data_1YV5
#
_model_server_result.job_id            VLnkZtkXJ_ondyHIaX_0_Q 
_model_server_result.datetime_utc      '2024-11-05 08:05:52' 
_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          1yv5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":901}' 
#
_entry.id    1YV5 
#
_exptl.entry_id    1YV5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              283.112 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID' 
_entity.pdbx_number_of_molecules    1 
_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            1YV5 
_cell.length_a            110.946 
_cell.length_b            110.946 
_cell.length_c            70.264 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YV5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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    1,2 
#
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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             G 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 124 A ASP 117 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc2 A OD2 ASP 124 A ASP 117 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? 
metalc ? metalc3 A OD1 ASP 124 A ASP 117 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc4 A OD2 ASP 128 A ASP 121 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? 
metalc ? metalc5 A OD2 ASP 128 A ASP 121 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc6 A OD2 ASP 264 A ASP 257 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc7 G O15 RIS . A RIS 901 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc8 G O12 RIS . A RIS 901 1_555 B MG MG . A MG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc9 G O16 RIS . A RIS 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc10 G O11 RIS . A RIS 901 1_555 C MG MG . A MG 908 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc11 G O15 RIS . A RIS 901 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc12 B MG MG . A MG 907 1_555 D MG MG . A MG 909 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc13 B MG MG . A MG 907 1_555 H O HOH . A HOH 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? 
metalc ? metalc14 B MG MG . A MG 907 1_555 H O HOH . A HOH 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc15 C MG MG . A MG 908 1_555 H O HOH . A HOH 1045 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc16 C MG MG . A MG 908 1_555 H O HOH . A HOH 1046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc17 C MG MG . A MG 908 1_555 H O HOH . A HOH 1080 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc18 D MG MG . A MG 909 1_555 H O HOH . A HOH 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc19 D MG MG . A MG 909 1_555 H O HOH . A HOH 1034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc20 D MG MG . A MG 909 1_555 H O HOH . A HOH 1049 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
#
_chem_comp.formula           'C7 H11 N O7 P2' 
_chem_comp.formula_weight    283.112 
_chem_comp.id                RIS 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Risedronate 
#
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
O12 P9 RIS sing 281 n n 
O12 H12 RIS sing 282 n n 
P9 O11 RIS doub 283 n n 
P9 O10 RIS sing 284 n n 
P9 C8 RIS sing 285 n n 
C8 O13 RIS sing 286 n n 
C8 P14 RIS sing 287 n n 
C8 C7 RIS sing 288 n n 
O13 H13 RIS sing 289 n n 
P14 O16 RIS sing 290 n n 
P14 O15 RIS sing 291 n n 
P14 O17 RIS doub 292 n n 
O16 H16 RIS sing 293 n n 
O15 H15 RIS sing 294 n n 
C7 C2 RIS sing 295 n n 
C7 HC71 RIS sing 296 n n 
C7 HC72 RIS sing 297 n n 
C2 C1 RIS doub 298 n y 
C2 C3 RIS sing 299 n y 
C1 C6 RIS sing 300 n y 
C1 HC1 RIS sing 301 n n 
C6 C5 RIS doub 302 n y 
C6 HC6 RIS sing 303 n n 
C5 N4 RIS sing 304 n y 
C5 HC5 RIS sing 305 n n 
N4 C3 RIS doub 306 n y 
C3 HC3 RIS sing 307 n n 
HO1 O10 RIS sing 308 n n 
#
_atom_sites.entry_id                     1YV5 
_atom_sites.fract_transf_matrix[1][1]    0.009013 
_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]    0.009013 
_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]    0.014232 
_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
B 2 MG A 1 907 907 MG MG . 
C 2 MG A 1 908 908 MG MG . 
D 2 MG A 1 909 909 MG MG . 
E 3 PO4 A 1 1001 1 PO4 PO4 . 
F 3 PO4 A 1 1002 2 PO4 PO4 . 
G 4 RIS A 1 901 901 RIS RIS . 
H 5 HOH A 1 1003 1 HOH HOH . 
H 5 HOH A 2 1004 2 HOH HOH . 
H 5 HOH A 3 1005 4 HOH HOH . 
H 5 HOH A 4 1006 6 HOH HOH . 
H 5 HOH A 5 1007 7 HOH HOH . 
H 5 HOH A 6 1008 9 HOH HOH . 
H 5 HOH A 7 1009 11 HOH HOH . 
H 5 HOH A 8 1010 13 HOH HOH . 
H 5 HOH A 9 1011 14 HOH HOH . 
H 5 HOH A 10 1012 15 HOH HOH . 
H 5 HOH A 11 1013 16 HOH HOH . 
H 5 HOH A 12 1014 17 HOH HOH . 
H 5 HOH A 13 1015 19 HOH HOH . 
H 5 HOH A 14 1016 21 HOH HOH . 
H 5 HOH A 15 1017 22 HOH HOH . 
H 5 HOH A 16 1018 23 HOH HOH . 
H 5 HOH A 17 1019 24 HOH HOH . 
H 5 HOH A 18 1020 25 HOH HOH . 
H 5 HOH A 19 1021 26 HOH HOH . 
H 5 HOH A 20 1022 27 HOH HOH . 
H 5 HOH A 21 1023 28 HOH HOH . 
H 5 HOH A 22 1024 29 HOH HOH . 
H 5 HOH A 23 1025 30 HOH HOH . 
H 5 HOH A 24 1026 32 HOH HOH . 
H 5 HOH A 25 1027 33 HOH HOH . 
H 5 HOH A 26 1028 34 HOH HOH . 
H 5 HOH A 27 1029 35 HOH HOH . 
H 5 HOH A 28 1030 36 HOH HOH . 
H 5 HOH A 29 1031 38 HOH HOH . 
H 5 HOH A 30 1032 39 HOH HOH . 
H 5 HOH A 31 1033 40 HOH HOH . 
H 5 HOH A 32 1034 41 HOH HOH . 
H 5 HOH A 33 1035 42 HOH HOH . 
H 5 HOH A 34 1036 43 HOH HOH . 
H 5 HOH A 35 1037 44 HOH HOH . 
H 5 HOH A 36 1038 45 HOH HOH . 
H 5 HOH A 37 1039 46 HOH HOH . 
H 5 HOH A 38 1040 47 HOH HOH . 
H 5 HOH A 39 1041 48 HOH HOH . 
H 5 HOH A 40 1042 49 HOH HOH . 
H 5 HOH A 41 1043 51 HOH HOH . 
H 5 HOH A 42 1044 53 HOH HOH . 
H 5 HOH A 43 1045 54 HOH HOH . 
H 5 HOH A 44 1046 55 HOH HOH . 
H 5 HOH A 45 1047 56 HOH HOH . 
H 5 HOH A 46 1048 59 HOH HOH . 
H 5 HOH A 47 1049 60 HOH HOH . 
H 5 HOH A 48 1050 61 HOH HOH . 
H 5 HOH A 49 1051 63 HOH HOH . 
H 5 HOH A 50 1052 64 HOH HOH . 
H 5 HOH A 51 1053 66 HOH HOH . 
H 5 HOH A 52 1054 67 HOH HOH . 
H 5 HOH A 53 1055 68 HOH HOH . 
H 5 HOH A 54 1056 69 HOH HOH . 
H 5 HOH A 55 1057 70 HOH HOH . 
H 5 HOH A 56 1058 71 HOH HOH . 
H 5 HOH A 57 1059 72 HOH HOH . 
H 5 HOH A 58 1060 73 HOH HOH . 
H 5 HOH A 59 1061 75 HOH HOH . 
H 5 HOH A 60 1062 76 HOH HOH . 
H 5 HOH A 61 1063 78 HOH HOH . 
H 5 HOH A 62 1064 80 HOH HOH . 
H 5 HOH A 63 1065 81 HOH HOH . 
H 5 HOH A 64 1066 82 HOH HOH . 
H 5 HOH A 65 1067 84 HOH HOH . 
H 5 HOH A 66 1068 85 HOH HOH . 
H 5 HOH A 67 1069 86 HOH HOH . 
H 5 HOH A 68 1070 87 HOH HOH . 
H 5 HOH A 69 1071 88 HOH HOH . 
H 5 HOH A 70 1072 89 HOH HOH . 
H 5 HOH A 71 1073 91 HOH HOH . 
H 5 HOH A 72 1074 92 HOH HOH . 
H 5 HOH A 73 1075 93 HOH HOH . 
H 5 HOH A 74 1076 95 HOH HOH . 
H 5 HOH A 75 1077 97 HOH HOH . 
H 5 HOH A 76 1078 98 HOH HOH . 
H 5 HOH A 77 1079 99 HOH HOH . 
H 5 HOH A 78 1080 100 HOH HOH . 
H 5 HOH A 79 1081 101 HOH HOH . 
H 5 HOH A 80 1082 103 HOH HOH . 
H 5 HOH A 81 1083 104 HOH HOH . 
H 5 HOH A 82 1084 105 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 O O12 RIS . . . G 4 16.929 35.805 -6.922 1 12.7 ? O12 RIS 901 A 1 
HETATM 2 P P9 RIS . . . G 4 15.496 35.801 -7.494 1 15.7 ? P9 RIS 901 A 1 
HETATM 3 O O11 RIS . . . G 4 15.215 36.987 -8.331 1 11.89 ? O11 RIS 901 A 1 
HETATM 4 O O10 RIS . . . G 4 14.544 35.764 -6.318 1 12.63 ? O10 RIS 901 A 1 
HETATM 5 C C8 RIS . . . G 4 15.21 34.3 -8.499 1 12.31 ? C8 RIS 901 A 1 
HETATM 6 O O13 RIS . . . G 4 13.898 34.372 -9.059 1 15.74 ? O13 RIS 901 A 1 
HETATM 7 P P14 RIS . . . G 4 16.442 34.167 -9.835 1 16.49 ? P14 RIS 901 A 1 
HETATM 8 O O16 RIS . . . G 4 16.471 35.438 -10.67 1 12.18 ? O16 RIS 901 A 1 
HETATM 9 O O15 RIS . . . G 4 17.641 34.105 -8.984 1 11.39 ? O15 RIS 901 A 1 
HETATM 10 O O17 RIS . . . G 4 16.399 32.964 -10.729 1 12.74 ? O17 RIS 901 A 1 
HETATM 11 C C7 RIS . . . G 4 15.228 33.176 -7.469 1 14.54 ? C7 RIS 901 A 1 
HETATM 12 C C2 RIS . . . G 4 15.083 31.753 -7.968 1 20.46 ? C2 RIS 901 A 1 
HETATM 13 C C1 RIS . . . G 4 15.697 30.773 -7.192 1 14.89 ? C1 RIS 901 A 1 
HETATM 14 C C6 RIS . . . G 4 15.621 29.442 -7.559 1 17.7 ? C6 RIS 901 A 1 
HETATM 15 C C5 RIS . . . G 4 14.893 29.113 -8.695 1 12.2 ? C5 RIS 901 A 1 
HETATM 16 N N4 RIS . . . G 4 14.274 30.058 -9.417 1 19.77 ? N4 RIS 901 A 1 
HETATM 17 C C3 RIS . . . G 4 14.351 31.369 -9.095 1 18.04 ? C3 RIS 901 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           17 
#