data_8PYM
#
_model_server_result.job_id            wtYxsEhaqS3l8Ea7dxrNeQ 
_model_server_result.datetime_utc      '2024-11-22 21:54:17' 
_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          8pym 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":1302}' 
#
_entry.id    8PYM 
#
_exptl.entry_id    8PYM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              58.693 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NICKEL (II) 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            8PYM 
_cell.length_a            69.35 
_cell.length_b            69.35 
_cell.length_c            142.85 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8PYM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_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                      3 
_struct_asym.id                             C 
_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 SG CYS 87 AAA CYS 1059 1_555 D CD CD . AAA CD 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? 
metalc ? metalc2 A NE2 HIS 88 AAA HIS 1060 1_555 C NI NI . AAA NI 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc3 A NE2 HIS 89 AAA HIS 1061 1_555 C NI NI . AAA NI 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc4 A OD1 ASP 149 AAA ASP 1121 1_555 D CD CD . AAA CD 1303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc5 A OE1 GLU 190 AAA GLU 1162 1_555 D CD CD . AAA CD 1303 3_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.658 ? 
metalc ? metalc6 A OE2 GLU 190 AAA GLU 1162 1_555 D CD CD . AAA CD 1303 3_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc7 C NI NI . AAA NI 1302 1_555 E O HOH . AAA HOH 1428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
#
_chem_comp.formula           'Ni 2' 
_chem_comp.formula_weight    58.693 
_chem_comp.id                NI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NICKEL (II) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     8PYM 
_atom_sites.fract_transf_matrix[1][1]    0.01442 
_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]    0.01442 
_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]    0.007 
_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 IED AAA 1 1301 3000 IED INH . 
C 3 NI AAA 1 1302 1 NI NI . 
D 4 CD AAA 1 1303 1 CD CD . 
E 5 HOH AAA 1 1401 56 HOH HOH . 
E 5 HOH AAA 2 1402 21 HOH HOH . 
E 5 HOH AAA 3 1403 12 HOH HOH . 
E 5 HOH AAA 4 1404 47 HOH HOH . 
E 5 HOH AAA 5 1405 10 HOH HOH . 
E 5 HOH AAA 6 1406 57 HOH HOH . 
E 5 HOH AAA 7 1407 59 HOH HOH . 
E 5 HOH AAA 8 1408 30 HOH HOH . 
E 5 HOH AAA 9 1409 23 HOH HOH . 
E 5 HOH AAA 10 1410 58 HOH HOH . 
E 5 HOH AAA 11 1411 32 HOH HOH . 
E 5 HOH AAA 12 1412 19 HOH HOH . 
E 5 HOH AAA 13 1413 25 HOH HOH . 
E 5 HOH AAA 14 1414 50 HOH HOH . 
E 5 HOH AAA 15 1415 34 HOH HOH . 
E 5 HOH AAA 16 1416 3 HOH HOH . 
E 5 HOH AAA 17 1417 52 HOH HOH . 
E 5 HOH AAA 18 1418 46 HOH HOH . 
E 5 HOH AAA 19 1419 18 HOH HOH . 
E 5 HOH AAA 20 1420 7 HOH HOH . 
E 5 HOH AAA 21 1421 24 HOH HOH . 
E 5 HOH AAA 22 1422 29 HOH HOH . 
E 5 HOH AAA 23 1423 39 HOH HOH . 
E 5 HOH AAA 24 1424 48 HOH HOH . 
E 5 HOH AAA 25 1425 28 HOH HOH . 
E 5 HOH AAA 26 1426 17 HOH HOH . 
E 5 HOH AAA 27 1427 6 HOH HOH . 
E 5 HOH AAA 28 1428 53 HOH HOH . 
E 5 HOH AAA 29 1429 2 HOH HOH . 
E 5 HOH AAA 30 1430 33 HOH HOH . 
E 5 HOH AAA 31 1431 11 HOH HOH . 
E 5 HOH AAA 32 1432 26 HOH HOH . 
E 5 HOH AAA 33 1433 36 HOH HOH . 
E 5 HOH AAA 34 1434 13 HOH HOH . 
E 5 HOH AAA 35 1435 41 HOH HOH . 
E 5 HOH AAA 36 1436 42 HOH HOH . 
E 5 HOH AAA 37 1437 22 HOH HOH . 
E 5 HOH AAA 38 1438 49 HOH HOH . 
E 5 HOH AAA 39 1439 20 HOH HOH . 
E 5 HOH AAA 40 1440 16 HOH HOH . 
E 5 HOH AAA 41 1441 55 HOH HOH . 
E 5 HOH AAA 42 1442 14 HOH HOH . 
E 5 HOH AAA 43 1443 37 HOH HOH . 
E 5 HOH AAA 44 1444 44 HOH HOH . 
E 5 HOH AAA 45 1445 45 HOH HOH . 
E 5 HOH AAA 46 1446 38 HOH HOH . 
E 5 HOH AAA 47 1447 54 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           NI 
_atom_site.label_atom_id         NI 
_atom_site.label_comp_id         NI 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         C 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               -33.101 
_atom_site.Cartn_y               8.395 
_atom_site.Cartn_z               -2.319 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        29.12 
_atom_site.pdbx_formal_charge    0 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           1302 
_atom_site.auth_asym_id          AAA 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              14 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#