data_6YRB # _model_server_result.job_id iz9O98lu3cOTeQgJhDnhjw _model_server_result.datetime_utc '2024-11-04 19:46:37' _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 6yrb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":605}' # _entry.id 6YRB # _exptl.entry_id 6YRB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 126.904 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'IODIDE ION' _entity.pdbx_number_of_molecules 6 _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 6YRB _cell.length_a 67.854 _cell.length_b 67.854 _cell.length_c 121.891 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YRB _symmetry.cell_setting ? _symmetry.Int_Tables_number 79 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,L,N,O 1 1,2,3,4 B,C,D,I,J,K,M,N,O 1 5,6,7,8 # 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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_545 x+1/2,y-1/2,z+1/2 1 0 0 0 1 0 0 0 1 33.927 -33.927 60.9455 6 'crystal symmetry operation' 6_455 -x-1/2,-y+1/2,z+1/2 -1 0 0 0 -1 0 0 0 1 -33.927 33.927 60.9455 7 'crystal symmetry operation' 7_555 -y+1/2,x+1/2,z+1/2 0 -1 0 1 0 0 0 0 1 33.927 33.927 60.9455 8 'crystal symmetry operation' 8_445 y-1/2,-x-1/2,z+1/2 0 1 0 -1 0 0 0 0 1 -33.927 -33.927 60.9455 # 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 I N N ? 4 J N N ? 4 K N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 1 FUC NAG C1 O1 . O6 HO6 . 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 3 n E NAG 1 E 1 NAG A 1483 NAG 3 n E NAG 2 E 2 NAG A 1484 NAG 3 n E BMA 3 E 3 BMA A 1485 BMA 3 n E FUC 4 E 4 FUC A 1486 FUC # 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 5 A CYS 379 1_555 A SG CYS 64 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 9 A CYS 383 1_555 A SG CYS 18 A CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 34 A CYS 408 1_555 A SG CYS 53 A CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 81 A CYS 455 1_555 A SG CYS 104 A CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 B SG CYS 5 B CYS 379 1_555 B SG CYS 64 B CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 9 B CYS 383 1_555 B SG CYS 18 B CYS 392 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 B SG CYS 34 B CYS 408 1_555 B SG CYS 53 B CYS 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 81 B CYS 455 1_555 B SG CYS 104 B CYS 478 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? covale ? covale1 A ND2 ASN 28 A ASN 402 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 E O6 NAG . E NAG 1 1_555 E C1 FUC . E FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _chem_comp.formula 'I -1' _chem_comp.formula_weight 126.904 _chem_comp.id IOD _chem_comp.mon_nstd_flag . _chem_comp.name 'IODIDE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 6YRB _atom_sites.fract_transf_matrix[1][1] 0.014738 _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] 0.014738 _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] 0.008204 _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 F 4 IOD A 1 605 1 IOD IOD . G 4 IOD A 1 606 2 IOD IOD . H 4 IOD A 1 607 5 IOD IOD . I 4 IOD B 1 601 3 IOD IOD . J 4 IOD B 1 602 4 IOD IOD . K 4 IOD B 1 603 6 IOD IOD . L 5 HOH A 1 701 14 HOH HOH . L 5 HOH A 2 702 54 HOH HOH . L 5 HOH A 3 703 50 HOH HOH . L 5 HOH A 4 704 3 HOH HOH . L 5 HOH A 5 705 18 HOH HOH . L 5 HOH A 6 706 1 HOH HOH . L 5 HOH A 7 707 5 HOH HOH . L 5 HOH A 8 708 32 HOH HOH . L 5 HOH A 9 709 28 HOH HOH . L 5 HOH A 10 710 48 HOH HOH . L 5 HOH A 11 711 9 HOH HOH . L 5 HOH A 12 712 41 HOH HOH . L 5 HOH A 13 713 8 HOH HOH . L 5 HOH A 14 714 16 HOH HOH . L 5 HOH A 15 715 11 HOH HOH . L 5 HOH A 16 716 27 HOH HOH . L 5 HOH A 17 717 4 HOH HOH . L 5 HOH A 18 718 37 HOH HOH . L 5 HOH A 19 719 51 HOH HOH . L 5 HOH A 20 720 21 HOH HOH . L 5 HOH A 21 721 34 HOH HOH . L 5 HOH A 22 722 26 HOH HOH . L 5 HOH A 23 723 45 HOH HOH . L 5 HOH A 24 724 22 HOH HOH . L 5 HOH A 25 725 49 HOH HOH . L 5 HOH A 26 726 40 HOH HOH . L 5 HOH A 27 727 47 HOH HOH . L 5 HOH A 28 728 42 HOH HOH . L 5 HOH A 29 729 52 HOH HOH . L 5 HOH A 30 730 53 HOH HOH . L 5 HOH A 31 731 46 HOH HOH . M 5 HOH B 1 701 36 HOH HOH . M 5 HOH B 2 702 7 HOH HOH . M 5 HOH B 3 703 35 HOH HOH . M 5 HOH B 4 704 30 HOH HOH . M 5 HOH B 5 705 44 HOH HOH . M 5 HOH B 6 706 24 HOH HOH . M 5 HOH B 7 707 17 HOH HOH . M 5 HOH B 8 708 31 HOH HOH . M 5 HOH B 9 709 23 HOH HOH . M 5 HOH B 10 710 2 HOH HOH . M 5 HOH B 11 711 10 HOH HOH . M 5 HOH B 12 712 20 HOH HOH . M 5 HOH B 13 713 12 HOH HOH . M 5 HOH B 14 714 13 HOH HOH . M 5 HOH B 15 715 39 HOH HOH . M 5 HOH B 16 716 33 HOH HOH . M 5 HOH B 17 717 38 HOH HOH . M 5 HOH B 18 718 43 HOH HOH . M 5 HOH B 19 719 29 HOH HOH . M 5 HOH B 20 720 55 HOH HOH . M 5 HOH B 21 721 19 HOH HOH . N 5 HOH C 1 101 6 HOH HOH . O 5 HOH D 1 101 25 HOH HOH . O 5 HOH D 2 102 15 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol I _atom_site.label_atom_id I _atom_site.label_comp_id IOD _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 9.341 _atom_site.Cartn_y 23.431 _atom_site.Cartn_z -34.54 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 80.64 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id I _atom_site.auth_comp_id IOD _atom_site.auth_seq_id 605 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #