data_8YPY
#
_model_server_result.job_id            TL0sltJjzR96iHlRaCo-IQ 
_model_server_result.datetime_utc      '2025-07-17 15:20:30' 
_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          8ypy 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1005}' 
#
_entry.id    8YPY 
#
_exptl.entry_id    8YPY 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              94.971 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHATE ION' 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          94.44 
_cell.angle_gamma         90 
_cell.entry_id            8YPY 
_cell.length_a            94.701 
_cell.length_b            73.598 
_cell.length_c            170.5 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8YPY 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA 
_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
? 5 K N N 
? 5 L N N 
? 5 M N N 
? 5 W N N 
? 5 CA 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 223 A ASP 223 1_555 I CD CD . A CD 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.677 ? 
metalc ? metalc2 B OD2 ASP 174 B ASP 174 1_555 O CD CD . B CD 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc3 C OD1 ASP 174 C ASP 174 1_555 S CD CD . C CD 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.599 ? 
metalc ? metalc4 C OD2 ASP 174 C ASP 174 1_555 S CD CD . C CD 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? 
metalc ? metalc5 D OD2 ASP 223 D ASP 223 1_555 V CD CD . D CD 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.595 ? 
metalc ? metalc6 F OD2 ASP 174 F ASP 174 1_555 BA CD CD . F CD 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? 
#
_chem_comp.formula           'O4 P -3' 
_chem_comp.formula_weight    94.971 
_chem_comp.id                PO4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHATE 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
P O1 PO4 doub 336 n n 
P O2 PO4 sing 337 n n 
P O3 PO4 sing 338 n n 
P O4 PO4 sing 339 n n 
#
_atom_sites.entry_id                     8YPY 
_atom_sites.fract_transf_matrix[1][1]    0.01056 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000819 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013587 
_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]    0.005883 
_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 APC A 1 1001 1001 APC APC . 
H 3 HSX A 1 1002 1002 HSX HSX . 
I 4 CD A 1 1003 1003 CD CD . 
J 2 APC A 1 1004 1004 APC APC . 
K 5 PO4 A 1 1005 1005 PO4 PO4 . 
L 5 PO4 A 1 1006 1006 PO4 PO4 . 
M 5 PO4 A 1 1007 1007 PO4 PO4 . 
N 3 HSX B 1 2001 2001 HSX HSX . 
O 4 CD B 1 2002 2002 CD CD . 
P 2 APC C 1 1001 1001 APC APC . 
Q 2 APC C 1 1002 1002 APC APC . 
R 3 HSX C 1 1003 1003 HSX HSX . 
S 4 CD C 1 1004 1004 CD CD . 
T 2 APC D 1 1001 1001 APC APC . 
U 3 HSX D 1 1002 1002 HSX HSX . 
V 4 CD D 1 1003 1003 CD CD . 
W 5 PO4 D 1 1004 1004 PO4 PO4 . 
X 2 APC E 1 1001 1001 APC APC . 
Y 3 HSX E 1 1002 1002 HSX HSX . 
Z 4 CD E 1 1003 1003 CD CD . 
AA 3 HSX F 1 2001 2001 HSX HSX . 
BA 4 CD F 1 2002 2002 CD CD . 
CA 5 PO4 F 1 2003 2003 PO4 PO4 . 
DA 6 HOH A 1 1101 1101 HOH HOH . 
DA 6 HOH A 2 1102 1102 HOH HOH . 
DA 6 HOH A 3 1103 1103 HOH HOH . 
DA 6 HOH A 4 1104 1104 HOH HOH . 
DA 6 HOH A 5 1105 1105 HOH HOH . 
DA 6 HOH A 6 1106 1106 HOH HOH . 
DA 6 HOH A 7 1107 1107 HOH HOH . 
DA 6 HOH A 8 1108 1108 HOH HOH . 
DA 6 HOH A 9 1109 1109 HOH HOH . 
DA 6 HOH A 10 1110 1110 HOH HOH . 
DA 6 HOH A 11 1111 1111 HOH HOH . 
DA 6 HOH A 12 1112 1112 HOH HOH . 
DA 6 HOH A 13 1113 1113 HOH HOH . 
DA 6 HOH A 14 1114 1114 HOH HOH . 
DA 6 HOH A 15 1115 1115 HOH HOH . 
DA 6 HOH A 16 1116 1116 HOH HOH . 
DA 6 HOH A 17 1117 1117 HOH HOH . 
DA 6 HOH A 18 1118 1118 HOH HOH . 
DA 6 HOH A 19 1119 1119 HOH HOH . 
DA 6 HOH A 20 1120 1120 HOH HOH . 
DA 6 HOH A 21 1121 1121 HOH HOH . 
DA 6 HOH A 22 1122 1122 HOH HOH . 
DA 6 HOH A 23 1123 1123 HOH HOH . 
DA 6 HOH A 24 1124 1124 HOH HOH . 
DA 6 HOH A 25 1125 1125 HOH HOH . 
DA 6 HOH A 26 1126 1126 HOH HOH . 
DA 6 HOH A 27 1127 1127 HOH HOH . 
DA 6 HOH A 28 1128 1128 HOH HOH . 
DA 6 HOH A 29 1129 1129 HOH HOH . 
DA 6 HOH A 30 1130 1130 HOH HOH . 
DA 6 HOH A 31 1131 1131 HOH HOH . 
DA 6 HOH A 32 1132 1132 HOH HOH . 
DA 6 HOH A 33 1133 1133 HOH HOH . 
DA 6 HOH A 34 1134 1134 HOH HOH . 
DA 6 HOH A 35 1135 1135 HOH HOH . 
DA 6 HOH A 36 1136 1136 HOH HOH . 
DA 6 HOH A 37 1137 1137 HOH HOH . 
DA 6 HOH A 38 1138 1138 HOH HOH . 
DA 6 HOH A 39 1139 1139 HOH HOH . 
DA 6 HOH A 40 1140 1140 HOH HOH . 
DA 6 HOH A 41 1141 1141 HOH HOH . 
DA 6 HOH A 42 1142 1142 HOH HOH . 
DA 6 HOH A 43 1143 1143 HOH HOH . 
DA 6 HOH A 44 1144 1144 HOH HOH . 
DA 6 HOH A 45 1145 1145 HOH HOH . 
DA 6 HOH A 46 1146 1146 HOH HOH . 
DA 6 HOH A 47 1147 1147 HOH HOH . 
DA 6 HOH A 48 1148 1148 HOH HOH . 
DA 6 HOH A 49 1149 1149 HOH HOH . 
DA 6 HOH A 50 1150 1150 HOH HOH . 
DA 6 HOH A 51 1151 1151 HOH HOH . 
DA 6 HOH A 52 1152 1152 HOH HOH . 
DA 6 HOH A 53 1153 1153 HOH HOH . 
DA 6 HOH A 54 1154 1154 HOH HOH . 
DA 6 HOH A 55 1155 1155 HOH HOH . 
DA 6 HOH A 56 1156 1156 HOH HOH . 
DA 6 HOH A 57 1157 1157 HOH HOH . 
DA 6 HOH A 58 1158 1158 HOH HOH . 
DA 6 HOH A 59 1159 1159 HOH HOH . 
DA 6 HOH A 60 1160 1160 HOH HOH . 
DA 6 HOH A 61 1161 1161 HOH HOH . 
EA 6 HOH B 1 2101 2101 HOH HOH . 
EA 6 HOH B 2 2102 2102 HOH HOH . 
EA 6 HOH B 3 2103 2103 HOH HOH . 
EA 6 HOH B 4 2104 2104 HOH HOH . 
EA 6 HOH B 5 2105 2105 HOH HOH . 
EA 6 HOH B 6 2106 2106 HOH HOH . 
EA 6 HOH B 7 2107 2107 HOH HOH . 
EA 6 HOH B 8 2108 2108 HOH HOH . 
EA 6 HOH B 9 2109 2109 HOH HOH . 
EA 6 HOH B 10 2110 2110 HOH HOH . 
EA 6 HOH B 11 2111 2111 HOH HOH . 
EA 6 HOH B 12 2112 2112 HOH HOH . 
EA 6 HOH B 13 2113 2113 HOH HOH . 
EA 6 HOH B 14 2114 2114 HOH HOH . 
EA 6 HOH B 15 2115 2115 HOH HOH . 
EA 6 HOH B 16 2116 2116 HOH HOH . 
EA 6 HOH B 17 2117 2117 HOH HOH . 
EA 6 HOH B 18 2118 2118 HOH HOH . 
EA 6 HOH B 19 2119 2119 HOH HOH . 
EA 6 HOH B 20 2120 2120 HOH HOH . 
EA 6 HOH B 21 2121 2121 HOH HOH . 
EA 6 HOH B 22 2122 2122 HOH HOH . 
EA 6 HOH B 23 2123 2123 HOH HOH . 
EA 6 HOH B 24 2124 2124 HOH HOH . 
EA 6 HOH B 25 2125 2125 HOH HOH . 
EA 6 HOH B 26 2126 2126 HOH HOH . 
EA 6 HOH B 27 2127 2127 HOH HOH . 
EA 6 HOH B 28 2128 2128 HOH HOH . 
EA 6 HOH B 29 2129 2129 HOH HOH . 
EA 6 HOH B 30 2130 2130 HOH HOH . 
EA 6 HOH B 31 2131 2131 HOH HOH . 
EA 6 HOH B 32 2132 2132 HOH HOH . 
FA 6 HOH C 1 1101 1101 HOH HOH . 
FA 6 HOH C 2 1102 1102 HOH HOH . 
FA 6 HOH C 3 1103 1103 HOH HOH . 
FA 6 HOH C 4 1104 1104 HOH HOH . 
FA 6 HOH C 5 1105 1105 HOH HOH . 
FA 6 HOH C 6 1106 1106 HOH HOH . 
GA 6 HOH D 1 1101 1101 HOH HOH . 
GA 6 HOH D 2 1102 1102 HOH HOH . 
GA 6 HOH D 3 1103 1103 HOH HOH . 
GA 6 HOH D 4 1104 1104 HOH HOH . 
GA 6 HOH D 5 1105 1105 HOH HOH . 
GA 6 HOH D 6 1106 1106 HOH HOH . 
GA 6 HOH D 7 1107 1107 HOH HOH . 
GA 6 HOH D 8 1108 1108 HOH HOH . 
HA 6 HOH E 1 1101 1101 HOH HOH . 
HA 6 HOH E 2 1102 1102 HOH HOH . 
HA 6 HOH E 3 1103 1103 HOH HOH . 
HA 6 HOH E 4 1104 1104 HOH HOH . 
HA 6 HOH E 5 1105 1105 HOH HOH . 
HA 6 HOH E 6 1106 1106 HOH HOH . 
HA 6 HOH E 7 1107 1107 HOH HOH . 
HA 6 HOH E 8 1108 1108 HOH HOH . 
HA 6 HOH E 9 1109 1109 HOH HOH . 
HA 6 HOH E 10 1110 1110 HOH HOH . 
HA 6 HOH E 11 1111 1111 HOH HOH . 
HA 6 HOH E 12 1112 1112 HOH HOH . 
HA 6 HOH E 13 1113 1113 HOH HOH . 
HA 6 HOH E 14 1114 1114 HOH HOH . 
HA 6 HOH E 15 1115 1115 HOH HOH . 
HA 6 HOH E 16 1116 1116 HOH HOH . 
HA 6 HOH E 17 1117 1117 HOH HOH . 
HA 6 HOH E 18 1118 1118 HOH HOH . 
HA 6 HOH E 19 1119 1119 HOH HOH . 
HA 6 HOH E 20 1120 1120 HOH HOH . 
HA 6 HOH E 21 1121 1121 HOH HOH . 
HA 6 HOH E 22 1122 1122 HOH HOH . 
HA 6 HOH E 23 1123 1123 HOH HOH . 
HA 6 HOH E 24 1124 1124 HOH HOH . 
HA 6 HOH E 25 1125 1125 HOH HOH . 
IA 6 HOH F 1 2101 2101 HOH HOH . 
IA 6 HOH F 2 2102 2102 HOH HOH . 
IA 6 HOH F 3 2103 2103 HOH HOH . 
IA 6 HOH F 4 2104 2104 HOH HOH . 
IA 6 HOH F 5 2105 2105 HOH HOH . 
IA 6 HOH F 6 2106 2106 HOH HOH . 
IA 6 HOH F 7 2107 2107 HOH HOH . 
IA 6 HOH F 8 2108 2108 HOH HOH . 
IA 6 HOH F 9 2109 2109 HOH HOH . 
IA 6 HOH F 10 2110 2110 HOH HOH . 
IA 6 HOH F 11 2111 2111 HOH HOH . 
IA 6 HOH F 12 2112 2112 HOH HOH . 
IA 6 HOH F 13 2113 2113 HOH HOH . 
IA 6 HOH F 14 2114 2114 HOH HOH . 
IA 6 HOH F 15 2115 2115 HOH HOH . 
IA 6 HOH F 16 2116 2116 HOH HOH . 
IA 6 HOH F 17 2117 2117 HOH HOH . 
IA 6 HOH F 18 2118 2118 HOH HOH . 
IA 6 HOH F 19 2119 2119 HOH HOH . 
IA 6 HOH F 20 2120 2120 HOH HOH . 
IA 6 HOH F 21 2121 2121 HOH HOH . 
IA 6 HOH F 22 2122 2122 HOH HOH . 
IA 6 HOH F 23 2123 2123 HOH HOH . 
IA 6 HOH F 24 2124 2124 HOH HOH . 
IA 6 HOH F 25 2125 2125 HOH HOH . 
IA 6 HOH F 26 2126 2126 HOH HOH . 
IA 6 HOH F 27 2127 2127 HOH HOH . 
IA 6 HOH F 28 2128 2128 HOH HOH . 
IA 6 HOH F 29 2129 2129 HOH HOH . 
IA 6 HOH F 30 2130 2130 HOH HOH . 
IA 6 HOH F 31 2131 2131 HOH HOH . 
IA 6 HOH F 32 2132 2132 HOH HOH . 
IA 6 HOH F 33 2133 2133 HOH HOH . 
IA 6 HOH F 34 2134 2134 HOH HOH . 
IA 6 HOH F 35 2135 2135 HOH HOH . 
IA 6 HOH F 36 2136 2136 HOH HOH . 
IA 6 HOH F 37 2137 2137 HOH HOH . 
IA 6 HOH F 38 2138 2138 HOH HOH . 
IA 6 HOH F 39 2139 2139 HOH HOH . 
IA 6 HOH F 40 2140 2140 HOH HOH . 
IA 6 HOH F 41 2141 2141 HOH HOH . 
IA 6 HOH F 42 2142 2142 HOH HOH . 
IA 6 HOH F 43 2143 2143 HOH HOH . 
IA 6 HOH F 44 2144 2144 HOH HOH . 
IA 6 HOH F 45 2145 2145 HOH HOH . 
IA 6 HOH F 46 2146 2146 HOH HOH . 
IA 6 HOH F 47 2147 2147 HOH HOH . 
IA 6 HOH F 48 2148 2148 HOH HOH . 
IA 6 HOH F 49 2149 2149 HOH HOH . 
IA 6 HOH F 50 2150 2150 HOH HOH . 
IA 6 HOH F 51 2151 2151 HOH HOH . 
IA 6 HOH F 52 2152 2152 HOH HOH . 
IA 6 HOH F 53 2153 2153 HOH HOH . 
IA 6 HOH F 54 2154 2154 HOH HOH . 
IA 6 HOH F 55 2155 2155 HOH HOH . 
IA 6 HOH F 56 2156 2156 HOH HOH . 
IA 6 HOH F 57 2157 2157 HOH HOH . 
IA 6 HOH F 58 2158 2158 HOH HOH . 
IA 6 HOH F 59 2159 2159 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 P P PO4 . . . K 5 35.32 -25.553 12.549 1 79.01 ? P PO4 1005 A 1 
HETATM 2 O O1 PO4 . . . K 5 34.781 -25.433 11.187 1 46.91 ? O1 PO4 1005 A 1 
HETATM 3 O O2 PO4 . . . K 5 34.402 -25.863 13.626 1 54.15 ? O2 PO4 1005 A 1 
HETATM 4 O O3 PO4 . . . K 5 36.265 -26.659 12.525 1 56.12 ? O3 PO4 1005 A 1 
HETATM 5 O O4 PO4 . . . K 5 35.969 -24.327 13.057 1 54.17 ? O4 PO4 1005 A 1 
#
_model_server_stats.io_time_ms              192 
_model_server_stats.parse_time_ms           62 
_model_server_stats.create_model_time_ms    94 
_model_server_stats.query_time_ms           1458 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           5 
#