data_3EDD # _model_server_result.job_id BAK9T9qi2LATZNcvbbFLQw _model_server_result.datetime_utc '2025-08-31 05:55:48' _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 3edd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":701}' # _entry.id 3EDD # _exptl.entry_id 3EDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 4 _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 120 _cell.entry_id 3EDD _cell.length_a 183.758 _cell.length_b 183.758 _cell.length_c 233.272 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_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,D,E,H 1 1,2 B,C,F,G,I 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' 12_555 -x+2/3,-x+y+1/3,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 91.879 53.046365 77.757333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 G N N # _pdbx_entity_branch.entity_id 2 _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 ? 2 1 6 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 2 1 GLC GLC C1 O1 . O4 HO4 . sing 3 ? 2 3 2 GLC GLC C1 O1 . O4 HO4 . sing 4 ? 2 4 3 GLC GLC C1 O1 . O4 HO4 . sing 5 ? 2 5 4 GLC GLC C1 O1 . O4 HO4 . sing 6 ? 2 6 5 GLC GLC 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 GLC 1 C 1 GLC B 802 ACX 2 n C GLC 2 C 2 GLC B 802 ACX 2 n C GLC 3 C 3 GLC B 802 ACX 2 n C GLC 4 C 4 GLC B 802 ACX 2 n C GLC 5 C 5 GLC B 802 ACX 2 n C GLC 6 C 6 GLC B 802 ACX # 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 covale ? covale1 C O4 GLC . C GLC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 sing covale ? covale2 C C1 GLC . C GLC 1 1_555 C O4 GLC . C GLC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 sing covale ? covale3 C O4 GLC . C GLC 2 1_555 C C1 GLC . C GLC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 sing covale ? covale4 C O4 GLC . C GLC 3 1_555 C C1 GLC . C GLC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 sing covale ? covale5 C O4 GLC . C GLC 4 1_555 C C1 GLC . C GLC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 sing covale ? covale6 C O4 GLC . C GLC 5 1_555 C C1 GLC . C GLC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 sing metalc ? metalc1 A OD1 ASN 119 A ASN 119 1_555 D CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc2 A O ASP 121 A ASP 121 1_555 D CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc3 A OD1 ASN 124 A ASN 124 1_555 D CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc4 A OD1 ASP 125 A ASP 125 1_555 D CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc5 A O GLY 144 A GLY 144 1_555 D CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc6 A OD1 ASP 146 A ASP 146 1_555 D CA CA . A CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc7 A O THR 270 A THR 270 1_555 E CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.254 ? metalc ? metalc8 A OD1 ASP 280 A ASP 280 1_555 E CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc9 A OD2 ASP 280 A ASP 280 1_555 E CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc10 A O TYR 315 A TYR 315 1_555 E CA CA . A CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? metalc ? metalc11 B OD1 ASN 119 B ASN 119 1_555 F CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.946 ? metalc ? metalc12 B O ASP 121 B ASP 121 1_555 F CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc13 B OD1 ASN 124 B ASN 124 1_555 F CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc14 B OD1 ASP 125 B ASP 125 1_555 F CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc15 B O GLY 144 B GLY 144 1_555 F CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc16 B OD1 ASP 146 B ASP 146 1_555 F CA CA . B CA 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc17 B O THR 270 B THR 270 1_555 G CA CA . B CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc18 B OD2 ASP 280 B ASP 280 1_555 G CA CA . B CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc19 B O TYR 315 B TYR 315 1_555 G CA CA . B CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc20 G CA CA . B CA 701 1_555 I O HOH . B HOH 845 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 3EDD _atom_sites.fract_transf_matrix[1][1] 0.005442 _atom_sites.fract_transf_matrix[1][2] 0.003142 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006284 _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] 0.004287 _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 D 3 CA A 1 700 700 CA CA2 . E 3 CA A 1 701 701 CA CA2 . F 3 CA B 1 700 700 CA CA2 . G 3 CA B 1 701 701 CA CA2 . H 4 HOH A 1 702 1 HOH HOH . H 4 HOH A 2 703 2 HOH HOH . H 4 HOH A 3 704 3 HOH HOH . H 4 HOH A 4 705 6 HOH HOH . H 4 HOH A 5 706 7 HOH HOH . H 4 HOH A 6 707 8 HOH HOH . H 4 HOH A 7 708 9 HOH HOH . H 4 HOH A 8 709 10 HOH HOH . H 4 HOH A 9 710 13 HOH HOH . H 4 HOH A 10 711 15 HOH HOH . H 4 HOH A 11 712 17 HOH HOH . H 4 HOH A 12 713 20 HOH HOH . H 4 HOH A 13 714 23 HOH HOH . H 4 HOH A 14 715 25 HOH HOH . H 4 HOH A 15 716 26 HOH HOH . H 4 HOH A 16 717 27 HOH HOH . H 4 HOH A 17 718 30 HOH HOH . H 4 HOH A 18 719 31 HOH HOH . H 4 HOH A 19 720 34 HOH HOH . H 4 HOH A 20 721 35 HOH HOH . H 4 HOH A 21 722 36 HOH HOH . H 4 HOH A 22 723 38 HOH HOH . H 4 HOH A 23 724 39 HOH HOH . H 4 HOH A 24 725 41 HOH HOH . H 4 HOH A 25 726 42 HOH HOH . H 4 HOH A 26 727 45 HOH HOH . H 4 HOH A 27 728 47 HOH HOH . H 4 HOH A 28 729 50 HOH HOH . H 4 HOH A 29 730 52 HOH HOH . H 4 HOH A 30 731 53 HOH HOH . H 4 HOH A 31 732 56 HOH HOH . H 4 HOH A 32 733 57 HOH HOH . H 4 HOH A 33 734 61 HOH HOH . H 4 HOH A 34 735 62 HOH HOH . H 4 HOH A 35 736 63 HOH HOH . H 4 HOH A 36 737 65 HOH HOH . H 4 HOH A 37 738 69 HOH HOH . H 4 HOH A 38 739 70 HOH HOH . H 4 HOH A 39 740 71 HOH HOH . H 4 HOH A 40 741 72 HOH HOH . H 4 HOH A 41 742 73 HOH HOH . H 4 HOH A 42 743 75 HOH HOH . H 4 HOH A 43 744 77 HOH HOH . H 4 HOH A 44 745 80 HOH HOH . H 4 HOH A 45 746 83 HOH HOH . H 4 HOH A 46 747 84 HOH HOH . H 4 HOH A 47 748 88 HOH HOH . H 4 HOH A 48 749 90 HOH HOH . H 4 HOH A 49 750 92 HOH HOH . H 4 HOH A 50 751 94 HOH HOH . H 4 HOH A 51 752 97 HOH HOH . H 4 HOH A 52 753 99 HOH HOH . H 4 HOH A 53 754 100 HOH HOH . H 4 HOH A 54 755 101 HOH HOH . H 4 HOH A 55 756 102 HOH HOH . H 4 HOH A 56 757 103 HOH HOH . H 4 HOH A 57 758 104 HOH HOH . H 4 HOH A 58 759 106 HOH HOH . H 4 HOH A 59 760 107 HOH HOH . H 4 HOH A 60 761 108 HOH HOH . H 4 HOH A 61 762 114 HOH HOH . H 4 HOH A 62 763 117 HOH HOH . H 4 HOH A 63 764 118 HOH HOH . H 4 HOH A 64 765 119 HOH HOH . H 4 HOH A 65 766 121 HOH HOH . I 4 HOH B 1 803 4 HOH HOH . I 4 HOH B 2 804 5 HOH HOH . I 4 HOH B 3 805 11 HOH HOH . I 4 HOH B 4 806 12 HOH HOH . I 4 HOH B 5 807 14 HOH HOH . I 4 HOH B 6 808 16 HOH HOH . I 4 HOH B 7 809 18 HOH HOH . I 4 HOH B 8 810 19 HOH HOH . I 4 HOH B 9 811 21 HOH HOH . I 4 HOH B 10 812 22 HOH HOH . I 4 HOH B 11 813 24 HOH HOH . I 4 HOH B 12 814 28 HOH HOH . I 4 HOH B 13 815 29 HOH HOH . I 4 HOH B 14 816 32 HOH HOH . I 4 HOH B 15 817 33 HOH HOH . I 4 HOH B 16 818 37 HOH HOH . I 4 HOH B 17 819 40 HOH HOH . I 4 HOH B 18 820 43 HOH HOH . I 4 HOH B 19 821 44 HOH HOH . I 4 HOH B 20 822 46 HOH HOH . I 4 HOH B 21 823 48 HOH HOH . I 4 HOH B 22 824 49 HOH HOH . I 4 HOH B 23 825 51 HOH HOH . I 4 HOH B 24 826 54 HOH HOH . I 4 HOH B 25 827 55 HOH HOH . I 4 HOH B 26 828 58 HOH HOH . I 4 HOH B 27 829 59 HOH HOH . I 4 HOH B 28 830 60 HOH HOH . I 4 HOH B 29 831 64 HOH HOH . I 4 HOH B 30 832 66 HOH HOH . I 4 HOH B 31 833 67 HOH HOH . I 4 HOH B 32 834 68 HOH HOH . I 4 HOH B 33 835 74 HOH HOH . I 4 HOH B 34 836 76 HOH HOH . I 4 HOH B 35 837 78 HOH HOH . I 4 HOH B 36 838 79 HOH HOH . I 4 HOH B 37 839 81 HOH HOH . I 4 HOH B 38 840 82 HOH HOH . I 4 HOH B 39 841 85 HOH HOH . I 4 HOH B 40 842 86 HOH HOH . I 4 HOH B 41 843 87 HOH HOH . I 4 HOH B 42 844 89 HOH HOH . I 4 HOH B 43 845 91 HOH HOH . I 4 HOH B 44 846 93 HOH HOH . I 4 HOH B 45 847 95 HOH HOH . I 4 HOH B 46 848 96 HOH HOH . I 4 HOH B 47 849 98 HOH HOH . I 4 HOH B 48 850 105 HOH HOH . I 4 HOH B 49 851 109 HOH HOH . I 4 HOH B 50 852 110 HOH HOH . I 4 HOH B 51 853 111 HOH HOH . I 4 HOH B 52 854 112 HOH HOH . I 4 HOH B 53 855 113 HOH HOH . I 4 HOH B 54 856 115 HOH HOH . I 4 HOH B 55 857 116 HOH HOH . I 4 HOH B 56 858 120 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _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 3 _atom_site.Cartn_x 31.854 _atom_site.Cartn_y 1.729 _atom_site.Cartn_z 43.966 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 49.14 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 701 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 349 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 1 #