data_6YDD # _model_server_result.job_id vk86MJuFPIe3f9Tgn-9nNA _model_server_result.datetime_utc '2025-04-19 02:06:41' _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 6ydd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 6YDD # _exptl.entry_id 6YDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 63.546 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'COPPER (II) ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 93.49 _cell.angle_gamma 90 _cell.entry_id 6YDD _cell.length_a 52.14 _cell.length_b 39.7 _cell.length_c 120.65 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G 1 1 B,D,F,H 2 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 E N N ? 4 F N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 BGC BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BGC BGC C1 O1 . O4 HO4 . sing 3 ? 2 4 3 BGC BGC C1 O1 . O4 HO4 . sing 4 ? 3 2 1 BGC BGC C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n C BGC 1 C 1 BGC A 409 BGC 2 n C BGC 2 C 2 BGC A 408 BGC 2 n C BGC 3 C 3 BGC A 407 BGC 2 n C BGC 4 C 4 BGC A 406 BGC 3 n D BGC 1 D 1 BGC B 400 BGC 3 n D BGC 2 D 2 BGC B 401 BGC # 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 disulf ? disulf1 A SG CYS 41 A CYS 41 1_555 A SG CYS 172 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? disulf ? disulf2 B SG CYS 41 B CYS 41 1_555 B SG CYS 172 B CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? covale ? covale1 A N THR 2 A THR 2 1_555 A C HIC 1 A HIC 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale2 B N THR 2 B THR 2 1_555 B C HIC 1 B HIC 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale3 C O4 BGC . C BGC 1 1_555 C C1 BGC . C BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale4 C O4 BGC . C BGC 2 1_555 C C1 BGC . C BGC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 C O4 BGC . C BGC 3 1_555 C C1 BGC . C BGC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale6 D O4 BGC . D BGC 1 1_555 D C1 BGC . D BGC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? metalc ? metalc1 A NE2 HIS 79 A HIS 79 1_555 E CU CU . A CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc2 A N HIC 1 A HIC 306 1_555 E CU CU . A CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc3 A ND1 HIC 1 A HIC 306 1_555 E CU CU . A CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc4 B NE2 HIS 79 B HIS 79 1_555 F CU CU . B CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc5 B N HIC 1 B HIC 304 1_555 F CU CU . B CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc6 B ND1 HIC 1 B HIC 304 1_555 F CU CU . B CU 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? # _chem_comp.formula 'Cu 2' _chem_comp.formula_weight 63.546 _chem_comp.id CU _chem_comp.mon_nstd_flag . _chem_comp.name 'COPPER (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6YDD _atom_sites.fract_transf_matrix[1][1] 0.019179 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00117 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.025189 _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] 0.008304 _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 E 4 CU A 1 401 301 CU CU . F 4 CU B 1 401 301 CU CU . G 5 HOH A 1 501 18 HOH HOH . G 5 HOH A 2 502 88 HOH HOH . G 5 HOH A 3 503 20 HOH HOH . G 5 HOH A 4 504 8 HOH HOH . G 5 HOH A 5 505 16 HOH HOH . G 5 HOH A 6 506 12 HOH HOH . G 5 HOH A 7 507 77 HOH HOH . G 5 HOH A 8 508 7 HOH HOH . G 5 HOH A 9 509 87 HOH HOH . G 5 HOH A 10 510 4 HOH HOH . G 5 HOH A 11 511 57 HOH HOH . G 5 HOH A 12 512 9 HOH HOH . G 5 HOH A 13 513 27 HOH HOH . G 5 HOH A 14 514 50 HOH HOH . G 5 HOH A 15 515 42 HOH HOH . G 5 HOH A 16 516 65 HOH HOH . G 5 HOH A 17 517 72 HOH HOH . G 5 HOH A 18 518 70 HOH HOH . G 5 HOH A 19 519 21 HOH HOH . G 5 HOH A 20 520 82 HOH HOH . G 5 HOH A 21 521 56 HOH HOH . G 5 HOH A 22 522 83 HOH HOH . G 5 HOH A 23 523 29 HOH HOH . G 5 HOH A 24 524 76 HOH HOH . G 5 HOH A 25 525 28 HOH HOH . G 5 HOH A 26 526 38 HOH HOH . G 5 HOH A 27 527 32 HOH HOH . G 5 HOH A 28 528 69 HOH HOH . G 5 HOH A 29 529 33 HOH HOH . G 5 HOH A 30 530 45 HOH HOH . G 5 HOH A 31 531 79 HOH HOH . G 5 HOH A 32 532 78 HOH HOH . G 5 HOH A 33 533 48 HOH HOH . G 5 HOH A 34 534 81 HOH HOH . G 5 HOH A 35 535 74 HOH HOH . G 5 HOH A 36 536 46 HOH HOH . G 5 HOH A 37 537 43 HOH HOH . H 5 HOH B 1 501 17 HOH HOH . H 5 HOH B 2 502 86 HOH HOH . H 5 HOH B 3 503 2 HOH HOH . H 5 HOH B 4 504 60 HOH HOH . H 5 HOH B 5 505 59 HOH HOH . H 5 HOH B 6 506 11 HOH HOH . H 5 HOH B 7 507 3 HOH HOH . H 5 HOH B 8 508 51 HOH HOH . H 5 HOH B 9 509 63 HOH HOH . H 5 HOH B 10 510 37 HOH HOH . H 5 HOH B 11 511 22 HOH HOH . H 5 HOH B 12 512 15 HOH HOH . H 5 HOH B 13 513 5 HOH HOH . H 5 HOH B 14 514 31 HOH HOH . H 5 HOH B 15 515 90 HOH HOH . H 5 HOH B 16 516 19 HOH HOH . H 5 HOH B 17 517 40 HOH HOH . H 5 HOH B 18 518 41 HOH HOH . H 5 HOH B 19 519 13 HOH HOH . H 5 HOH B 20 520 84 HOH HOH . H 5 HOH B 21 521 61 HOH HOH . H 5 HOH B 22 522 55 HOH HOH . H 5 HOH B 23 523 62 HOH HOH . H 5 HOH B 24 524 49 HOH HOH . H 5 HOH B 25 525 89 HOH HOH . H 5 HOH B 26 526 25 HOH HOH . H 5 HOH B 27 527 26 HOH HOH . H 5 HOH B 28 528 34 HOH HOH . H 5 HOH B 29 529 52 HOH HOH . H 5 HOH B 30 530 91 HOH HOH . H 5 HOH B 31 531 85 HOH HOH . H 5 HOH B 32 532 68 HOH HOH . H 5 HOH B 33 533 54 HOH HOH . H 5 HOH B 34 534 44 HOH HOH . H 5 HOH B 35 535 58 HOH HOH . H 5 HOH B 36 536 10 HOH HOH . H 5 HOH B 37 537 23 HOH HOH . H 5 HOH B 38 538 39 HOH HOH . H 5 HOH B 39 539 14 HOH HOH . H 5 HOH B 40 540 36 HOH HOH . H 5 HOH B 41 541 71 HOH HOH . H 5 HOH B 42 542 75 HOH HOH . H 5 HOH B 43 543 53 HOH HOH . H 5 HOH B 44 544 73 HOH HOH . H 5 HOH B 45 545 80 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CU _atom_site.label_atom_id CU _atom_site.label_comp_id CU _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id E _atom_site.label_entity_id 4 _atom_site.Cartn_x 0.554 _atom_site.Cartn_y -6.325 _atom_site.Cartn_z 45.791 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 20.06 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CU _atom_site.auth_comp_id CU _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #