data_4YDX
#
_model_server_result.job_id            YwiGfuOgG6wv1gUh-9tmpQ 
_model_server_result.datetime_utc      '2024-11-13 08:34:44' 
_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          4ydx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":103}' 
#
_entry.id    4YDX 
#
_exptl.entry_id    4YDX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              250.186 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "3,3',3''-phosphanetriyltripropanoic 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         120 
_cell.entry_id            4YDX 
_cell.length_a            54.07 
_cell.length_b            54.07 
_cell.length_c            55.578 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YDX 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 N CYS 11 A CYS 12 1_555 B PT PT . A PT 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc2 A SG CYS 11 A CYS 12 1_555 B PT PT . A PT 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc3 A SG CYS 14 A CYS 15 1_555 B PT PT . A PT 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
#
_chem_comp.formula           'C9 H15 O6 P' 
_chem_comp.formula_weight    250.186 
_chem_comp.id                TCE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "3,3',3''-phosphanetriyltripropanoic acid" 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     '3-[bis(2-carboxyethyl)phosphanyl]propanoic acid' 
#
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
O16 C14 TCE doub 275 n n 
C14 O15 TCE sing 276 n n 
C14 C5 TCE sing 277 n n 
O15 HO15 TCE sing 278 n n 
C2 C5 TCE sing 279 n n 
C5 H5 TCE sing 280 n n 
C5 H5A TCE sing 281 n n 
C2 P TCE sing 282 n n 
C2 H2 TCE sing 283 n n 
C2 H2A TCE sing 284 n n 
C1 P TCE sing 285 n n 
P C3 TCE sing 286 n n 
C3 C6 TCE sing 287 n n 
C3 H3 TCE sing 288 n n 
C3 H3A TCE sing 289 n n 
C6 C8 TCE sing 290 n n 
C6 H6 TCE sing 291 n n 
C6 H6A TCE sing 292 n n 
O10 C8 TCE doub 293 n n 
C8 O9 TCE sing 294 n n 
O9 HO9 TCE sing 295 n n 
C4 C1 TCE sing 296 n n 
C1 H1 TCE sing 297 n n 
C1 H1A TCE sing 298 n n 
C11 C4 TCE sing 299 n n 
C4 H4 TCE sing 300 n n 
C4 H4A TCE sing 301 n n 
O13 C11 TCE doub 302 n n 
O12 C11 TCE sing 303 n n 
O12 HO12 TCE sing 304 n n 
#
_atom_sites.entry_id                     4YDX 
_atom_sites.fract_transf_matrix[1][1]    0.018495 
_atom_sites.fract_transf_matrix[1][2]    0.010678 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021356 
_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]    0.017993 
_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 PT A 1 101 69 PT PT . 
C 3 SO4 A 1 102 70 SO4 SO4 . 
D 4 TCE A 1 103 71 TCE TCE . 
E 5 HOH A 1 201 115 HOH HOH . 
E 5 HOH A 2 202 126 HOH HOH . 
E 5 HOH A 3 203 163 HOH HOH . 
E 5 HOH A 4 204 117 HOH HOH . 
E 5 HOH A 5 205 119 HOH HOH . 
E 5 HOH A 6 206 123 HOH HOH . 
E 5 HOH A 7 207 136 HOH HOH . 
E 5 HOH A 8 208 134 HOH HOH . 
E 5 HOH A 9 209 137 HOH HOH . 
E 5 HOH A 10 210 135 HOH HOH . 
E 5 HOH A 11 211 251 HOH HOH . 
E 5 HOH A 12 212 114 HOH HOH . 
E 5 HOH A 13 213 231 HOH HOH . 
E 5 HOH A 14 214 110 HOH HOH . 
E 5 HOH A 15 215 120 HOH HOH . 
E 5 HOH A 16 216 116 HOH HOH . 
E 5 HOH A 17 217 164 HOH HOH . 
E 5 HOH A 18 218 103 HOH HOH . 
E 5 HOH A 19 219 256 HOH HOH . 
E 5 HOH A 20 220 229 HOH HOH . 
E 5 HOH A 21 221 230 HOH HOH . 
E 5 HOH A 22 222 124 HOH HOH . 
E 5 HOH A 23 223 107 HOH HOH . 
E 5 HOH A 24 224 244 HOH HOH . 
E 5 HOH A 25 225 139 HOH HOH . 
E 5 HOH A 26 226 131 HOH HOH . 
E 5 HOH A 27 227 147 HOH HOH . 
E 5 HOH A 28 228 253 HOH HOH . 
E 5 HOH A 29 229 241 HOH HOH . 
E 5 HOH A 30 230 108 HOH HOH . 
E 5 HOH A 31 231 152 HOH HOH . 
E 5 HOH A 32 232 104 HOH HOH . 
E 5 HOH A 33 233 169 HOH HOH . 
E 5 HOH A 34 234 132 HOH HOH . 
E 5 HOH A 35 235 249 HOH HOH . 
E 5 HOH A 36 236 254 HOH HOH . 
E 5 HOH A 37 237 240 HOH HOH . 
E 5 HOH A 38 238 156 HOH HOH . 
E 5 HOH A 39 239 159 HOH HOH . 
E 5 HOH A 40 240 257 HOH HOH . 
E 5 HOH A 41 241 233 HOH HOH . 
E 5 HOH A 42 242 238 HOH HOH . 
E 5 HOH A 43 243 153 HOH HOH . 
E 5 HOH A 44 244 109 HOH HOH . 
E 5 HOH A 45 245 146 HOH HOH . 
E 5 HOH A 46 246 234 HOH HOH . 
E 5 HOH A 47 247 101 HOH HOH . 
E 5 HOH A 48 248 102 HOH HOH . 
E 5 HOH A 49 249 106 HOH HOH . 
E 5 HOH A 50 250 111 HOH HOH . 
E 5 HOH A 51 251 112 HOH HOH . 
E 5 HOH A 52 252 113 HOH HOH . 
E 5 HOH A 53 253 118 HOH HOH . 
E 5 HOH A 54 254 121 HOH HOH . 
E 5 HOH A 55 255 122 HOH HOH . 
E 5 HOH A 56 256 125 HOH HOH . 
E 5 HOH A 57 257 127 HOH HOH . 
E 5 HOH A 58 258 128 HOH HOH . 
E 5 HOH A 59 259 129 HOH HOH . 
E 5 HOH A 60 260 130 HOH HOH . 
E 5 HOH A 61 261 133 HOH HOH . 
E 5 HOH A 62 262 138 HOH HOH . 
E 5 HOH A 63 263 140 HOH HOH . 
E 5 HOH A 64 264 141 HOH HOH . 
E 5 HOH A 65 265 142 HOH HOH . 
E 5 HOH A 66 266 143 HOH HOH . 
E 5 HOH A 67 267 144 HOH HOH . 
E 5 HOH A 68 268 145 HOH HOH . 
E 5 HOH A 69 269 149 HOH HOH . 
E 5 HOH A 70 270 150 HOH HOH . 
E 5 HOH A 71 271 151 HOH HOH . 
E 5 HOH A 72 272 157 HOH HOH . 
E 5 HOH A 73 273 158 HOH HOH . 
E 5 HOH A 74 274 160 HOH HOH . 
E 5 HOH A 75 275 161 HOH HOH . 
E 5 HOH A 76 276 162 HOH HOH . 
E 5 HOH A 77 277 165 HOH HOH . 
E 5 HOH A 78 278 166 HOH HOH . 
E 5 HOH A 79 279 167 HOH HOH . 
E 5 HOH A 80 280 170 HOH HOH . 
E 5 HOH A 81 281 171 HOH HOH . 
E 5 HOH A 82 282 232 HOH HOH . 
E 5 HOH A 83 283 235 HOH HOH . 
E 5 HOH A 84 284 236 HOH HOH . 
E 5 HOH A 85 285 237 HOH HOH . 
E 5 HOH A 86 286 239 HOH HOH . 
E 5 HOH A 87 287 242 HOH HOH . 
E 5 HOH A 88 288 245 HOH HOH . 
E 5 HOH A 89 289 246 HOH HOH . 
E 5 HOH A 90 290 247 HOH HOH . 
E 5 HOH A 91 291 248 HOH HOH . 
E 5 HOH A 92 292 250 HOH HOH . 
E 5 HOH A 93 293 255 HOH HOH . 
E 5 HOH A 94 294 258 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 O16 TCE . . . D 4 40.84 30.347 12.298 0.9 39.55 ? O16 TCE 103 A 1 
HETATM 2 C C14 TCE . . . D 4 41.155 29.159 12.521 0.9 36.11 ? C14 TCE 103 A 1 
HETATM 3 O O15 TCE . . . D 4 41.446 28.755 13.668 0.9 34.65 ? O15 TCE 103 A 1 
HETATM 4 C C5 TCE . . . D 4 41.162 28.213 11.339 0.9 33.76 ? C5 TCE 103 A 1 
HETATM 5 C C2 TCE . . . D 4 41.235 26.75 11.757 0.9 33.26 ? C2 TCE 103 A 1 
HETATM 6 P P TCE . . . D 4 40.869 25.587 10.375 0.9 22.76 ? P TCE 103 A 1 
HETATM 7 C C3 TCE . . . D 4 41.807 26.231 8.916 0.9 38.6 ? C3 TCE 103 A 1 
HETATM 8 C C6 TCE . . . D 4 43.326 26.228 9.105 0.9 41.26 ? C6 TCE 103 A 1 
HETATM 9 C C8 TCE . . . D 4 44.003 26.923 7.935 0.9 44.33 ? C8 TCE 103 A 1 
HETATM 10 O O10 TCE . . . D 4 43.67 26.611 6.768 0.9 44.33 ? O10 TCE 103 A 1 
HETATM 11 O O9 TCE . . . D 4 44.886 27.781 8.174 0.9 45.82 ? O9 TCE 103 A 1 
HETATM 12 C C1 TCE . . . D 4 41.861 24.138 10.949 0.9 30.6 ? C1 TCE 103 A 1 
HETATM 13 C C4 TCE . . . D 4 41.844 23.041 9.893 0.9 29.16 ? C4 TCE 103 A 1 
HETATM 14 C C11 TCE . . . D 4 42.469 21.746 10.364 0.9 30.07 ? C11 TCE 103 A 1 
HETATM 15 O O12 TCE . . . D 4 42.3 21.366 11.542 0.9 28.39 ? O12 TCE 103 A 1 
HETATM 16 O O13 TCE . . . D 4 43.133 21.084 9.537 0.9 31.74 ? O13 TCE 103 A 1 
#
_model_server_stats.io_time_ms              63 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           16 
#