data_7TPV # _model_server_result.job_id IhRKHi-eoZEYrMtxD4siIg _model_server_result.datetime_utc '2024-11-27 19:56:32' _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 7tpv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7TPV # _exptl.entry_id 7TPV _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 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 7TPV _cell.length_a 45.363 _cell.length_b 73.691 _cell.length_c 74.17 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7TPV _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 2 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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_565 x,-y+1,-z 1 0 0 0 -1 0 0 0 -1 0 73.691 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 # 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 A OG SER 17 A SER 16 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc2 A SG CYS 98 A CYS 97 1_555 C FE1 SF4 . A SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc3 A SG CYS 133 A CYS 132 1_555 C FE2 SF4 . A SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc4 B O2B ADP . A ADP 301 1_555 D MG MG . A MG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc5 D MG MG . A MG 303 1_555 E O HOH . A HOH 437 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc6 D MG MG . A MG 303 1_555 E O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc7 D MG MG . A MG 303 1_555 E O HOH . A HOH 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc8 D MG MG . A MG 303 1_555 E O HOH . A HOH 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? # _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 7TPV _atom_sites.fract_transf_matrix[1][1] 0.022044 _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] 0.01357 _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] 0.013483 _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 ADP A 1 301 305 ADP ADP . C 3 SF4 A 1 302 301 SF4 SF4 . D 4 MG A 1 303 306 MG MG . E 5 HOH A 1 401 117 HOH HOH . E 5 HOH A 2 402 129 HOH HOH . E 5 HOH A 3 403 73 HOH HOH . E 5 HOH A 4 404 29 HOH HOH . E 5 HOH A 5 405 87 HOH HOH . E 5 HOH A 6 406 128 HOH HOH . E 5 HOH A 7 407 41 HOH HOH . E 5 HOH A 8 408 46 HOH HOH . E 5 HOH A 9 409 137 HOH HOH . E 5 HOH A 10 410 47 HOH HOH . E 5 HOH A 11 411 79 HOH HOH . E 5 HOH A 12 412 109 HOH HOH . E 5 HOH A 13 413 35 HOH HOH . E 5 HOH A 14 414 114 HOH HOH . E 5 HOH A 15 415 32 HOH HOH . E 5 HOH A 16 416 18 HOH HOH . E 5 HOH A 17 417 61 HOH HOH . E 5 HOH A 18 418 16 HOH HOH . E 5 HOH A 19 419 84 HOH HOH . E 5 HOH A 20 420 89 HOH HOH . E 5 HOH A 21 421 80 HOH HOH . E 5 HOH A 22 422 130 HOH HOH . E 5 HOH A 23 423 111 HOH HOH . E 5 HOH A 24 424 21 HOH HOH . E 5 HOH A 25 425 132 HOH HOH . E 5 HOH A 26 426 24 HOH HOH . E 5 HOH A 27 427 14 HOH HOH . E 5 HOH A 28 428 118 HOH HOH . E 5 HOH A 29 429 60 HOH HOH . E 5 HOH A 30 430 52 HOH HOH . E 5 HOH A 31 431 12 HOH HOH . E 5 HOH A 32 432 91 HOH HOH . E 5 HOH A 33 433 19 HOH HOH . E 5 HOH A 34 434 93 HOH HOH . E 5 HOH A 35 435 26 HOH HOH . E 5 HOH A 36 436 7 HOH HOH . E 5 HOH A 37 437 3 HOH HOH . E 5 HOH A 38 438 37 HOH HOH . E 5 HOH A 39 439 71 HOH HOH . E 5 HOH A 40 440 13 HOH HOH . E 5 HOH A 41 441 9 HOH HOH . E 5 HOH A 42 442 125 HOH HOH . E 5 HOH A 43 443 88 HOH HOH . E 5 HOH A 44 444 136 HOH HOH . E 5 HOH A 45 445 56 HOH HOH . E 5 HOH A 46 446 4 HOH HOH . E 5 HOH A 47 447 107 HOH HOH . E 5 HOH A 48 448 99 HOH HOH . E 5 HOH A 49 449 22 HOH HOH . E 5 HOH A 50 450 76 HOH HOH . E 5 HOH A 51 451 55 HOH HOH . E 5 HOH A 52 452 42 HOH HOH . E 5 HOH A 53 453 92 HOH HOH . E 5 HOH A 54 454 5 HOH HOH . E 5 HOH A 55 455 20 HOH HOH . E 5 HOH A 56 456 98 HOH HOH . E 5 HOH A 57 457 100 HOH HOH . E 5 HOH A 58 458 11 HOH HOH . E 5 HOH A 59 459 2 HOH HOH . E 5 HOH A 60 460 53 HOH HOH . E 5 HOH A 61 461 119 HOH HOH . E 5 HOH A 62 462 34 HOH HOH . E 5 HOH A 63 463 1 HOH HOH . E 5 HOH A 64 464 44 HOH HOH . E 5 HOH A 65 465 113 HOH HOH . E 5 HOH A 66 466 6 HOH HOH . E 5 HOH A 67 467 17 HOH HOH . E 5 HOH A 68 468 102 HOH HOH . E 5 HOH A 69 469 124 HOH HOH . E 5 HOH A 70 470 39 HOH HOH . E 5 HOH A 71 471 28 HOH HOH . E 5 HOH A 72 472 50 HOH HOH . E 5 HOH A 73 473 38 HOH HOH . E 5 HOH A 74 474 48 HOH HOH . E 5 HOH A 75 475 62 HOH HOH . E 5 HOH A 76 476 8 HOH HOH . E 5 HOH A 77 477 123 HOH HOH . E 5 HOH A 78 478 69 HOH HOH . E 5 HOH A 79 479 51 HOH HOH . E 5 HOH A 80 480 134 HOH HOH . E 5 HOH A 81 481 23 HOH HOH . E 5 HOH A 82 482 142 HOH HOH . E 5 HOH A 83 483 81 HOH HOH . E 5 HOH A 84 484 45 HOH HOH . E 5 HOH A 85 485 94 HOH HOH . E 5 HOH A 86 486 36 HOH HOH . E 5 HOH A 87 487 131 HOH HOH . E 5 HOH A 88 488 65 HOH HOH . E 5 HOH A 89 489 27 HOH HOH . E 5 HOH A 90 490 106 HOH HOH . E 5 HOH A 91 491 59 HOH HOH . E 5 HOH A 92 492 54 HOH HOH . E 5 HOH A 93 493 101 HOH HOH . E 5 HOH A 94 494 90 HOH HOH . E 5 HOH A 95 495 43 HOH HOH . E 5 HOH A 96 496 82 HOH HOH . E 5 HOH A 97 497 15 HOH HOH . E 5 HOH A 98 498 103 HOH HOH . E 5 HOH A 99 499 75 HOH HOH . E 5 HOH A 100 500 68 HOH HOH . E 5 HOH A 101 501 78 HOH HOH . E 5 HOH A 102 502 25 HOH HOH . E 5 HOH A 103 503 74 HOH HOH . E 5 HOH A 104 504 86 HOH HOH . E 5 HOH A 105 505 72 HOH HOH . E 5 HOH A 106 506 121 HOH HOH . E 5 HOH A 107 507 49 HOH HOH . E 5 HOH A 108 508 120 HOH HOH . E 5 HOH A 109 509 57 HOH HOH . E 5 HOH A 110 510 31 HOH HOH . E 5 HOH A 111 511 96 HOH HOH . E 5 HOH A 112 512 30 HOH HOH . E 5 HOH A 113 513 67 HOH HOH . E 5 HOH A 114 514 115 HOH HOH . E 5 HOH A 115 515 133 HOH HOH . E 5 HOH A 116 516 40 HOH HOH . E 5 HOH A 117 517 108 HOH HOH . E 5 HOH A 118 518 64 HOH HOH . E 5 HOH A 119 519 70 HOH HOH . E 5 HOH A 120 520 105 HOH HOH . E 5 HOH A 121 521 83 HOH HOH . E 5 HOH A 122 522 63 HOH HOH . E 5 HOH A 123 523 33 HOH HOH . E 5 HOH A 124 524 66 HOH HOH . E 5 HOH A 125 525 122 HOH HOH . E 5 HOH A 126 526 140 HOH HOH . E 5 HOH A 127 527 10 HOH HOH . E 5 HOH A 128 528 126 HOH HOH . E 5 HOH A 129 529 95 HOH HOH . E 5 HOH A 130 530 110 HOH HOH . E 5 HOH A 131 531 85 HOH HOH . E 5 HOH A 132 532 135 HOH HOH . E 5 HOH A 133 533 144 HOH HOH . E 5 HOH A 134 534 104 HOH HOH . E 5 HOH A 135 535 141 HOH HOH . E 5 HOH A 136 536 58 HOH HOH . E 5 HOH A 137 537 145 HOH HOH . E 5 HOH A 138 538 143 HOH HOH . E 5 HOH A 139 539 97 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 . . . B 2 18.386 28.736 1.54 1 13.71 ? PB ADP 301 A 1 HETATM 2 O O1B ADP . . . B 2 18.379 29.058 0.066 1 14.26 ? O1B ADP 301 A 1 HETATM 3 O O2B ADP . . . B 2 18.971 27.381 1.865 1 13.89 ? O2B ADP 301 A 1 HETATM 4 O O3B ADP . . . B 2 18.896 29.878 2.389 1 15.92 ? O3B ADP 301 A 1 HETATM 5 P PA ADP . . . B 2 16.045 27.436 2.658 1 15.42 ? PA ADP 301 A 1 HETATM 6 O O1A ADP . . . B 2 16.029 26.157 1.874 1 16.22 ? O1A ADP 301 A 1 HETATM 7 O O2A ADP . . . B 2 16.589 27.425 4.066 1 15.65 ? O2A ADP 301 A 1 HETATM 8 O O3A ADP . . . B 2 16.809 28.621 1.857 1 13.79 ? O3A ADP 301 A 1 HETATM 9 O O5' ADP . . . B 2 14.527 27.956 2.651 1 14.9 ? O5' ADP 301 A 1 HETATM 10 C C5' ADP . . . B 2 14.255 29.176 3.327 1 17.34 ? C5' ADP 301 A 1 HETATM 11 C C4' ADP . . . B 2 12.886 29.119 3.985 1 19.07 ? C4' ADP 301 A 1 HETATM 12 O O4' ADP . . . B 2 11.899 28.98 2.943 1 19.29 ? O4' ADP 301 A 1 HETATM 13 C C3' ADP . . . B 2 12.687 27.951 4.927 1 22.21 ? C3' ADP 301 A 1 HETATM 14 O O3' ADP . . . B 2 11.927 28.446 6.033 1 28.25 ? O3' ADP 301 A 1 HETATM 15 C C2' ADP . . . B 2 11.807 26.957 4.236 1 20.81 ? C2' ADP 301 A 1 HETATM 16 O O2' ADP . . . B 2 10.905 26.307 5.094 1 27.91 ? O2' ADP 301 A 1 HETATM 17 C C1' ADP . . . B 2 11.055 27.864 3.267 1 22 ? C1' ADP 301 A 1 HETATM 18 N N9 ADP . . . B 2 10.711 27.234 1.996 1 19.58 ? N9 ADP 301 A 1 HETATM 19 C C8 ADP . . . B 2 11.581 26.901 1.035 1 15.94 ? C8 ADP 301 A 1 HETATM 20 N N7 ADP . . . B 2 10.925 26.342 -0.005 1 18.6 ? N7 ADP 301 A 1 HETATM 21 C C5 ADP . . . B 2 9.615 26.351 0.29 1 20.24 ? C5 ADP 301 A 1 HETATM 22 C C6 ADP . . . B 2 8.394 25.91 -0.38 1 21.02 ? C6 ADP 301 A 1 HETATM 23 N N6 ADP . . . B 2 8.48 25.369 -1.612 1 17.98 ? N6 ADP 301 A 1 HETATM 24 N N1 ADP . . . B 2 7.225 26.091 0.276 1 20.05 ? N1 ADP 301 A 1 HETATM 25 C C2 ADP . . . B 2 7.166 26.645 1.507 1 20.04 ? C2 ADP 301 A 1 HETATM 26 N N3 ADP . . . B 2 8.253 27.069 2.175 1 19.76 ? N3 ADP 301 A 1 HETATM 27 C C4 ADP . . . B 2 9.478 26.95 1.61 1 19.73 ? C4 ADP 301 A 1 HETATM 28 H "H5'1" ADP . . . B 2 14.286 30.005 2.616 1 20.85 ? "H5'1" ADP 301 A 1 HETATM 29 H "H5'2" ADP . . . B 2 15.02 29.355 4.085 1 20.85 ? "H5'2" ADP 301 A 1 HETATM 30 H H4' ADP . . . B 2 12.788 30.041 4.574 1 22.93 ? H4' ADP 301 A 1 HETATM 31 H H3' ADP . . . B 2 13.646 27.512 5.235 1 26.7 ? H3' ADP 301 A 1 HETATM 32 H HO3' ADP . . . B 2 11.815 27.744 6.687 1 33.95 ? HO3' ADP 301 A 1 HETATM 33 H H2' ADP . . . B 2 12.371 26.129 3.784 1 25.02 ? H2' ADP 301 A 1 HETATM 34 H HO2' ADP . . . B 2 10.943 25.353 4.939 1 33.53 ? HO2' ADP 301 A 1 HETATM 35 H H1' ADP . . . B 2 10.126 28.132 3.79 1 26.45 ? H1' ADP 301 A 1 HETATM 36 H H8 ADP . . . B 2 12.652 27.056 1.084 1 19.17 ? H8 ADP 301 A 1 HETATM 37 H HN61 ADP . . . B 2 7.657 25.057 -2.075 1 21.62 ? HN61 ADP 301 A 1 HETATM 38 H HN62 ADP . . . B 2 9.379 25.254 -2.054 1 21.62 ? HN62 ADP 301 A 1 HETATM 39 H H2 ADP . . . B 2 6.197 26.754 1.977 1 24.09 ? H2 ADP 301 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 39 #