data_6D3K # _model_server_result.job_id Fqn8cm5qY7uI7fyL8LXWDA _model_server_result.datetime_utc '2024-11-14 18:56:53' _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 6d3k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":601}' # _entry.id 6D3K # _exptl.entry_id 6D3K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 6D3K _cell.length_a 106.48 _cell.length_b 159.6 _cell.length_c 172.99 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6D3K _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 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,B,D,E,F,G,H,I,J,K,L,M,U,V 1 1 A,C,D,E,F,G,N,O,P,Q,R,S,T,U,W 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 ? 2 D N N ? 2 H N N ? 2 N N N # 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 metalc ? metalc1 A OD1 ASN 191 B ASN 419 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc2 A OD2 ASP 204 B ASP 432 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? metalc ? metalc3 D O3B ADP . B ADP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc4 D O2A ADP . B ADP 601 1_555 F MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc5 B OD1 ASN 191 A ASN 419 1_555 J MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc6 B OD2 ASP 204 A ASP 432 1_555 J MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc7 H O1A ADP . A ADP 601 1_555 J MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc8 H O3A ADP . A ADP 601 1_555 J MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc9 C OD1 ASN 191 C ASN 419 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc10 C OD2 ASP 204 C ASP 432 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc11 N O2B ADP . C ADP 601 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc12 N O1A ADP . C ADP 601 1_555 P MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _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 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6D3K _atom_sites.fract_transf_matrix[1][1] 0.009391 _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] 0.006266 _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] 0.005781 _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 2 ADP B 1 601 600 ADP ADP . E 3 PO4 B 1 602 650 PO4 PO4 . F 4 MG B 1 603 700 MG MG . G 5 SO4 B 1 604 11 SO4 SO4 . H 2 ADP A 1 601 600 ADP ADP . I 3 PO4 A 1 602 650 PO4 PO4 . J 4 MG A 1 603 701 MG MG . K 5 SO4 A 1 604 2 SO4 SO4 . L 5 SO4 A 1 605 6 SO4 SO4 . M 5 SO4 A 1 606 7 SO4 SO4 . N 2 ADP C 1 601 601 ADP ADP . O 3 PO4 C 1 602 650 PO4 PO4 . P 4 MG C 1 603 700 MG MG . Q 5 SO4 C 1 604 1 SO4 SO4 . R 5 SO4 C 1 605 9 SO4 SO4 . S 5 SO4 C 1 606 10 SO4 SO4 . T 3 PO4 C 1 607 1 PO4 PO4 . U 6 HOH B 1 701 125 HOH HOH . U 6 HOH B 2 702 117 HOH HOH . U 6 HOH B 3 703 99 HOH HOH . U 6 HOH B 4 704 76 HOH HOH . U 6 HOH B 5 705 100 HOH HOH . U 6 HOH B 6 706 116 HOH HOH . U 6 HOH B 7 707 74 HOH HOH . U 6 HOH B 8 708 9 HOH HOH . U 6 HOH B 9 709 95 HOH HOH . U 6 HOH B 10 710 118 HOH HOH . U 6 HOH B 11 711 89 HOH HOH . U 6 HOH B 12 712 98 HOH HOH . U 6 HOH B 13 713 91 HOH HOH . U 6 HOH B 14 714 94 HOH HOH . U 6 HOH B 15 715 124 HOH HOH . V 6 HOH A 1 701 113 HOH HOH . V 6 HOH A 2 702 107 HOH HOH . V 6 HOH A 3 703 97 HOH HOH . V 6 HOH A 4 704 119 HOH HOH . V 6 HOH A 5 705 106 HOH HOH . V 6 HOH A 6 706 110 HOH HOH . V 6 HOH A 7 707 112 HOH HOH . V 6 HOH A 8 708 105 HOH HOH . V 6 HOH A 9 709 78 HOH HOH . V 6 HOH A 10 710 123 HOH HOH . V 6 HOH A 11 711 31 HOH HOH . V 6 HOH A 12 712 115 HOH HOH . V 6 HOH A 13 713 81 HOH HOH . V 6 HOH A 14 714 122 HOH HOH . V 6 HOH A 15 715 28 HOH HOH . V 6 HOH A 16 716 102 HOH HOH . V 6 HOH A 17 717 79 HOH HOH . V 6 HOH A 18 718 114 HOH HOH . V 6 HOH A 19 719 85 HOH HOH . V 6 HOH A 20 720 88 HOH HOH . V 6 HOH A 21 721 90 HOH HOH . W 6 HOH C 1 701 121 HOH HOH . W 6 HOH C 2 702 61 HOH HOH . W 6 HOH C 3 703 93 HOH HOH . W 6 HOH C 4 704 70 HOH HOH . W 6 HOH C 5 705 35 HOH HOH . W 6 HOH C 6 706 27 HOH HOH . W 6 HOH C 7 707 69 HOH HOH . W 6 HOH C 8 708 104 HOH HOH . W 6 HOH C 9 709 120 HOH HOH . W 6 HOH C 10 710 67 HOH HOH . W 6 HOH C 11 711 12 HOH HOH . W 6 HOH C 12 712 73 HOH HOH . W 6 HOH C 13 713 26 HOH HOH . W 6 HOH C 14 714 36 HOH HOH . W 6 HOH C 15 715 53 HOH HOH . W 6 HOH C 16 716 44 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 . . . H 2 6.416 -66.281 -14.598 1 82.66 ? PB ADP 601 A 1 HETATM 2 O O1B ADP . . . H 2 6.607 -66.278 -16.105 1 65.47 ? O1B ADP 601 A 1 HETATM 3 O O2B ADP . . . H 2 6.004 -65.058 -13.774 1 72.8 ? O2B ADP 601 A 1 HETATM 4 O O3B ADP . . . H 2 7.515 -67.088 -13.913 1 92.65 ? O3B ADP 601 A 1 HETATM 5 P PA ADP . . . H 2 4.66 -68.489 -13.862 1 71.37 ? PA ADP 601 A 1 HETATM 6 O O1A ADP . . . H 2 3.18 -68.369 -14.071 1 83.91 ? O1A ADP 601 A 1 HETATM 7 O O2A ADP . . . H 2 5.262 -68.689 -12.497 1 59.92 ? O2A ADP 601 A 1 HETATM 8 O O3A ADP . . . H 2 5.002 -67.046 -14.518 1 84.07 ? O3A ADP 601 A 1 HETATM 9 O O5' ADP . . . H 2 5.245 -69.597 -14.885 1 62.37 ? O5' ADP 601 A 1 HETATM 10 C C5' ADP . . . H 2 5.087 -69.468 -16.3 1 70.94 ? C5' ADP 601 A 1 HETATM 11 C C4' ADP . . . H 2 4.338 -70.61 -16.989 1 71.54 ? C4' ADP 601 A 1 HETATM 12 O O4' ADP . . . H 2 4.905 -71.871 -16.637 1 73.09 ? O4' ADP 601 A 1 HETATM 13 C C3' ADP . . . H 2 2.847 -70.716 -16.667 1 73.72 ? C3' ADP 601 A 1 HETATM 14 O O3' ADP . . . H 2 1.959 -69.869 -17.42 1 65.3 ? O3' ADP 601 A 1 HETATM 15 C C2' ADP . . . H 2 2.628 -72.187 -16.964 1 73.29 ? C2' ADP 601 A 1 HETATM 16 O O2' ADP . . . H 2 2.539 -72.448 -18.364 1 73.47 ? O2' ADP 601 A 1 HETATM 17 C C1' ADP . . . H 2 3.885 -72.838 -16.447 1 69.59 ? C1' ADP 601 A 1 HETATM 18 N N9 ADP . . . H 2 3.768 -73.218 -15.016 1 66.62 ? N9 ADP 601 A 1 HETATM 19 C C8 ADP . . . H 2 4.237 -72.591 -13.923 1 71.07 ? C8 ADP 601 A 1 HETATM 20 N N7 ADP . . . H 2 3.963 -73.259 -12.777 1 69.1 ? N7 ADP 601 A 1 HETATM 21 C C5 ADP . . . H 2 3.307 -74.35 -13.16 1 70.57 ? C5 ADP 601 A 1 HETATM 22 C C6 ADP . . . H 2 2.728 -75.497 -12.477 1 68.36 ? C6 ADP 601 A 1 HETATM 23 N N6 ADP . . . H 2 2.803 -75.574 -11.147 1 77.35 ? N6 ADP 601 A 1 HETATM 24 N N1 ADP . . . H 2 2.143 -76.436 -13.23 1 67.46 ? N1 ADP 601 A 1 HETATM 25 C C2 ADP . . . H 2 2.069 -76.349 -14.576 1 65.55 ? C2 ADP 601 A 1 HETATM 26 N N3 ADP . . . H 2 2.569 -75.336 -15.282 1 66.74 ? N3 ADP 601 A 1 HETATM 27 C C4 ADP . . . H 2 3.179 -74.323 -14.624 1 70.07 ? C4 ADP 601 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 228 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #