data_4WDG # _model_server_result.job_id bJWmR_Y4EZaR245AC4ZyRg _model_server_result.datetime_utc '2024-11-25 13:25:04' _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 4wdg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4WDG # _exptl.entry_id 4WDG _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-2'-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 4WDG _cell.length_a 41.33 _cell.length_b 46.94 _cell.length_c 106.89 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WDG _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id A2P _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-2'-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 P1 O1P A2P doub 1 n n P1 O2P A2P sing 2 n n P1 O3P A2P sing 3 n n P1 O2' A2P sing 4 n n O2P HOP2 A2P sing 5 n n O3P HOP3 A2P sing 6 n n P2 O4P A2P doub 7 n n P2 O5P A2P sing 8 n n P2 O6P A2P sing 9 n n P2 O5' A2P sing 10 n n O5P HOP5 A2P sing 11 n n O6P HOP6 A2P sing 12 n n O5' C5' A2P sing 13 n n C5' C4' A2P sing 14 n n C5' "H5'1" A2P sing 15 n n C5' "H5'2" A2P sing 16 n n C4' O4' A2P sing 17 n n C4' C3' A2P sing 18 n n C4' H4' A2P sing 19 n n O4' C1' A2P sing 20 n n C3' O3' A2P sing 21 n n C3' C2' A2P sing 22 n n C3' H3' A2P sing 23 n n O3' HO3' A2P sing 24 n n C2' O2' A2P sing 25 n n C2' C1' A2P sing 26 n n C2' H2' A2P sing 27 n n C1' N9 A2P sing 28 n n C1' H1' A2P sing 29 n n N9 C8 A2P sing 30 n y N9 C4 A2P sing 31 n y C8 N7 A2P doub 32 n y C8 H8 A2P sing 33 n n N7 C5 A2P sing 34 n y C5 C6 A2P sing 35 n y C5 C4 A2P doub 36 n y C6 N6 A2P sing 37 n n C6 N1 A2P doub 38 n y N6 HN61 A2P sing 39 n n N6 HN62 A2P sing 40 n n N1 C2 A2P sing 41 n y C2 N3 A2P doub 42 n y C2 H2 A2P sing 43 n n N3 C4 A2P sing 44 n y # _atom_sites.entry_id 4WDG _atom_sites.fract_transf_matrix[1][1] 0.024195 _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] 0.021304 _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] 0.009355 _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 B 2 A2P A 1 401 1 A2P A2P . C 3 HOH A 1 501 8 HOH HOH . C 3 HOH A 2 502 16 HOH HOH . C 3 HOH A 3 503 21 HOH HOH . C 3 HOH A 4 504 25 HOH HOH . C 3 HOH A 5 505 40 HOH HOH . C 3 HOH A 6 506 7 HOH HOH . C 3 HOH A 7 507 14 HOH HOH . C 3 HOH A 8 508 3 HOH HOH . C 3 HOH A 9 509 39 HOH HOH . C 3 HOH A 10 510 11 HOH HOH . C 3 HOH A 11 511 37 HOH HOH . C 3 HOH A 12 512 41 HOH HOH . C 3 HOH A 13 513 1 HOH HOH . C 3 HOH A 14 514 2 HOH HOH . C 3 HOH A 15 515 4 HOH HOH . C 3 HOH A 16 516 6 HOH HOH . C 3 HOH A 17 517 9 HOH HOH . C 3 HOH A 18 518 10 HOH HOH . C 3 HOH A 19 519 12 HOH HOH . C 3 HOH A 20 520 13 HOH HOH . C 3 HOH A 21 521 15 HOH HOH . C 3 HOH A 22 522 17 HOH HOH . C 3 HOH A 23 523 18 HOH HOH . C 3 HOH A 24 524 19 HOH HOH . C 3 HOH A 25 525 20 HOH HOH . C 3 HOH A 26 526 23 HOH HOH . C 3 HOH A 27 527 24 HOH HOH . C 3 HOH A 28 528 26 HOH HOH . C 3 HOH A 29 529 27 HOH HOH . C 3 HOH A 30 530 28 HOH HOH . C 3 HOH A 31 531 29 HOH HOH . C 3 HOH A 32 532 30 HOH HOH . C 3 HOH A 33 533 31 HOH HOH . C 3 HOH A 34 534 32 HOH HOH . C 3 HOH A 35 535 33 HOH HOH . C 3 HOH A 36 536 34 HOH HOH . C 3 HOH A 37 537 36 HOH HOH . C 3 HOH A 38 538 42 HOH HOH . C 3 HOH A 39 539 43 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 P1 A2P . . . B 2 -5.55 4.215 -21.3 1 86.41 ? P1 A2P 401 A 1 HETATM 2 O O1P A2P . . . B 2 -4.916 3.064 -22.06 1 84.4 ? O1P A2P 401 A 1 HETATM 3 O O2P A2P . . . B 2 -4.589 5.381 -21.256 1 84.91 ? O2P A2P 401 A 1 HETATM 4 O O3P A2P . . . B 2 -5.873 3.748 -19.83 1 81.84 ? O3P A2P 401 A 1 HETATM 5 P P2 A2P . . . B 2 -4.773 3.98 -27.868 1 87.33 ? P2 A2P 401 A 1 HETATM 6 O O4P A2P . . . B 2 -3.887 4.504 -28.927 1 86.24 ? O4P A2P 401 A 1 HETATM 7 O O5P A2P . . . B 2 -6.048 3.492 -28.493 1 89.07 ? O5P A2P 401 A 1 HETATM 8 O O6P A2P . . . B 2 -4.099 2.86 -27.2 1 87.73 ? O6P A2P 401 A 1 HETATM 9 O O5' A2P . . . B 2 -5.094 5.165 -26.78 1 77.57 ? O5' A2P 401 A 1 HETATM 10 C C5' A2P . . . B 2 -6.443 5.615 -26.622 1 76.48 ? C5' A2P 401 A 1 HETATM 11 C C4' A2P . . . B 2 -6.678 6.359 -25.297 1 75.57 ? C4' A2P 401 A 1 HETATM 12 O O4' A2P . . . B 2 -7.963 6.311 -25.001 1 72 ? O4' A2P 401 A 1 HETATM 13 C C3' A2P . . . B 2 -5.984 5.696 -24.118 1 78.8 ? C3' A2P 401 A 1 HETATM 14 O O3' A2P . . . B 2 -5.633 6.649 -23.168 1 77.21 ? O3' A2P 401 A 1 HETATM 15 C C2' A2P . . . B 2 -7.018 4.711 -23.554 1 82.06 ? C2' A2P 401 A 1 HETATM 16 O O2' A2P . . . B 2 -6.94 4.692 -22.053 1 82.69 ? O2' A2P 401 A 1 HETATM 17 C C1' A2P . . . B 2 -8.198 5.145 -23.942 1 82.5 ? C1' A2P 401 A 1 HETATM 18 N N9 A2P . . . B 2 -8.972 4.117 -24.522 1 81.64 ? N9 A2P 401 A 1 HETATM 19 C C8 A2P . . . B 2 -8.84 3.268 -25.537 1 81.12 ? C8 A2P 401 A 1 HETATM 20 N N7 A2P . . . B 2 -9.969 2.519 -25.58 1 79.37 ? N7 A2P 401 A 1 HETATM 21 C C5 A2P . . . B 2 -10.787 2.926 -24.583 1 79.14 ? C5 A2P 401 A 1 HETATM 22 C C6 A2P . . . B 2 -12.024 2.495 -24.208 1 76.46 ? C6 A2P 401 A 1 HETATM 23 N N6 A2P . . . B 2 -12.887 1.502 -24.693 1 75.43 ? N6 A2P 401 A 1 HETATM 24 N N1 A2P . . . B 2 -12.643 3.065 -23.169 1 76.25 ? N1 A2P 401 A 1 HETATM 25 C C2 A2P . . . B 2 -12.046 4.058 -22.499 1 77.58 ? C2 A2P 401 A 1 HETATM 26 N N3 A2P . . . B 2 -10.818 4.487 -22.869 1 79.09 ? N3 A2P 401 A 1 HETATM 27 C C4 A2P . . . B 2 -10.188 3.914 -23.919 1 80.43 ? C4 A2P 401 A 1 HETATM 28 H "H5'1" A2P . . . B 2 -7.036 4.844 -26.664 1 91.77 ? "H5'1" A2P 401 A 1 HETATM 29 H "H5'2" A2P . . . B 2 -6.666 6.224 -27.364 1 91.77 ? "H5'2" A2P 401 A 1 HETATM 30 H H4' A2P . . . B 2 -6.409 7.232 -25.373 1 90.69 ? H4' A2P 401 A 1 HETATM 31 H H3' A2P . . . B 2 -5.161 5.196 -24.434 1 94.55 ? H3' A2P 401 A 1 HETATM 32 H HO3' A2P . . . B 2 -4.758 6.618 -23.028 1 92.65 ? HO3' A2P 401 A 1 HETATM 33 H H2' A2P . . . B 2 -6.85 3.777 -23.927 1 98.47 ? H2' A2P 401 A 1 HETATM 34 H H1' A2P . . . B 2 -8.698 5.523 -23.132 1 99 ? H1' A2P 401 A 1 HETATM 35 H H8 A2P . . . B 2 -8.063 3.196 -26.144 1 97.35 ? H8 A2P 401 A 1 HETATM 36 H HN61 A2P . . . B 2 -13.54 1.119 -24.119 1 90.52 ? HN61 A2P 401 A 1 HETATM 37 H HN62 A2P . . . B 2 -12.819 1.216 -25.578 1 90.52 ? HN62 A2P 401 A 1 HETATM 38 H H2 A2P . . . B 2 -12.492 4.467 -21.752 1 93.1 ? H2 A2P 401 A 1 # _model_server_stats.io_time_ms 70 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #