data_4PYJ
#
_model_server_result.job_id            r4ev51mlpx9iMajHblTWXA 
_model_server_result.datetime_utc      '2024-11-22 06:11:52' 
_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          4pyj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    4PYJ 
#
_exptl.entry_id    4PYJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              22.99 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SODIUM ION' 
_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            4PYJ 
_cell.length_a            54.882 
_cell.length_b            67.165 
_cell.length_c            128.827 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PYJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E 1 1 
A,B,C,D,E 2 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' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_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 OD1 ASP 141 A ASP 191 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc2 A OD2 ASP 169 A ASP 219 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? 
metalc ? metalc3 A OD1 ASN 170 A ASN 220 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc4 A O VAL 183 A VAL 233 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? 
metalc ? metalc5 A O ARG 184 A ARG 234 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? 
metalc ? metalc6 A O SER 186 A SER 236 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc7 A O PHE 189 A PHE 239 1_555 B NA NA . A NA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? 
metalc ? metalc8 A OE2 GLU 202 A GLU 252 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? 
metalc ? metalc9 B NA NA . A NA 301 1_555 E O HOH . A HOH 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? 
metalc ? metalc10 B NA NA . A NA 301 1_555 E O HOH . A HOH 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? 
metalc ? metalc11 C MG MG . A MG 302 1_555 E O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? 
#
_chem_comp.formula           'Na 1' 
_chem_comp.formula_weight    22.99 
_chem_comp.id                NA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SODIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     4PYJ 
_atom_sites.fract_transf_matrix[1][1]    0.018221 
_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]    0.014889 
_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]    0.007762 
_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 NA A 1 301 301 NA NA . 
C 3 MG A 1 302 302 MG MG . 
D 4 CL A 1 303 303 CL CL . 
E 5 HOH A 1 401 1 HOH HOH . 
E 5 HOH A 2 402 2 HOH HOH . 
E 5 HOH A 3 403 3 HOH HOH . 
E 5 HOH A 4 404 4 HOH HOH . 
E 5 HOH A 5 405 5 HOH HOH . 
E 5 HOH A 6 406 6 HOH HOH . 
E 5 HOH A 7 407 7 HOH HOH . 
E 5 HOH A 8 408 8 HOH HOH . 
E 5 HOH A 9 409 9 HOH HOH . 
E 5 HOH A 10 410 10 HOH HOH . 
E 5 HOH A 11 411 11 HOH HOH . 
E 5 HOH A 12 412 12 HOH HOH . 
E 5 HOH A 13 413 13 HOH HOH . 
E 5 HOH A 14 414 14 HOH HOH . 
E 5 HOH A 15 415 15 HOH HOH . 
E 5 HOH A 16 416 16 HOH HOH . 
E 5 HOH A 17 417 17 HOH HOH . 
E 5 HOH A 18 418 18 HOH HOH . 
E 5 HOH A 19 419 19 HOH HOH . 
E 5 HOH A 20 420 20 HOH HOH . 
E 5 HOH A 21 421 21 HOH HOH . 
E 5 HOH A 22 422 22 HOH HOH . 
E 5 HOH A 23 423 23 HOH HOH . 
E 5 HOH A 24 424 24 HOH HOH . 
E 5 HOH A 25 425 25 HOH HOH . 
E 5 HOH A 26 426 26 HOH HOH . 
E 5 HOH A 27 427 27 HOH HOH . 
E 5 HOH A 28 428 28 HOH HOH . 
E 5 HOH A 29 429 29 HOH HOH . 
E 5 HOH A 30 430 30 HOH HOH . 
E 5 HOH A 31 431 31 HOH HOH . 
E 5 HOH A 32 432 32 HOH HOH . 
E 5 HOH A 33 433 33 HOH HOH . 
E 5 HOH A 34 434 34 HOH HOH . 
E 5 HOH A 35 435 35 HOH HOH . 
E 5 HOH A 36 436 36 HOH HOH . 
E 5 HOH A 37 437 37 HOH HOH . 
E 5 HOH A 38 438 38 HOH HOH . 
E 5 HOH A 39 439 39 HOH HOH . 
E 5 HOH A 40 440 40 HOH HOH . 
E 5 HOH A 41 441 41 HOH HOH . 
E 5 HOH A 42 442 42 HOH HOH . 
E 5 HOH A 43 443 43 HOH HOH . 
E 5 HOH A 44 444 44 HOH HOH . 
E 5 HOH A 45 445 45 HOH HOH . 
E 5 HOH A 46 446 46 HOH HOH . 
E 5 HOH A 47 447 47 HOH HOH . 
E 5 HOH A 48 448 48 HOH HOH . 
E 5 HOH A 49 449 49 HOH HOH . 
E 5 HOH A 50 450 50 HOH HOH . 
E 5 HOH A 51 451 51 HOH HOH . 
E 5 HOH A 52 452 52 HOH HOH . 
E 5 HOH A 53 453 53 HOH HOH . 
E 5 HOH A 54 454 54 HOH HOH . 
E 5 HOH A 55 455 55 HOH HOH . 
E 5 HOH A 56 456 56 HOH HOH . 
E 5 HOH A 57 457 57 HOH HOH . 
E 5 HOH A 58 458 58 HOH HOH . 
E 5 HOH A 59 459 59 HOH HOH . 
E 5 HOH A 60 460 60 HOH HOH . 
E 5 HOH A 61 461 61 HOH HOH . 
E 5 HOH A 62 462 62 HOH HOH . 
E 5 HOH A 63 463 63 HOH HOH . 
E 5 HOH A 64 464 64 HOH HOH . 
E 5 HOH A 65 465 65 HOH HOH . 
E 5 HOH A 66 466 66 HOH HOH . 
E 5 HOH A 67 467 67 HOH HOH . 
E 5 HOH A 68 468 68 HOH HOH . 
E 5 HOH A 69 469 69 HOH HOH . 
E 5 HOH A 70 470 70 HOH HOH . 
E 5 HOH A 71 471 72 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           NA 
_atom_site.label_atom_id         NA 
_atom_site.label_comp_id         NA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         B 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               7.011 
_atom_site.Cartn_y               6.193 
_atom_site.Cartn_z               -22.126 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        45.03 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NA 
_atom_site.auth_comp_id          NA 
_atom_site.auth_seq_id           301 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           246 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#