data_6GNG # _model_server_result.job_id lBiAwhEDkd6eaQPha5cfww _model_server_result.datetime_utc '2025-01-22 01:51:25' _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":"F","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 . . . F 3 32.844 7.744 -36.717 1 47.53 ? PB ADP 602 B 1 HETATM 2 O O1B ADP . . . F 3 33.691 8.15 -37.902 1 51.05 ? O1B ADP 602 B 1 HETATM 3 O O2B ADP . . . F 3 31.667 6.855 -36.998 1 46.52 ? O2B ADP 602 B 1 HETATM 4 O O3B ADP . . . F 3 32.521 8.886 -35.803 1 47.1 ? O3B ADP 602 B 1 HETATM 5 P PA ADP . . . F 3 34.502 5.453 -36.453 1 47.62 ? PA ADP 602 B 1 HETATM 6 O O1A ADP . . . F 3 35.992 5.691 -36.378 1 44.92 ? O1A ADP 602 B 1 HETATM 7 O O2A ADP . . . F 3 33.934 4.264 -35.727 1 47.36 ? O2A ADP 602 B 1 HETATM 8 O O3A ADP . . . F 3 33.81 6.786 -35.868 1 47.65 ? O3A ADP 602 B 1 HETATM 9 O O5' ADP . . . F 3 34.061 5.309 -37.998 1 52.76 ? O5' ADP 602 B 1 HETATM 10 C C5' ADP . . . F 3 35.044 5.041 -39.003 1 59.07 ? C5' ADP 602 B 1 HETATM 11 C C4' ADP . . . F 3 34.39 4.612 -40.306 1 62.12 ? C4' ADP 602 B 1 HETATM 12 O O4' ADP . . . F 3 33.812 5.772 -40.902 1 66.42 ? O4' ADP 602 B 1 HETATM 13 C C3' ADP . . . F 3 35.358 4.047 -41.346 1 64.78 ? C3' ADP 602 B 1 HETATM 14 O O3' ADP . . . F 3 34.883 2.751 -41.745 1 65.09 ? O3' ADP 602 B 1 HETATM 15 C C2' ADP . . . F 3 35.378 5.07 -42.489 1 66.1 ? C2' ADP 602 B 1 HETATM 16 O O2' ADP . . . F 3 35.538 4.513 -43.803 1 64.69 ? O2' ADP 602 B 1 HETATM 17 C C1' ADP . . . F 3 34.01 5.706 -42.32 1 67.15 ? C1' ADP 602 B 1 HETATM 18 N N9 ADP . . . F 3 33.755 7.033 -42.959 1 67.56 ? N9 ADP 602 B 1 HETATM 19 C C8 ADP . . . F 3 34.438 8.195 -42.832 1 65.55 ? C8 ADP 602 B 1 HETATM 20 N N7 ADP . . . F 3 33.843 9.177 -43.569 1 64.22 ? N7 ADP 602 B 1 HETATM 21 C C5 ADP . . . F 3 32.751 8.648 -44.173 1 66.73 ? C5 ADP 602 B 1 HETATM 22 C C6 ADP . . . F 3 31.653 9.086 -45.093 1 66.93 ? C6 ADP 602 B 1 HETATM 23 N N6 ADP . . . F 3 31.57 10.349 -45.56 1 68.31 ? N6 ADP 602 B 1 HETATM 24 N N1 ADP . . . F 3 30.715 8.181 -45.472 1 66.46 ? N1 ADP 602 B 1 HETATM 25 C C2 ADP . . . F 3 30.732 6.904 -45.043 1 65.67 ? C2 ADP 602 B 1 HETATM 26 N N3 ADP . . . F 3 31.687 6.444 -44.215 1 67.36 ? N3 ADP 602 B 1 HETATM 27 C C4 ADP . . . F 3 32.7 7.239 -43.756 1 67.96 ? C4 ADP 602 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #