data_4Y1D
#
_model_server_result.job_id            pR0sKgCqcxWDTyUwmkSyYA 
_model_server_result.datetime_utc      '2024-11-04 23:07:55' 
_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          4y1d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":302}' 
#
_entry.id    4Y1D 
#
_exptl.entry_id    4Y1D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              112.411 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CADMIUM 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          90 
_cell.angle_gamma         90 
_cell.entry_id            4Y1D 
_cell.length_a            60.8 
_cell.length_b            62.6 
_cell.length_c            82 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Y1D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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 D N N 
? 3 E N N 
? 3 I N N 
? 3 J 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
covale ? covale1 C C LYS 1 D LYS 1 1_555 C N NLE 2 D NLE 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale2 C N LYS 1 D LYS 1 1_555 C C 45W 6 D 45W 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.496 ? 
covale ? covale3 C C NLE 2 D NLE 2 1_555 C N ASP 3 D ASP 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
covale ? covale4 C C ASN 4 D ASN 4 1_555 C N DVA 5 D DVA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? 
covale ? covale5 C C DVA 5 D DVA 5 1_555 C N 45W 6 D 45W 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? 
metalc ? metalc1 A SG CYS 20 A CYS 65 1_555 D CD CD . A CD 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? 
metalc ? metalc2 A SG CYS 20 A CYS 65 1_555 E CD CD . A CD 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? 
metalc ? metalc3 A NE2 HIS 22 A HIS 67 1_555 D CD CD . A CD 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc4 A OE1 GLU 47 A GLU 92 1_555 D CD CD . A CD 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? 
metalc ? metalc5 A OE2 GLU 47 A GLU 92 1_555 E CD CD . A CD 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? 
metalc ? metalc6 A OD2 ASP 71 A ASP 116 1_555 E CD CD . A CD 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc7 A O ASP 86 A ASP 131 1_555 I CD CD . B CD 301 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc8 A OD1 ASP 86 A ASP 131 1_555 I CD CD . B CD 301 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? 
metalc ? metalc9 A OD1 ASP 86 A ASP 131 1_555 J CD CD . B CD 302 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? 
metalc ? metalc10 E CD CD . A CD 1002 1_555 N O HOH . A HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc11 N O HOH . A HOH 1147 4_456 I CD CD . B CD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? 
metalc ? metalc12 B SG CYS 20 B CYS 65 1_555 I CD CD . B CD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? 
metalc ? metalc13 B SG CYS 20 B CYS 65 1_555 J CD CD . B CD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? 
metalc ? metalc14 B NE2 HIS 22 B HIS 67 1_555 I CD CD . B CD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc15 B OE1 GLU 47 B GLU 92 1_555 I CD CD . B CD 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc16 B OE2 GLU 47 B GLU 92 1_555 J CD CD . B CD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc17 B OD2 ASP 71 B ASP 116 1_555 J CD CD . B CD 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? 
metalc ? metalc18 J CD CD . B CD 302 1_555 O O HOH . B HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
#
_chem_comp.formula           'Cd 2' 
_chem_comp.formula_weight    112.411 
_chem_comp.id                CD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CADMIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     4Y1D 
_atom_sites.fract_transf_matrix[1][1]    0.016447 
_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]    0.015974 
_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]    0.012195 
_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
D 3 CD A 1 1001 1001 CD CD . 
E 3 CD A 1 1002 1002 CD CD . 
F 4 CL A 1 1003 501 CL CL . 
G 5 SO4 A 1 1004 750 SO4 SO4 . 
H 5 SO4 A 1 1005 753 SO4 SO4 . 
I 3 CD B 1 301 1003 CD CD . 
J 3 CD B 1 302 1004 CD CD . 
K 4 CL B 1 303 502 CL CL . 
L 5 SO4 B 1 304 751 SO4 SO4 . 
M 5 SO4 B 1 305 752 SO4 SO4 . 
N 6 HOH A 1 1101 123 HOH HOH . 
N 6 HOH A 2 1102 75 HOH HOH . 
N 6 HOH A 3 1103 103 HOH HOH . 
N 6 HOH A 4 1104 115 HOH HOH . 
N 6 HOH A 5 1105 12 HOH HOH . 
N 6 HOH A 6 1106 1 HOH HOH . 
N 6 HOH A 7 1107 27 HOH HOH . 
N 6 HOH A 8 1108 94 HOH HOH . 
N 6 HOH A 9 1109 36 HOH HOH . 
N 6 HOH A 10 1110 86 HOH HOH . 
N 6 HOH A 11 1111 30 HOH HOH . 
N 6 HOH A 12 1112 101 HOH HOH . 
N 6 HOH A 13 1113 44 HOH HOH . 
N 6 HOH A 14 1114 25 HOH HOH . 
N 6 HOH A 15 1115 20 HOH HOH . 
N 6 HOH A 16 1116 47 HOH HOH . 
N 6 HOH A 17 1117 124 HOH HOH . 
N 6 HOH A 18 1118 42 HOH HOH . 
N 6 HOH A 19 1119 122 HOH HOH . 
N 6 HOH A 20 1120 121 HOH HOH . 
N 6 HOH A 21 1121 51 HOH HOH . 
N 6 HOH A 22 1122 8 HOH HOH . 
N 6 HOH A 23 1123 9 HOH HOH . 
N 6 HOH A 24 1124 56 HOH HOH . 
N 6 HOH A 25 1125 95 HOH HOH . 
N 6 HOH A 26 1126 76 HOH HOH . 
N 6 HOH A 27 1127 110 HOH HOH . 
N 6 HOH A 28 1128 19 HOH HOH . 
N 6 HOH A 29 1129 108 HOH HOH . 
N 6 HOH A 30 1130 117 HOH HOH . 
N 6 HOH A 31 1131 106 HOH HOH . 
N 6 HOH A 32 1132 11 HOH HOH . 
N 6 HOH A 33 1133 118 HOH HOH . 
N 6 HOH A 34 1134 29 HOH HOH . 
N 6 HOH A 35 1135 112 HOH HOH . 
N 6 HOH A 36 1136 74 HOH HOH . 
N 6 HOH A 37 1137 111 HOH HOH . 
N 6 HOH A 38 1138 79 HOH HOH . 
N 6 HOH A 39 1139 18 HOH HOH . 
N 6 HOH A 40 1140 49 HOH HOH . 
N 6 HOH A 41 1141 38 HOH HOH . 
N 6 HOH A 42 1142 90 HOH HOH . 
N 6 HOH A 43 1143 78 HOH HOH . 
N 6 HOH A 44 1144 97 HOH HOH . 
N 6 HOH A 45 1145 41 HOH HOH . 
N 6 HOH A 46 1146 31 HOH HOH . 
N 6 HOH A 47 1147 7 HOH HOH . 
N 6 HOH A 48 1148 63 HOH HOH . 
N 6 HOH A 49 1149 84 HOH HOH . 
N 6 HOH A 50 1150 128 HOH HOH . 
N 6 HOH A 51 1151 22 HOH HOH . 
N 6 HOH A 52 1152 40 HOH HOH . 
N 6 HOH A 53 1153 34 HOH HOH . 
N 6 HOH A 54 1154 127 HOH HOH . 
N 6 HOH A 55 1155 65 HOH HOH . 
N 6 HOH A 56 1156 119 HOH HOH . 
N 6 HOH A 57 1157 125 HOH HOH . 
N 6 HOH A 58 1158 120 HOH HOH . 
N 6 HOH A 59 1159 89 HOH HOH . 
O 6 HOH B 1 401 96 HOH HOH . 
O 6 HOH B 2 402 50 HOH HOH . 
O 6 HOH B 3 403 98 HOH HOH . 
O 6 HOH B 4 404 16 HOH HOH . 
O 6 HOH B 5 405 92 HOH HOH . 
O 6 HOH B 6 406 104 HOH HOH . 
O 6 HOH B 7 407 15 HOH HOH . 
O 6 HOH B 8 408 73 HOH HOH . 
O 6 HOH B 9 409 6 HOH HOH . 
O 6 HOH B 10 410 23 HOH HOH . 
O 6 HOH B 11 411 26 HOH HOH . 
O 6 HOH B 12 412 21 HOH HOH . 
O 6 HOH B 13 413 61 HOH HOH . 
O 6 HOH B 14 414 37 HOH HOH . 
O 6 HOH B 15 415 105 HOH HOH . 
O 6 HOH B 16 416 53 HOH HOH . 
O 6 HOH B 17 417 28 HOH HOH . 
O 6 HOH B 18 418 17 HOH HOH . 
O 6 HOH B 19 419 109 HOH HOH . 
O 6 HOH B 20 420 32 HOH HOH . 
O 6 HOH B 21 421 10 HOH HOH . 
O 6 HOH B 22 422 13 HOH HOH . 
O 6 HOH B 23 423 57 HOH HOH . 
O 6 HOH B 24 424 129 HOH HOH . 
O 6 HOH B 25 425 113 HOH HOH . 
O 6 HOH B 26 426 5 HOH HOH . 
O 6 HOH B 27 427 91 HOH HOH . 
O 6 HOH B 28 428 100 HOH HOH . 
O 6 HOH B 29 429 102 HOH HOH . 
O 6 HOH B 30 430 3 HOH HOH . 
O 6 HOH B 31 431 14 HOH HOH . 
O 6 HOH B 32 432 2 HOH HOH . 
O 6 HOH B 33 433 4 HOH HOH . 
O 6 HOH B 34 434 24 HOH HOH . 
O 6 HOH B 35 435 39 HOH HOH . 
O 6 HOH B 36 436 116 HOH HOH . 
O 6 HOH B 37 437 126 HOH HOH . 
O 6 HOH B 38 438 54 HOH HOH . 
O 6 HOH B 39 439 85 HOH HOH . 
O 6 HOH B 40 440 107 HOH HOH . 
O 6 HOH B 41 441 46 HOH HOH . 
O 6 HOH B 42 442 52 HOH HOH . 
O 6 HOH B 43 443 68 HOH HOH . 
O 6 HOH B 44 444 114 HOH HOH . 
O 6 HOH B 45 445 93 HOH HOH . 
O 6 HOH B 46 446 81 HOH HOH . 
P 6 HOH D 1 101 99 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           CD 
_atom_site.label_atom_id         CD 
_atom_site.label_comp_id         CD 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         J 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               -2.905 
_atom_site.Cartn_y               11.754 
_atom_site.Cartn_z               31.466 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        31.4 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CD 
_atom_site.auth_comp_id          CD 
_atom_site.auth_seq_id           302 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#