data_6GNE # _model_server_result.job_id CZT6F8A8Avze_RB76rVWFQ _model_server_result.datetime_utc '2024-12-26 20:32:49' _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 6gne # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":601}' # _entry.id 6GNE # _exptl.entry_id 6GNE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 90 _cell.angle_gamma 90 _cell.entry_id 6GNE _cell.length_a 129.76 _cell.length_b 166.94 _cell.length_c 47.94 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GNE _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 ? 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,D,F,H 1 1 B,E,G,I 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 F N N ? 4 G 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 GLC GLC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 AC1 GLC C1 O1 . O4 HO4 . sing 3 ? 3 2 1 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 C 2 ACR 2 n C GLC 2 C 2 GLC C 2 ACR 2 n C AC1 3 C 3 AC1 C 2 ACR 3 n D GLC 1 D 1 GLC E 1 MAL 3 n D GLC 2 D 2 GLC E 1 MAL 2 n E GLC 1 E 1 GLC C 4 ACR 2 n E GLC 2 E 2 GLC C 4 ACR 2 n E AC1 3 E 3 AC1 C 4 ACR # 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 sing covale ? covale2 C O4 GLC . C GLC 2 1_555 C C1 AC1 . C AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 sing covale ? covale3 D O4 GLC . D GLC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 sing covale ? covale4 E O4 GLC . E GLC 1 1_555 E C1 GLC . E GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 sing covale ? covale5 E O4 GLC . E GLC 2 1_555 E C1 AC1 . E AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 sing # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PB O1B ADP doub 47 n n PB O2B ADP sing 48 n n PB O3B ADP sing 49 n n PB O3A ADP sing 50 n n O2B HOB2 ADP sing 51 n n O3B HOB3 ADP sing 52 n n PA O1A ADP doub 53 n n PA O2A ADP sing 54 n n PA O3A ADP sing 55 n n PA O5' ADP sing 56 n n O2A HOA2 ADP sing 57 n n O5' C5' ADP sing 58 n n C5' C4' ADP sing 59 n n C5' "H5'1" ADP sing 60 n n C5' "H5'2" ADP sing 61 n n C4' O4' ADP sing 62 n n C4' C3' ADP sing 63 n n C4' H4' ADP sing 64 n n O4' C1' ADP sing 65 n n C3' O3' ADP sing 66 n n C3' C2' ADP sing 67 n n C3' H3' ADP sing 68 n n O3' HO3' ADP sing 69 n n C2' O2' ADP sing 70 n n C2' C1' ADP sing 71 n n C2' H2' ADP sing 72 n n O2' HO2' ADP sing 73 n n C1' N9 ADP sing 74 n n C1' H1' ADP sing 75 n n N9 C8 ADP sing 76 n y N9 C4 ADP sing 77 n y C8 N7 ADP doub 78 n y C8 H8 ADP sing 79 n n N7 C5 ADP sing 80 n y C5 C6 ADP sing 81 n y C5 C4 ADP doub 82 n y C6 N6 ADP sing 83 n n C6 N1 ADP doub 84 n y N6 HN61 ADP sing 85 n n N6 HN62 ADP sing 86 n n N1 C2 ADP sing 87 n y C2 N3 ADP doub 88 n y C2 H2 ADP sing 89 n n N3 C4 ADP sing 90 n y # _atom_sites.entry_id 6GNE _atom_sites.fract_transf_matrix[1][1] 0.007707 _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] 0.00599 _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] 0.020859 _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 ADP A 1 601 1 ADP ADP . G 4 ADP B 1 601 3 ADP ADP . H 5 HOH A 1 701 74 HOH HOH . H 5 HOH A 2 702 102 HOH HOH . H 5 HOH A 3 703 98 HOH HOH . H 5 HOH A 4 704 82 HOH HOH . H 5 HOH A 5 705 14 HOH HOH . H 5 HOH A 6 706 113 HOH HOH . H 5 HOH A 7 707 39 HOH HOH . H 5 HOH A 8 708 78 HOH HOH . H 5 HOH A 9 709 61 HOH HOH . H 5 HOH A 10 710 81 HOH HOH . H 5 HOH A 11 711 116 HOH HOH . H 5 HOH A 12 712 59 HOH HOH . H 5 HOH A 13 713 109 HOH HOH . H 5 HOH A 14 714 35 HOH HOH . H 5 HOH A 15 715 87 HOH HOH . H 5 HOH A 16 716 94 HOH HOH . H 5 HOH A 17 717 112 HOH HOH . H 5 HOH A 18 718 68 HOH HOH . H 5 HOH A 19 719 93 HOH HOH . H 5 HOH A 20 720 48 HOH HOH . H 5 HOH A 21 721 47 HOH HOH . H 5 HOH A 22 722 107 HOH HOH . H 5 HOH A 23 723 75 HOH HOH . H 5 HOH A 24 724 57 HOH HOH . H 5 HOH A 25 725 38 HOH HOH . H 5 HOH A 26 726 92 HOH HOH . H 5 HOH A 27 727 83 HOH HOH . H 5 HOH A 28 728 66 HOH HOH . H 5 HOH A 29 729 46 HOH HOH . H 5 HOH A 30 730 64 HOH HOH . H 5 HOH A 31 731 77 HOH HOH . H 5 HOH A 32 732 119 HOH HOH . H 5 HOH A 33 733 4 HOH HOH . H 5 HOH A 34 734 13 HOH HOH . H 5 HOH A 35 735 62 HOH HOH . H 5 HOH A 36 736 20 HOH HOH . H 5 HOH A 37 737 114 HOH HOH . H 5 HOH A 38 738 51 HOH HOH . H 5 HOH A 39 739 80 HOH HOH . H 5 HOH A 40 740 110 HOH HOH . H 5 HOH A 41 741 96 HOH HOH . H 5 HOH A 42 742 45 HOH HOH . H 5 HOH A 43 743 34 HOH HOH . H 5 HOH A 44 744 12 HOH HOH . H 5 HOH A 45 745 42 HOH HOH . H 5 HOH A 46 746 73 HOH HOH . H 5 HOH A 47 747 70 HOH HOH . H 5 HOH A 48 748 106 HOH HOH . H 5 HOH A 49 749 10 HOH HOH . H 5 HOH A 50 750 120 HOH HOH . H 5 HOH A 51 751 65 HOH HOH . H 5 HOH A 52 752 97 HOH HOH . H 5 HOH A 53 753 121 HOH HOH . H 5 HOH A 54 754 118 HOH HOH . H 5 HOH A 55 755 115 HOH HOH . H 5 HOH A 56 756 36 HOH HOH . H 5 HOH A 57 757 60 HOH HOH . H 5 HOH A 58 758 19 HOH HOH . H 5 HOH A 59 759 6 HOH HOH . H 5 HOH A 60 760 18 HOH HOH . H 5 HOH A 61 761 72 HOH HOH . H 5 HOH A 62 762 21 HOH HOH . I 5 HOH B 1 701 26 HOH HOH . I 5 HOH B 2 702 40 HOH HOH . I 5 HOH B 3 703 11 HOH HOH . I 5 HOH B 4 704 44 HOH HOH . I 5 HOH B 5 705 99 HOH HOH . I 5 HOH B 6 706 85 HOH HOH . I 5 HOH B 7 707 117 HOH HOH . I 5 HOH B 8 708 27 HOH HOH . I 5 HOH B 9 709 69 HOH HOH . I 5 HOH B 10 710 104 HOH HOH . I 5 HOH B 11 711 101 HOH HOH . I 5 HOH B 12 712 33 HOH HOH . I 5 HOH B 13 713 89 HOH HOH . I 5 HOH B 14 714 24 HOH HOH . I 5 HOH B 15 715 91 HOH HOH . I 5 HOH B 16 716 28 HOH HOH . I 5 HOH B 17 717 43 HOH HOH . I 5 HOH B 18 718 53 HOH HOH . I 5 HOH B 19 719 55 HOH HOH . I 5 HOH B 20 720 5 HOH HOH . I 5 HOH B 21 721 41 HOH HOH . I 5 HOH B 22 722 31 HOH HOH . I 5 HOH B 23 723 71 HOH HOH . I 5 HOH B 24 724 9 HOH HOH . I 5 HOH B 25 725 37 HOH HOH . I 5 HOH B 26 726 22 HOH HOH . I 5 HOH B 27 727 32 HOH HOH . I 5 HOH B 28 728 103 HOH HOH . I 5 HOH B 29 729 105 HOH HOH . I 5 HOH B 30 730 90 HOH HOH . I 5 HOH B 31 731 88 HOH HOH . I 5 HOH B 32 732 76 HOH HOH . I 5 HOH B 33 733 108 HOH HOH . I 5 HOH B 34 734 23 HOH HOH . I 5 HOH B 35 735 2 HOH HOH . I 5 HOH B 36 736 58 HOH HOH . I 5 HOH B 37 737 15 HOH HOH . I 5 HOH B 38 738 111 HOH HOH . I 5 HOH B 39 739 95 HOH HOH . I 5 HOH B 40 740 54 HOH HOH . I 5 HOH B 41 741 29 HOH HOH . I 5 HOH B 42 742 1 HOH HOH . I 5 HOH B 43 743 63 HOH HOH . I 5 HOH B 44 744 67 HOH HOH . I 5 HOH B 45 745 52 HOH HOH . I 5 HOH B 46 746 49 HOH HOH . I 5 HOH B 47 747 86 HOH HOH . I 5 HOH B 48 748 50 HOH HOH . I 5 HOH B 49 749 16 HOH HOH . I 5 HOH B 50 750 25 HOH HOH . I 5 HOH B 51 751 84 HOH HOH . I 5 HOH B 52 752 30 HOH HOH . I 5 HOH B 53 753 56 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PB ADP . . . F 4 -32.988 15.933 -9.354 1 27.46 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . F 4 -31.505 15.875 -9.572 1 28.85 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . F 4 -33.64 14.683 -8.838 1 27.4 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . F 4 -33.365 17.135 -8.519 1 28.09 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . F 4 -33.02 15.809 -12.236 1 28.5 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . F 4 -34.109 16.07 -13.236 1 29.64 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . F 4 -31.734 16.553 -12.487 1 30.69 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . F 4 -33.658 16.156 -10.799 1 27.33 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . F 4 -32.659 14.246 -12.158 1 28.95 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . F 4 -33.639 13.251 -11.858 1 29.36 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . F 4 -33.265 11.834 -12.33 1 28.85 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . F 4 -33.759 10.864 -11.394 1 28.56 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . F 4 -33.915 11.446 -13.642 1 28.13 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . F 4 -33.113 10.46 -14.27 1 27.88 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . F 4 -35.216 10.814 -13.221 1 27.7 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . F 4 -35.738 9.925 -14.192 1 28.75 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . F 4 -34.785 10.072 -11.991 1 28.36 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . F 4 -35.862 9.886 -10.994 1 29.82 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . F 4 -36.334 10.794 -10.131 1 29.22 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . F 4 -37.283 10.246 -9.339 1 29.29 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . F 4 -37.427 8.959 -9.692 1 29.69 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . F 4 -38.27 7.798 -9.267 1 29.92 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . F 4 -39.181 7.943 -8.272 1 28.33 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . F 4 -38.085 6.616 -9.921 1 29.74 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . F 4 -37.182 6.503 -10.929 1 30.03 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . F 4 -36.407 7.514 -11.354 1 29.05 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . F 4 -36.486 8.735 -10.788 1 29.65 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 284 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #