data_3AP3 # _model_server_result.job_id B1Yj9gXVRkJButbY-D0l7Q _model_server_result.datetime_utc '2024-11-23 05:37:28' _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 3ap3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1}' # _entry.id 3AP3 # _exptl.entry_id 3AP3 _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-3'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 3AP3 _cell.length_a 71.432 _cell.length_b 81.326 _cell.length_c 226.659 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AP3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 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 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,E,F 1 1 C,D,G,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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 H 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 disulf ? disulf1 A SG CYS 74 A CYS 96 1_555 A SG CYS 134 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf2 A SG CYS 203 A CYS 225 1_555 A SG CYS 211 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 B SG CYS 74 B CYS 96 1_555 B SG CYS 134 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf4 B SG CYS 203 B CYS 225 1_555 B SG CYS 211 B CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf5 C SG CYS 74 C CYS 96 1_555 C SG CYS 134 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 C SG CYS 203 C CYS 225 1_555 C SG CYS 211 C CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 D SG CYS 74 D CYS 96 1_555 D SG CYS 134 D CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf8 D SG CYS 203 D CYS 225 1_555 D SG CYS 211 D CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A3P _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-3'-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 P1 O1P A3P doub 1 n n P1 O2P A3P sing 2 n n P1 O3P A3P sing 3 n n P1 O3' A3P sing 4 n n O2P HOP2 A3P sing 5 n n O3P HOP3 A3P sing 6 n n P2 O4P A3P doub 7 n n P2 O5P A3P sing 8 n n P2 O6P A3P sing 9 n n P2 O5' A3P sing 10 n n O5P HOP5 A3P sing 11 n n O6P HOP6 A3P sing 12 n n O5' C5' A3P sing 13 n n C5' C4' A3P sing 14 n n C5' "H5'1" A3P sing 15 n n C5' "H5'2" A3P sing 16 n n C4' O4' A3P sing 17 n n C4' C3' A3P sing 18 n n C4' H4' A3P sing 19 n n O4' C1' A3P sing 20 n n C3' O3' A3P sing 21 n n C3' C2' A3P sing 22 n n C3' H3' A3P sing 23 n n C2' O2' A3P sing 24 n n C2' C1' A3P sing 25 n n C2' H2' A3P sing 26 n n O2' HO2' A3P sing 27 n n C1' N9 A3P sing 28 n n C1' H1' A3P sing 29 n n N9 C8 A3P sing 30 n y N9 C4 A3P sing 31 n y C8 N7 A3P doub 32 n y C8 H8 A3P sing 33 n n N7 C5 A3P sing 34 n y C5 C6 A3P sing 35 n y C5 C4 A3P doub 36 n y C6 N6 A3P sing 37 n n C6 N1 A3P doub 38 n y N6 HN61 A3P sing 39 n n N6 HN62 A3P sing 40 n n N1 C2 A3P sing 41 n y C2 N3 A3P doub 42 n y C2 H2 A3P sing 43 n n N3 C4 A3P sing 44 n y # _atom_sites.entry_id 3AP3 _atom_sites.fract_transf_matrix[1][1] 0.013999 _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] 0.012296 _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] 0.004412 _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 2 A3P A 1 1 1 A3P A3P . F 2 A3P B 1 1 1 A3P A3P . G 2 A3P C 1 1 1 A3P A3P . H 2 A3P D 1 1 1 A3P A3P . # 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 P1 A3P . . . F 2 -11.694 -25.416 -45.426 1 119.03 ? P1 A3P 1 B 1 HETATM 2 O O1P A3P . . . F 2 -12.673 -25.277 -44.263 1 116.41 ? O1P A3P 1 B 1 HETATM 3 O O2P A3P . . . F 2 -11.809 -26.739 -46.163 1 117.67 ? O2P A3P 1 B 1 HETATM 4 O O3P A3P . . . F 2 -11.707 -24.239 -46.418 1 116.26 ? O3P A3P 1 B 1 HETATM 5 P P2 A3P . . . F 2 -7.44 -25.541 -39.371 1 118.7 ? P2 A3P 1 B 1 HETATM 6 O O4P A3P . . . F 2 -8.823 -25.06 -38.936 1 117.45 ? O4P A3P 1 B 1 HETATM 7 O O5P A3P . . . F 2 -6.378 -24.459 -39.55 1 117.59 ? O5P A3P 1 B 1 HETATM 8 O O6P A3P . . . F 2 -6.974 -26.753 -38.589 1 118.12 ? O6P A3P 1 B 1 HETATM 9 O O5' A3P . . . F 2 -7.603 -26.155 -40.85 1 115.86 ? O5' A3P 1 B 1 HETATM 10 C C5' A3P . . . F 2 -8.881 -26.273 -41.458 1 116.41 ? C5' A3P 1 B 1 HETATM 11 C C4' A3P . . . F 2 -8.567 -26.254 -42.941 1 117.96 ? C4' A3P 1 B 1 HETATM 12 O O4' A3P . . . F 2 -7.499 -27.215 -43.13 1 118.97 ? O4' A3P 1 B 1 HETATM 13 C C3' A3P . . . F 2 -9.764 -26.612 -43.848 1 117.98 ? C3' A3P 1 B 1 HETATM 14 O O3' A3P . . . F 2 -10.218 -25.508 -44.687 1 117.72 ? O3' A3P 1 B 1 HETATM 15 C C2' A3P . . . F 2 -9.249 -27.819 -44.638 1 118.24 ? C2' A3P 1 B 1 HETATM 16 O O2' A3P . . . F 2 -9.54 -27.758 -46.044 1 114.85 ? O2' A3P 1 B 1 HETATM 17 C C1' A3P . . . F 2 -7.726 -27.885 -44.389 1 120.12 ? C1' A3P 1 B 1 HETATM 18 N N9 A3P . . . F 2 -7.22 -29.307 -44.538 1 120.51 ? N9 A3P 1 B 1 HETATM 19 C C8 A3P . . . F 2 -7.298 -30.319 -43.625 1 119.74 ? C8 A3P 1 B 1 HETATM 20 N N7 A3P . . . F 2 -6.769 -31.476 -44.124 1 119.02 ? N7 A3P 1 B 1 HETATM 21 C C5 A3P . . . F 2 -6.34 -31.228 -45.391 1 119.4 ? C5 A3P 1 B 1 HETATM 22 C C6 A3P . . . F 2 -5.685 -31.999 -46.496 1 118.66 ? C6 A3P 1 B 1 HETATM 23 N N6 A3P . . . F 2 -5.375 -33.307 -46.319 1 118.2 ? N6 A3P 1 B 1 HETATM 24 N N1 A3P . . . F 2 -5.409 -31.36 -47.672 1 117.21 ? N1 A3P 1 B 1 HETATM 25 C C2 A3P . . . F 2 -5.713 -30.058 -47.859 1 117.23 ? C2 A3P 1 B 1 HETATM 26 N N3 A3P . . . F 2 -6.308 -29.293 -46.916 1 118.23 ? N3 A3P 1 B 1 HETATM 27 C C4 A3P . . . F 2 -6.643 -29.8 -45.675 1 119.88 ? C4 A3P 1 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 413 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #