data_4XCD # _model_server_result.job_id 3dfk_NZ1Xpvc2TtMUCqPNw _model_server_result.datetime_utc '2025-04-12 22:30:53' _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 4xcd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":600}' # _entry.id 4XCD # _exptl.entry_id 4XCD _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 6 _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 4XCD _cell.length_a 163.36 _cell.length_b 163.36 _cell.length_c 327.29 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XCD _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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' 2_645 -y+1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 245.04 -141.47391 0 3 'crystal symmetry operation' 3_765 -x+y+2,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 245.04 141.47391 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N # _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 4XCD _atom_sites.fract_transf_matrix[1][1] 0.006121 _atom_sites.fract_transf_matrix[1][2] 0.003534 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007068 _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] 0.003055 _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 G 2 ADP A 1 600 600 ADP ADP . H 2 ADP B 1 600 600 ADP ADP . I 2 ADP C 1 600 600 ADP ADP . J 2 ADP D 1 600 600 ADP ADP . K 2 ADP E 1 600 600 ADP ADP . L 2 ADP F 1 600 600 ADP ADP . # 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 . . . I 2 155.247 61.9 52.363 1 228.9 ? PB ADP 600 C 1 HETATM 2 O O1B ADP . . . I 2 154.994 61.035 51.122 1 224.69 ? O1B ADP 600 C 1 HETATM 3 O O2B ADP . . . I 2 155.069 61.08 53.625 1 226.87 -1 O2B ADP 600 C 1 HETATM 4 O O3B ADP . . . I 2 154.49 63.18 52.395 1 228.46 -1 O3B ADP 600 C 1 HETATM 5 P PA ADP . . . I 2 157.702 62.46 53.674 1 206.48 ? PA ADP 600 C 1 HETATM 6 O O1A ADP . . . I 2 159.098 62.73 53.276 1 219.46 -1 O1A ADP 600 C 1 HETATM 7 O O2A ADP . . . I 2 157.653 61.184 54.497 1 192.14 ? O2A ADP 600 C 1 HETATM 8 O O3A ADP . . . I 2 156.803 62.225 52.384 1 217.05 ? O3A ADP 600 C 1 HETATM 9 O O5' ADP . . . I 2 157.004 63.657 54.479 1 189.78 ? O5' ADP 600 C 1 HETATM 10 C C5' ADP . . . I 2 155.931 63.43 55.41 1 178.28 ? C5' ADP 600 C 1 HETATM 11 C C4' ADP . . . I 2 155.894 64.518 56.455 1 170.45 ? C4' ADP 600 C 1 HETATM 12 O O4' ADP . . . I 2 157.162 65.194 56.51 1 164.53 ? O4' ADP 600 C 1 HETATM 13 C C3' ADP . . . I 2 154.843 65.6 56.217 1 170.95 ? C3' ADP 600 C 1 HETATM 14 O O3' ADP . . . I 2 153.696 65.369 57.03 1 170.45 ? O3' ADP 600 C 1 HETATM 15 C C2' ADP . . . I 2 155.545 66.914 56.605 1 169.89 ? C2' ADP 600 C 1 HETATM 16 O O2' ADP . . . I 2 154.83 67.57 57.65 1 172.7 ? O2' ADP 600 C 1 HETATM 17 C C1' ADP . . . I 2 156.949 66.479 57.05 1 163.46 ? C1' ADP 600 C 1 HETATM 18 N N9 ADP . . . I 2 158.021 67.358 56.577 1 154.02 ? N9 ADP 600 C 1 HETATM 19 C C8 ADP . . . I 2 158.485 67.459 55.292 1 145.64 ? C8 ADP 600 C 1 HETATM 20 N N7 ADP . . . I 2 159.436 68.349 55.133 1 138.86 ? N7 ADP 600 C 1 HETATM 21 C C5 ADP . . . I 2 159.612 68.872 56.405 1 145.66 ? C5 ADP 600 C 1 HETATM 22 C C6 ADP . . . I 2 160.463 69.877 56.91 1 147.51 ? C6 ADP 600 C 1 HETATM 23 N N6 ADP . . . I 2 161.333 70.563 56.164 1 150.61 ? N6 ADP 600 C 1 HETATM 24 N N1 ADP . . . I 2 160.376 70.172 58.227 1 143.71 ? N1 ADP 600 C 1 HETATM 25 C C2 ADP . . . I 2 159.494 69.504 58.977 1 147.96 ? C2 ADP 600 C 1 HETATM 26 N N3 ADP . . . I 2 158.643 68.538 58.614 1 152.28 ? N3 ADP 600 C 1 HETATM 27 C C4 ADP . . . I 2 158.75 68.267 57.307 1 149.59 ? C4 ADP 600 C 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 374 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #