH B 10 111 111 HOH HOH . 
H 4 HOH B 11 112 112 HOH HOH . 
H 4 HOH B 12 118 118 HOH HOH . 
H 4 HOH B 13 126 126 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         F 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               16.187 
_atom_site.Cartn_y               -13.94 
_atom_site.Cartn_z               3.032 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        8.05 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           154 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           440 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#