data_6GNG # _model_server_result.job_id ZUTYRZ-OtldxlYhpMh1gWg _model_server_result.datetime_utc '2025-01-22 01:51:15' _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 6gng # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":602}' # _entry.id 6GNG # _exptl.entry_id 6GNG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 6GNG _cell.length_a 69.3 _cell.length_b 106.1 _cell.length_c 175.5 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GNG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 ? 3 E N N ? 3 F 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 2 1 GLC BGC C1 O1 . O4 HO4 . sing 2 ? 2 3 2 AC1 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 BGC 1 C 1 BGC D 1 ACR 2 n C GLC 2 C 2 GLC D 1 ACR 2 n C AC1 3 C 3 AC1 D 1 ACR 2 n D BGC 1 D 1 BGC D 2 ACR 2 n D GLC 2 D 2 GLC D 2 ACR 2 n D AC1 3 D 3 AC1 D 2 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 BGC . C BGC 1 1_555 C C1 GLC . C GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 sing covale ? covale2 C O4 GLC . C GLC 2 1_555 C C1 AC1 . C AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 sing covale ? covale3 D O4 BGC . D BGC 1 1_555 D C1 GLC . D GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 sing covale ? covale4 D O4 GLC . D GLC 2 1_555 D C1 AC1 . D AC1 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 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 6GNG _atom_sites.fract_transf_matrix[1][1] 0.01443 _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] 0.009425 _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] 0.005698 _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 3 ADP A 1 602 2 ADP ADP . F 3 ADP B 1 602 1 ADP ADP . G 4 HOH A 1 701 2 HOH HOH . G 4 HOH A 2 702 4 HOH HOH . H 4 HOH B 1 701 3 HOH HOH . H 4 HOH B 2 702 5 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 . . . E 3 0.793 3.929 9.409 1 52.2 ? PB ADP 602 A 1 HETATM 2 O O1B ADP . . . E 3 0.895 5.059 8.428 1 51.62 ? O1B ADP 602 A 1 HETATM 3 O O2B ADP . . . E 3 2.026 3.076 9.492 1 52.97 ? O2B ADP 602 A 1 HETATM 4 O O3B ADP . . . E 3 0.171 4.338 10.729 1 55.73 ? O3B ADP 602 A 1 HETATM 5 P PA ADP . . . E 3 -0.348 1.365 9.295 1 50.54 ? PA ADP 602 A 1 HETATM 6 O O1A ADP . . . E 3 0.634 0.536 8.501 1 47.34 ? O1A ADP 602 A 1 HETATM 7 O O2A ADP . . . E 3 -1.829 1.067 9.271 1 49.19 ? O2A ADP 602 A 1 HETATM 8 O O3A ADP . . . E 3 -0.24 2.882 8.765 1 51.76 ? O3A ADP 602 A 1 HETATM 9 O O5' ADP . . . E 3 0.158 1.368 10.84 1 56.65 ? O5' ADP 602 A 1 HETATM 10 C C5' ADP . . . E 3 -0.679 1.099 11.981 1 60.28 ? C5' ADP 602 A 1 HETATM 11 C C4' ADP . . . E 3 0.078 0.296 13.052 1 62.44 ? C4' ADP 602 A 1 HETATM 12 O O4' ADP . . . E 3 0.591 1.174 14.054 1 65.7 ? O4' ADP 602 A 1 HETATM 13 C C3' ADP . . . E 3 -0.757 -0.72 13.832 1 63.87 ? C3' ADP 602 A 1 HETATM 14 O O3' ADP . . . E 3 0.015 -1.916 13.995 1 64.74 ? O3' ADP 602 A 1 HETATM 15 C C2' ADP . . . E 3 -1.082 -0.074 15.174 1 63.6 ? C2' ADP 602 A 1 HETATM 16 O O2' ADP . . . E 3 -0.889 -0.982 16.257 1 60.24 ? O2' ADP 602 A 1 HETATM 17 C C1' ADP . . . E 3 -0.095 1.073 15.321 1 66.34 ? C1' ADP 602 A 1 HETATM 18 N N9 ADP . . . E 3 -0.608 2.443 15.576 1 68.11 ? N9 ADP 602 A 1 HETATM 19 C C8 ADP . . . E 3 -1.824 2.964 15.317 1 69.55 ? C8 ADP 602 A 1 HETATM 20 N N7 ADP . . . E 3 -1.859 4.276 15.646 1 68.98 ? N7 ADP 602 A 1 HETATM 21 C C5 ADP . . . E 3 -0.646 4.605 16.104 1 69.56 ? C5 ADP 602 A 1 HETATM 22 C C6 ADP . . . E 3 -0.006 5.829 16.622 1 73.03 ? C6 ADP 602 A 1 HETATM 23 N N6 ADP . . . E 3 -0.749 6.954 16.688 1 73.03 ? N6 ADP 602 A 1 HETATM 24 N N1 ADP . . . E 3 1.303 5.768 17.014 1 74.45 ? N1 ADP 602 A 1 HETATM 25 C C2 ADP . . . E 3 2.022 4.623 16.94 1 71.55 ? C2 ADP 602 A 1 HETATM 26 N N3 ADP . . . E 3 1.486 3.473 16.473 1 71.62 ? N3 ADP 602 A 1 HETATM 27 C C4 ADP . . . E 3 0.185 3.403 16.051 1 69.51 ? C4 ADP 602 A 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 27 #