data_4JKY # _model_server_result.job_id '_CCsvtrrV36JLdrTYGoBzQ' _model_server_result.datetime_utc '2024-12-21 13:01:55' _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 4jky # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 4JKY # _exptl.entry_id 4JKY _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 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 4JKY _cell.length_a 67.55 _cell.length_b 73.53 _cell.length_c 87.47 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JKY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,D,E,I 1 1 B,F,G,H,J 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 C N N ? 2 D N N ? 2 F N N ? 2 G 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 E CO CO . A CO 303 1_555 I O HOH . A HOH 409 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc2 E CO CO . A CO 303 1_555 I O HOH . A HOH 437 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc3 E CO CO . A CO 303 1_555 I O HOH . A HOH 482 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.355 ? metalc ? metalc4 H CO CO . B CO 303 1_555 J O HOH . B HOH 429 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc5 H CO CO . B CO 303 1_555 J O HOH . B HOH 437 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc6 H CO CO . B CO 303 1_555 J O HOH . B HOH 458 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.701 ? metalc ? metalc7 H CO CO . B CO 303 1_555 J O HOH . B HOH 459 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.396 ? # _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 4JKY _atom_sites.fract_transf_matrix[1][1] 0.014804 _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] 0.0136 _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] 0.011432 _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 C 2 ADP A 1 301 1 ADP ADP . D 2 ADP A 1 302 1 ADP ADP . E 3 CO A 1 303 1 CO CO . F 2 ADP B 1 301 1 ADP ADP . G 2 ADP B 1 302 1 ADP ADP . H 3 CO B 1 303 2 CO CO . I 4 HOH A 1 401 1 HOH HOH . I 4 HOH A 2 402 2 HOH HOH . I 4 HOH A 3 403 5 HOH HOH . I 4 HOH A 4 404 6 HOH HOH . I 4 HOH A 5 405 7 HOH HOH . I 4 HOH A 6 406 8 HOH HOH . I 4 HOH A 7 407 9 HOH HOH . I 4 HOH A 8 408 10 HOH HOH . I 4 HOH A 9 409 13 HOH HOH . I 4 HOH A 10 410 14 HOH HOH . I 4 HOH A 11 411 15 HOH HOH . I 4 HOH A 12 412 16 HOH HOH . I 4 HOH A 13 413 17 HOH HOH . I 4 HOH A 14 414 18 HOH HOH . I 4 HOH A 15 415 19 HOH HOH . I 4 HOH A 16 416 20 HOH HOH . I 4 HOH A 17 417 21 HOH HOH . I 4 HOH A 18 418 22 HOH HOH . I 4 HOH A 19 419 23 HOH HOH . I 4 HOH A 20 420 24 HOH HOH . I 4 HOH A 21 421 27 HOH HOH . I 4 HOH A 22 422 29 HOH HOH . I 4 HOH A 23 423 31 HOH HOH . I 4 HOH A 24 424 33 HOH HOH . I 4 HOH A 25 425 35 HOH HOH . I 4 HOH A 26 426 37 HOH HOH . I 4 HOH A 27 427 39 HOH HOH . I 4 HOH A 28 428 40 HOH HOH . I 4 HOH A 29 429 42 HOH HOH . I 4 HOH A 30 430 43 HOH HOH . I 4 HOH A 31 431 44 HOH HOH . I 4 HOH A 32 432 45 HOH HOH . I 4 HOH A 33 433 47 HOH HOH . I 4 HOH A 34 434 52 HOH HOH . I 4 HOH A 35 435 54 HOH HOH . I 4 HOH A 36 436 56 HOH HOH . I 4 HOH A 37 437 57 HOH HOH . I 4 HOH A 38 438 59 HOH HOH . I 4 HOH A 39 439 60 HOH HOH . I 4 HOH A 40 440 63 HOH HOH . I 4 HOH A 41 441 65 HOH HOH . I 4 HOH A 42 442 67 HOH HOH . I 4 HOH A 43 443 68 HOH HOH . I 4 HOH A 44 444 70 HOH HOH . I 4 HOH A 45 445 75 HOH HOH . I 4 HOH A 46 446 77 HOH HOH . I 4 HOH A 47 447 78 HOH HOH . I 4 HOH A 48 448 81 HOH HOH . I 4 HOH A 49 449 83 HOH HOH . I 4 HOH A 50 450 85 HOH HOH . I 4 HOH A 51 451 86 HOH HOH . I 4 HOH A 52 452 87 HOH HOH . I 4 HOH A 53 453 88 HOH HOH . I 4 HOH A 54 454 89 HOH HOH . I 4 HOH A 55 455 90 HOH HOH . I 4 HOH A 56 456 92 HOH HOH . I 4 HOH A 57 457 94 HOH HOH . I 4 HOH A 58 458 98 HOH HOH . I 4 HOH A 59 459 99 HOH HOH . I 4 HOH A 60 460 101 HOH HOH . I 4 HOH A 61 461 102 HOH HOH . I 4 HOH A 62 462 104 HOH HOH . I 4 HOH A 63 463 107 HOH HOH . I 4 HOH A 64 464 109 HOH HOH . I 4 HOH A 65 465 111 HOH HOH . I 4 HOH A 66 466 113 HOH HOH . I 4 HOH A 67 467 117 HOH HOH . I 4 HOH A 68 468 118 HOH HOH . I 4 HOH A 69 469 119 HOH HOH . I 4 HOH A 70 470 121 HOH HOH . I 4 HOH A 71 471 123 HOH HOH . I 4 HOH A 72 472 125 HOH HOH . I 4 HOH A 73 473 128 HOH HOH . I 4 HOH A 74 474 129 HOH HOH . I 4 HOH A 75 475 130 HOH HOH . I 4 HOH A 76 476 131 HOH HOH . I 4 HOH A 77 477 132 HOH HOH . I 4 HOH A 78 478 133 HOH HOH . I 4 HOH A 79 479 135 HOH HOH . I 4 HOH A 80 480 138 HOH HOH . I 4 HOH A 81 481 143 HOH HOH . I 4 HOH A 82 482 145 HOH HOH . I 4 HOH A 83 483 146 HOH HOH . J 4 HOH B 1 401 2 HOH HOH . J 4 HOH B 2 402 1 HOH HOH . J 4 HOH B 3 403 3 HOH HOH . J 4 HOH B 4 404 4 HOH HOH . J 4 HOH B 5 405 11 HOH HOH . J 4 HOH B 6 406 12 HOH HOH . J 4 HOH B 7 407 25 HOH HOH . J 4 HOH B 8 408 26 HOH HOH . J 4 HOH B 9 409 28 HOH HOH . J 4 HOH B 10 410 30 HOH HOH . J 4 HOH B 11 411 34 HOH HOH . J 4 HOH B 12 412 36 HOH HOH . J 4 HOH B 13 413 38 HOH HOH . J 4 HOH B 14 414 41 HOH HOH . J 4 HOH B 15 415 46 HOH HOH . J 4 HOH B 16 416 48 HOH HOH . J 4 HOH B 17 417 49 HOH HOH . J 4 HOH B 18 418 50 HOH HOH . J 4 HOH B 19 419 51 HOH HOH . J 4 HOH B 20 420 53 HOH HOH . J 4 HOH B 21 421 55 HOH HOH . J 4 HOH B 22 422 58 HOH HOH . J 4 HOH B 23 423 61 HOH HOH . J 4 HOH B 24 424 62 HOH HOH . J 4 HOH B 25 425 64 HOH HOH . J 4 HOH B 26 426 66 HOH HOH . J 4 HOH B 27 427 69 HOH HOH . J 4 HOH B 28 428 71 HOH HOH . J 4 HOH B 29 429 72 HOH HOH . J 4 HOH B 30 430 74 HOH HOH . J 4 HOH B 31 431 76 HOH HOH . J 4 HOH B 32 432 79 HOH HOH . J 4 HOH B 33 433 80 HOH HOH . J 4 HOH B 34 434 82 HOH HOH . J 4 HOH B 35 435 84 HOH HOH . J 4 HOH B 36 436 91 HOH HOH . J 4 HOH B 37 437 93 HOH HOH . J 4 HOH B 38 438 95 HOH HOH . J 4 HOH B 39 439 96 HOH HOH . J 4 HOH B 40 440 97 HOH HOH . J 4 HOH B 41 441 100 HOH HOH . J 4 HOH B 42 442 103 HOH HOH . J 4 HOH B 43 443 105 HOH HOH . J 4 HOH B 44 444 106 HOH HOH . J 4 HOH B 45 445 108 HOH HOH . J 4 HOH B 46 446 110 HOH HOH . J 4 HOH B 47 447 112 HOH HOH . J 4 HOH B 48 448 114 HOH HOH . J 4 HOH B 49 449 115 HOH HOH . J 4 HOH B 50 450 116 HOH HOH . J 4 HOH B 51 451 122 HOH HOH . J 4 HOH B 52 452 124 HOH HOH . J 4 HOH B 53 453 126 HOH HOH . J 4 HOH B 54 454 127 HOH HOH . J 4 HOH B 55 455 134 HOH HOH . J 4 HOH B 56 456 136 HOH HOH . J 4 HOH B 57 457 137 HOH HOH . J 4 HOH B 58 458 139 HOH HOH . J 4 HOH B 59 459 140 HOH HOH . J 4 HOH B 60 460 141 HOH HOH . J 4 HOH B 61 461 142 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 . . . D 2 47.161 32.158 40.911 0.38 38.56 ? PB ADP 302 A 1 HETATM 2 O O1B ADP . . . D 2 47.82 31.272 41.944 1 40.98 ? O1B ADP 302 A 1 HETATM 3 O O2B ADP . . . D 2 47.853 33.422 40.454 1 36.22 ? O2B ADP 302 A 1 HETATM 4 O O3B ADP . . . D 2 46.577 31.36 39.768 1 50.4 ? O3B ADP 302 A 1 HETATM 5 P PA ADP . . . D 2 45.467 32.381 43.165 1 29.42 ? PA ADP 302 A 1 HETATM 6 O O1A ADP . . . D 2 46.368 33.068 44.16 1 37.02 ? O1A ADP 302 A 1 HETATM 7 O O2A ADP . . . D 2 45.319 30.893 43.212 1 31.27 ? O2A ADP 302 A 1 HETATM 8 O O3A ADP . . . D 2 45.92 32.814 41.692 1 38.63 ? O3A ADP 302 A 1 HETATM 9 O O5' ADP . . . D 2 44.04 33.121 43.216 1 36.73 ? O5' ADP 302 A 1 HETATM 10 C C5' ADP . . . D 2 42.961 32.819 42.327 1 27.52 ? C5' ADP 302 A 1 HETATM 11 C C4' ADP . . . D 2 42.013 34.013 42.327 1 29.02 ? C4' ADP 302 A 1 HETATM 12 O O4' ADP . . . D 2 41.422 34.176 43.625 1 29.64 ? O4' ADP 302 A 1 HETATM 13 C C3' ADP . . . D 2 42.721 35.334 42.084 1 28.78 ? C3' ADP 302 A 1 HETATM 14 O O3' ADP . . . D 2 42.857 35.662 40.707 1 29.32 ? O3' ADP 302 A 1 HETATM 15 C C2' ADP . . . D 2 41.783 36.308 42.748 1 28.96 ? C2' ADP 302 A 1 HETATM 16 O O2' ADP . . . D 2 40.66 36.514 41.892 1 29.84 ? O2' ADP 302 A 1 HETATM 17 C C1' ADP . . . D 2 41.313 35.559 43.976 1 27.82 ? C1' ADP 302 A 1 HETATM 18 N N9 ADP . . . D 2 42.257 35.896 45.073 1 24.94 ? N9 ADP 302 A 1 HETATM 19 C C8 ADP . . . D 2 43.198 35.074 45.571 1 25.03 ? C8 ADP 302 A 1 HETATM 20 N N7 ADP . . . D 2 43.905 35.681 46.559 1 24.44 ? N7 ADP 302 A 1 HETATM 21 C C5 ADP . . . D 2 43.415 36.933 46.704 1 21.74 ? C5 ADP 302 A 1 HETATM 22 C C6 ADP . . . D 2 43.708 38.104 47.568 1 16.67 ? C6 ADP 302 A 1 HETATM 23 N N6 ADP . . . D 2 44.691 38.069 48.489 1 21.16 ? N6 ADP 302 A 1 HETATM 24 N N1 ADP . . . D 2 42.965 39.215 47.4 1 24.15 ? N1 ADP 302 A 1 HETATM 25 C C2 ADP . . . D 2 41.982 39.259 46.468 1 21.64 ? C2 ADP 302 A 1 HETATM 26 N N3 ADP . . . D 2 41.665 38.236 45.662 1 18.48 ? N3 ADP 302 A 1 HETATM 27 C C4 ADP . . . D 2 42.331 37.066 45.721 1 20.59 ? C4 ADP 302 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #