data_4WDF # _model_server_result.job_id Cs_Qlqa_OnvKhyFj4721QA _model_server_result.datetime_utc '2024-11-25 13:33:54' _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 4wdf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 4WDF # _exptl.entry_id 4WDF _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 95.67 _cell.angle_gamma 90 _cell.entry_id 4WDF _cell.length_a 41.09 _cell.length_b 47.01 _cell.length_c 53.65 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WDF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 4WDF _atom_sites.fract_transf_matrix[1][1] 0.024337 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002417 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021272 _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] 0.018731 _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 25 HOH HOH . C 3 HOH A 2 502 23 HOH HOH . C 3 HOH A 3 503 58 HOH HOH . C 3 HOH A 4 504 18 HOH HOH . C 3 HOH A 5 505 38 HOH HOH . C 3 HOH A 6 506 6 HOH HOH . C 3 HOH A 7 507 65 HOH HOH . C 3 HOH A 8 508 45 HOH HOH . C 3 HOH A 9 509 67 HOH HOH . C 3 HOH A 10 510 66 HOH HOH . C 3 HOH A 11 511 40 HOH HOH . C 3 HOH A 12 512 34 HOH HOH . C 3 HOH A 13 513 21 HOH HOH . C 3 HOH A 14 514 27 HOH HOH . C 3 HOH A 15 515 24 HOH HOH . C 3 HOH A 16 516 69 HOH HOH . C 3 HOH A 17 517 8 HOH HOH . C 3 HOH A 18 518 77 HOH HOH . C 3 HOH A 19 519 46 HOH HOH . C 3 HOH A 20 520 57 HOH HOH . C 3 HOH A 21 521 56 HOH HOH . C 3 HOH A 22 522 64 HOH HOH . C 3 HOH A 23 523 37 HOH HOH . C 3 HOH A 24 524 1 HOH HOH . C 3 HOH A 25 525 2 HOH HOH . C 3 HOH A 26 526 3 HOH HOH . C 3 HOH A 27 527 4 HOH HOH . C 3 HOH A 28 528 7 HOH HOH . C 3 HOH A 29 529 9 HOH HOH . C 3 HOH A 30 530 10 HOH HOH . C 3 HOH A 31 531 11 HOH HOH . C 3 HOH A 32 532 12 HOH HOH . C 3 HOH A 33 533 14 HOH HOH . C 3 HOH A 34 534 15 HOH HOH . C 3 HOH A 35 535 16 HOH HOH . C 3 HOH A 36 536 17 HOH HOH . C 3 HOH A 37 537 20 HOH HOH . C 3 HOH A 38 538 22 HOH HOH . C 3 HOH A 39 539 26 HOH HOH . C 3 HOH A 40 540 28 HOH HOH . C 3 HOH A 41 541 29 HOH HOH . C 3 HOH A 42 542 30 HOH HOH . C 3 HOH A 43 543 32 HOH HOH . C 3 HOH A 44 544 33 HOH HOH . C 3 HOH A 45 545 36 HOH HOH . C 3 HOH A 46 546 42 HOH HOH . C 3 HOH A 47 547 43 HOH HOH . C 3 HOH A 48 548 47 HOH HOH . C 3 HOH A 49 549 48 HOH HOH . C 3 HOH A 50 550 49 HOH HOH . C 3 HOH A 51 551 50 HOH HOH . C 3 HOH A 52 552 52 HOH HOH . C 3 HOH A 53 553 53 HOH HOH . C 3 HOH A 54 554 54 HOH HOH . C 3 HOH A 55 555 55 HOH HOH . C 3 HOH A 56 556 59 HOH HOH . C 3 HOH A 57 557 60 HOH HOH . C 3 HOH A 58 558 61 HOH HOH . C 3 HOH A 59 559 62 HOH HOH . C 3 HOH A 60 560 63 HOH HOH . C 3 HOH A 61 561 68 HOH HOH . C 3 HOH A 62 562 70 HOH HOH . C 3 HOH A 63 563 71 HOH HOH . C 3 HOH A 64 564 72 HOH HOH . C 3 HOH A 65 565 73 HOH HOH . C 3 HOH A 66 566 74 HOH HOH . C 3 HOH A 67 567 75 HOH HOH . C 3 HOH A 68 568 76 HOH HOH . C 3 HOH A 69 569 78 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 38.827 3.743 74.691 1 84.84 ? P1 A2P 401 A 1 HETATM 2 O O1P A2P . . . B 2 39.306 3.297 73.316 1 82.46 ? O1P A2P 401 A 1 HETATM 3 O O2P A2P . . . B 2 37.777 4.874 74.546 1 79.54 ? O2P A2P 401 A 1 HETATM 4 O O3P A2P . . . B 2 38.221 2.579 75.404 1 82.35 ? O3P A2P 401 A 1 HETATM 5 P P2 A2P . . . B 2 38.479 3.479 81.222 1 127.73 ? P2 A2P 401 A 1 HETATM 6 O O4P A2P . . . B 2 37.001 3.512 81.156 1 127.76 ? O4P A2P 401 A 1 HETATM 7 O O5P A2P . . . B 2 38.937 2.076 81.281 1 128.28 ? O5P A2P 401 A 1 HETATM 8 O O6P A2P . . . B 2 38.956 4.219 82.472 1 128.06 ? O6P A2P 401 A 1 HETATM 9 O O5' A2P . . . B 2 39.089 4.199 79.909 1 70.43 ? O5' A2P 401 A 1 HETATM 10 C C5' A2P . . . B 2 38.762 5.546 79.666 1 66.81 ? C5' A2P 401 A 1 HETATM 11 C C4' A2P . . . B 2 39.451 6.006 78.403 1 67.61 ? C4' A2P 401 A 1 HETATM 12 O O4' A2P . . . B 2 41.018 5.64 78.484 1 69.74 ? O4' A2P 401 A 1 HETATM 13 C C3' A2P . . . B 2 38.95 5.408 77.345 1 69.84 ? C3' A2P 401 A 1 HETATM 14 O O3' A2P . . . B 2 38.725 6.401 76.238 1 67.18 ? O3' A2P 401 A 1 HETATM 15 C C2' A2P . . . B 2 39.983 4.359 76.911 1 74.02 ? C2' A2P 401 A 1 HETATM 16 O O2' A2P . . . B 2 40.081 4.316 75.545 1 76.69 ? O2' A2P 401 A 1 HETATM 17 C C1' A2P . . . B 2 41.321 4.814 77.522 1 71.34 ? C1' A2P 401 A 1 HETATM 18 N N9 A2P . . . B 2 42.019 3.684 78.089 1 72.38 ? N9 A2P 401 A 1 HETATM 19 C C8 A2P . . . B 2 41.924 2.766 79.106 1 70.36 ? C8 A2P 401 A 1 HETATM 20 N N7 A2P . . . B 2 43.006 1.955 79.052 1 69.38 ? N7 A2P 401 A 1 HETATM 21 C C5 A2P . . . B 2 43.782 2.364 78 1 68.19 ? C5 A2P 401 A 1 HETATM 22 C C6 A2P . . . B 2 44.978 1.876 77.522 1 68.35 ? C6 A2P 401 A 1 HETATM 23 N N6 A2P . . . B 2 45.901 0.837 77.825 1 71.19 ? N6 A2P 401 A 1 HETATM 24 N N1 A2P . . . B 2 45.57 2.441 76.461 1 68.63 ? N1 A2P 401 A 1 HETATM 25 C C2 A2P . . . B 2 44.977 3.513 75.851 1 67.72 ? C2 A2P 401 A 1 HETATM 26 N N3 A2P . . . B 2 43.784 4.004 76.324 1 69.67 ? N3 A2P 401 A 1 HETATM 27 C C4 A2P . . . B 2 43.181 3.429 77.402 1 68.85 ? C4 A2P 401 A 1 HETATM 28 H "H5'1" A2P . . . B 2 39.046 6.071 80.387 1 80.17 ? "H5'1" A2P 401 A 1 HETATM 29 H "H5'2" A2P . . . B 2 37.808 5.631 79.563 1 80.17 ? "H5'2" A2P 401 A 1 HETATM 30 H H4' A2P . . . B 2 39.347 6.964 78.311 1 81.14 ? H4' A2P 401 A 1 HETATM 31 H H3' A2P . . . B 2 38.152 4.992 77.565 1 83.81 ? H3' A2P 401 A 1 HETATM 32 H HO3' A2P . . . B 2 37.829 6.538 76.13 1 80.62 ? HO3' A2P 401 A 1 HETATM 33 H H2' A2P . . . B 2 39.724 3.448 77.27 1 88.82 ? H2' A2P 401 A 1 HETATM 34 H H1' A2P . . . B 2 41.904 5.28 76.811 1 85.61 ? H1' A2P 401 A 1 HETATM 35 H H8 A2P . . . B 2 41.187 2.707 79.771 1 84.44 ? H8 A2P 401 A 1 HETATM 36 H HN61 A2P . . . B 2 46.735 1.045 78.224 1 85.42 ? HN61 A2P 401 A 1 HETATM 37 H HN62 A2P . . . B 2 45.683 -0.06 77.629 1 85.42 ? HN62 A2P 401 A 1 HETATM 38 H H2 A2P . . . B 2 45.412 3.938 75.063 1 81.27 ? H2 A2P 401 A 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #