data_5Y4A
#
_model_server_result.job_id            DZGZHROCEgrNjQaGel28oQ 
_model_server_result.datetime_utc      '2024-12-12 01:44:00' 
_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          5y4a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":404}' 
#
_entry.id    5Y4A 
#
_exptl.entry_id    5Y4A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              112.411 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CADMIUM 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          90 
_cell.angle_gamma         90 
_cell.entry_id            5Y4A 
_cell.length_a            60.216 
_cell.length_b            77.547 
_cell.length_c            90.388 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y4A 
_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    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,I,J,K,L,M,N 
_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
? 4 F N N 
? 4 G N N 
? 4 H N N 
? 4 K N N 
? 4 L 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 OE1 GLU 102 A GLU 102 1_555 G CD CD . A CD 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? 
metalc ? metalc2 A OE2 GLU 102 A GLU 102 1_555 G CD CD . A CD 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? 
metalc ? metalc3 A O THR 117 A THR 117 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc4 A O ILE 120 A ILE 120 1_555 C NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc5 A OD1 ASP 130 A ASP 130 1_555 F CD CD . A CD 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? 
metalc ? metalc6 A OD2 ASP 130 A ASP 130 1_555 F CD CD . A CD 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? 
metalc ? metalc7 A OD1 ASP 131 A ASP 131 1_555 F CD CD . A CD 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? 
metalc ? metalc8 A OE2 GLU 164 A GLU 164 1_555 G CD CD . A CD 405 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc9 A ND1 HIS 177 A HIS 177 1_555 H CD CD . B CD 201 3_555 ? B ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc10 A OD1 ASP 185 A ASP 185 1_555 G CD CD . A CD 405 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
metalc ? metalc11 A OD2 ASP 185 A ASP 185 1_555 G CD CD . A CD 405 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc12 A ND1 HIS 187 A HIS 187 1_555 G CD CD . A CD 405 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc13 C NA NA . A NA 401 1_555 M O HOH . A HOH 517 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? 
metalc ? metalc14 C NA NA . A NA 401 1_555 M O HOH . A HOH 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.524 ? 
metalc ? metalc15 F CD CD . A CD 404 1_555 M O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc16 F CD CD . A CD 404 1_555 M O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? 
metalc ? metalc17 F CD CD . A CD 404 1_555 M O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? 
metalc ? metalc18 F CD CD . A CD 404 1_555 M O HOH . A HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc19 B O THR 117 B THR 117 1_555 I NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.424 ? 
metalc ? metalc20 B O ILE 120 B ILE 120 1_555 I NA NA . B NA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc21 B OD1 ASP 130 B ASP 130 1_555 K CD CD . B CD 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc22 B OD1 ASP 131 B ASP 131 1_555 K CD CD . B CD 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? 
metalc ? metalc23 B NE2 HIS 155 B HIS 155 1_555 L CD CD . B CD 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc24 I NA NA . B NA 202 1_555 N O HOH . B HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc25 I NA NA . B NA 202 1_555 N O HOH . B HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? 
metalc ? metalc26 I NA NA . B NA 202 1_555 N O HOH . B HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? 
metalc ? metalc27 K CD CD . B CD 204 1_555 N O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc28 K CD CD . B CD 204 1_555 N O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? 
metalc ? metalc29 K CD CD . B CD 204 1_555 N O HOH . B HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc30 L CD CD . B CD 205 1_555 N O HOH . B HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
#
_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                     5Y4A 
_atom_sites.fract_transf_matrix[1][1]    0.016607 
_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]    0.012895 
_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]    0.011063 
_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 2 NA A 1 401 401 NA NA . 
D 3 SO4 A 1 402 501 SO4 SO4 . 
E 3 SO4 A 1 403 502 SO4 SO4 . 
F 4 CD A 1 404 503 CD CD . 
G 4 CD A 1 405 504 CD CD . 
H 4 CD B 1 201 505 CD CD . 
I 2 NA B 1 202 401 NA NA . 
J 3 SO4 B 1 203 501 SO4 SO4 . 
K 4 CD B 1 204 503 CD CD . 
L 4 CD B 1 205 504 CD CD . 
M 5 HOH A 1 501 22 HOH HOH . 
M 5 HOH A 2 502 47 HOH HOH . 
M 5 HOH A 3 503 24 HOH HOH . 
M 5 HOH A 4 504 48 HOH HOH . 
M 5 HOH A 5 505 12 HOH HOH . 
M 5 HOH A 6 506 35 HOH HOH . 
M 5 HOH A 7 507 9 HOH HOH . 
M 5 HOH A 8 508 5 HOH HOH . 
M 5 HOH A 9 509 33 HOH HOH . 
M 5 HOH A 10 510 15 HOH HOH . 
M 5 HOH A 11 511 37 HOH HOH . 
M 5 HOH A 12 512 49 HOH HOH . 
M 5 HOH A 13 513 41 HOH HOH . 
M 5 HOH A 14 514 21 HOH HOH . 
M 5 HOH A 15 515 11 HOH HOH . 
M 5 HOH A 16 516 32 HOH HOH . 
M 5 HOH A 17 517 23 HOH HOH . 
M 5 HOH A 18 518 6 HOH HOH . 
M 5 HOH A 19 519 34 HOH HOH . 
M 5 HOH A 20 520 25 HOH HOH . 
M 5 HOH A 21 521 20 HOH HOH . 
M 5 HOH A 22 522 16 HOH HOH . 
M 5 HOH A 23 523 45 HOH HOH . 
M 5 HOH A 24 524 26 HOH HOH . 
M 5 HOH A 25 525 19 HOH HOH . 
M 5 HOH A 26 526 13 HOH HOH . 
M 5 HOH A 27 527 46 HOH HOH . 
M 5 HOH A 28 528 40 HOH HOH . 
N 5 HOH B 1 301 14 HOH HOH . 
N 5 HOH B 2 302 7 HOH HOH . 
N 5 HOH B 3 303 28 HOH HOH . 
N 5 HOH B 4 304 31 HOH HOH . 
N 5 HOH B 5 305 50 HOH HOH . 
N 5 HOH B 6 306 42 HOH HOH . 
N 5 HOH B 7 307 30 HOH HOH . 
N 5 HOH B 8 308 36 HOH HOH . 
N 5 HOH B 9 309 8 HOH HOH . 
N 5 HOH B 10 310 10 HOH HOH . 
N 5 HOH B 11 311 3 HOH HOH . 
N 5 HOH B 12 312 29 HOH HOH . 
N 5 HOH B 13 313 51 HOH HOH . 
N 5 HOH B 14 314 38 HOH HOH . 
N 5 HOH B 15 315 27 HOH HOH . 
N 5 HOH B 16 316 44 HOH HOH . 
N 5 HOH B 17 317 43 HOH HOH . 
N 5 HOH B 18 318 52 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         F 
_atom_site.label_entity_id       4 
_atom_site.Cartn_x               -7.237 
_atom_site.Cartn_y               8.299 
_atom_site.Cartn_z               4.159 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        31.23 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CD 
_atom_site.auth_comp_id          CD 
_atom_site.auth_seq_id           404 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              78 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           312 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#