data_1GSA # _model_server_result.job_id p0rhdsJXJNDbLDDClVRQAw _model_server_result.datetime_utc '2024-11-25 20:50:34' _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 1gsa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":317}' # _entry.id 1GSA # _exptl.entry_id 1GSA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 120 _cell.entry_id 1GSA _cell.length_a 87.25 _cell.length_b 87.25 _cell.length_c 169.58 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GSA _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 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,C,D,E,F,G 1 1,2,3,4 A,B,C,D,E,F,G 2 1,3 # 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' 4_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 43.625 75.560716 0 3 'crystal symmetry operation' 7_555 y,x,-z+2/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 113.053333 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+2/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 43.625 75.560716 113.053333 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id E _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 OD2 ASP 273 A ASP 273 1_555 B MG MG . A MG 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc2 A OE2 GLU 281 A GLU 281 1_555 B MG MG . A MG 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc3 A OE2 GLU 281 A GLU 281 1_555 C MG MG . A MG 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc4 A OE1 GLU 281 A GLU 281 1_555 C MG MG . A MG 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc5 A OD1 ASN 283 A ASN 283 1_555 C MG MG . A MG 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc6 A ND2 ASN 283 A ASN 283 1_555 C MG MG . A MG 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc7 E O3B ADP . A ADP 317 1_555 B MG MG . A MG 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc8 E O1A ADP . A ADP 317 1_555 B MG MG . A MG 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc9 E O2B ADP . A ADP 317 1_555 C MG MG . A MG 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.862 ? metalc ? metalc10 E O1B ADP . A ADP 317 1_555 C MG MG . A MG 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.683 ? metalc ? metalc11 B MG MG . A MG 319 1_555 D O4 SO4 . A SO4 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc12 B MG MG . A MG 319 1_555 G O HOH . A HOH 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.112 ? metalc ? metalc13 C MG MG . A MG 320 1_555 D O2 SO4 . A SO4 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc14 C MG MG . A MG 320 1_555 D S SO4 . A SO4 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.865 ? metalc ? metalc15 C MG MG . A MG 320 1_555 D O1 SO4 . A SO4 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.07 ? metalc ? metalc16 C MG MG . A MG 320 1_555 G O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? # _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 1GSA _atom_sites.fract_transf_matrix[1][1] 0.011461 _atom_sites.fract_transf_matrix[1][2] 0.006617 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013234 _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] 0.005897 _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 MG A 1 319 319 MG MG . C 2 MG A 1 320 320 MG MG . D 3 SO4 A 1 400 400 SO4 SO4 . E 4 ADP A 1 317 317 ADP ADP . F 5 GSH A 1 318 318 GSH GTT . G 6 HOH A 1 401 401 HOH HOH . G 6 HOH A 2 402 402 HOH HOH . G 6 HOH A 3 403 403 HOH HOH . G 6 HOH A 4 404 404 HOH HOH . G 6 HOH A 5 405 405 HOH HOH . G 6 HOH A 6 406 406 HOH HOH . G 6 HOH A 7 407 407 HOH HOH . G 6 HOH A 8 408 408 HOH HOH . G 6 HOH A 9 409 409 HOH HOH . G 6 HOH A 10 410 410 HOH HOH . G 6 HOH A 11 411 411 HOH HOH . G 6 HOH A 12 412 412 HOH HOH . G 6 HOH A 13 413 413 HOH HOH . G 6 HOH A 14 414 414 HOH HOH . G 6 HOH A 15 415 415 HOH HOH . G 6 HOH A 16 416 416 HOH HOH . G 6 HOH A 17 417 417 HOH HOH . G 6 HOH A 18 418 418 HOH HOH . G 6 HOH A 19 419 419 HOH HOH . G 6 HOH A 20 420 420 HOH HOH . G 6 HOH A 21 421 421 HOH HOH . G 6 HOH A 22 422 422 HOH HOH . G 6 HOH A 23 423 423 HOH HOH . G 6 HOH A 24 424 424 HOH HOH . G 6 HOH A 25 425 425 HOH HOH . G 6 HOH A 26 426 426 HOH HOH . G 6 HOH A 27 427 427 HOH HOH . G 6 HOH A 28 428 428 HOH HOH . G 6 HOH A 29 429 429 HOH HOH . G 6 HOH A 30 430 430 HOH HOH . G 6 HOH A 31 431 431 HOH HOH . G 6 HOH A 32 432 432 HOH HOH . G 6 HOH A 33 433 433 HOH HOH . G 6 HOH A 34 434 434 HOH HOH . G 6 HOH A 35 435 435 HOH HOH . G 6 HOH A 36 436 436 HOH HOH . G 6 HOH A 37 437 437 HOH HOH . G 6 HOH A 38 438 438 HOH HOH . G 6 HOH A 39 439 439 HOH HOH . G 6 HOH A 40 440 440 HOH HOH . G 6 HOH A 41 441 441 HOH HOH . G 6 HOH A 42 442 442 HOH HOH . G 6 HOH A 43 443 443 HOH HOH . G 6 HOH A 44 444 444 HOH HOH . G 6 HOH A 45 445 445 HOH HOH . G 6 HOH A 46 446 446 HOH HOH . G 6 HOH A 47 447 447 HOH HOH . G 6 HOH A 48 448 448 HOH HOH . G 6 HOH A 49 449 449 HOH HOH . G 6 HOH A 50 450 450 HOH HOH . G 6 HOH A 51 451 451 HOH HOH . G 6 HOH A 52 452 452 HOH HOH . G 6 HOH A 53 453 453 HOH HOH . G 6 HOH A 54 454 454 HOH HOH . G 6 HOH A 55 455 455 HOH HOH . G 6 HOH A 56 456 456 HOH HOH . G 6 HOH A 57 457 457 HOH HOH . G 6 HOH A 58 458 458 HOH HOH . G 6 HOH A 59 459 459 HOH HOH . G 6 HOH A 60 460 460 HOH HOH . G 6 HOH A 61 461 461 HOH HOH . G 6 HOH A 62 462 462 HOH HOH . G 6 HOH A 63 463 463 HOH HOH . G 6 HOH A 64 464 464 HOH HOH . G 6 HOH A 65 465 465 HOH HOH . G 6 HOH A 66 466 466 HOH HOH . G 6 HOH A 67 467 467 HOH HOH . G 6 HOH A 68 468 468 HOH HOH . G 6 HOH A 69 469 469 HOH HOH . G 6 HOH A 70 470 470 HOH HOH . G 6 HOH A 71 471 471 HOH HOH . G 6 HOH A 72 472 472 HOH HOH . G 6 HOH A 73 473 473 HOH HOH . G 6 HOH A 74 474 474 HOH HOH . G 6 HOH A 75 475 475 HOH HOH . G 6 HOH A 76 476 476 HOH HOH . G 6 HOH A 77 478 478 HOH HOH . G 6 HOH A 78 479 479 HOH HOH . G 6 HOH A 79 480 480 HOH HOH . G 6 HOH A 80 481 481 HOH HOH . G 6 HOH A 81 482 482 HOH HOH . G 6 HOH A 82 483 483 HOH HOH . G 6 HOH A 83 484 484 HOH HOH . G 6 HOH A 84 485 485 HOH HOH . G 6 HOH A 85 486 486 HOH HOH . G 6 HOH A 86 487 487 HOH HOH . G 6 HOH A 87 488 488 HOH HOH . G 6 HOH A 88 489 489 HOH HOH . G 6 HOH A 89 490 490 HOH HOH . G 6 HOH A 90 491 491 HOH HOH . G 6 HOH A 91 492 492 HOH HOH . G 6 HOH A 92 493 493 HOH HOH . G 6 HOH A 93 494 494 HOH HOH . G 6 HOH A 94 495 495 HOH HOH . G 6 HOH A 95 496 496 HOH HOH . G 6 HOH A 96 497 497 HOH HOH . G 6 HOH A 97 498 498 HOH HOH . G 6 HOH A 98 499 499 HOH HOH . G 6 HOH A 99 500 500 HOH HOH . G 6 HOH A 100 501 501 HOH HOH . G 6 HOH A 101 502 502 HOH HOH . G 6 HOH A 102 503 503 HOH HOH . G 6 HOH A 103 504 504 HOH HOH . G 6 HOH A 104 505 505 HOH HOH . G 6 HOH A 105 506 506 HOH HOH . G 6 HOH A 106 507 507 HOH HOH . G 6 HOH A 107 508 508 HOH HOH . G 6 HOH A 108 509 509 HOH HOH . G 6 HOH A 109 510 510 HOH HOH . G 6 HOH A 110 511 511 HOH HOH . G 6 HOH A 111 512 512 HOH HOH . G 6 HOH A 112 513 513 HOH HOH . G 6 HOH A 113 514 514 HOH HOH . G 6 HOH A 114 515 515 HOH HOH . G 6 HOH A 115 516 516 HOH HOH . G 6 HOH A 116 517 517 HOH HOH . G 6 HOH A 117 518 518 HOH HOH . G 6 HOH A 118 519 519 HOH HOH . G 6 HOH A 119 520 520 HOH HOH . G 6 HOH A 120 521 521 HOH HOH . G 6 HOH A 121 522 522 HOH HOH . G 6 HOH A 122 523 523 HOH HOH . G 6 HOH A 123 524 524 HOH HOH . G 6 HOH A 124 525 525 HOH HOH . G 6 HOH A 125 526 526 HOH HOH . G 6 HOH A 126 527 527 HOH HOH . G 6 HOH A 127 528 528 HOH HOH . G 6 HOH A 128 529 529 HOH HOH . G 6 HOH A 129 530 530 HOH HOH . G 6 HOH A 130 531 531 HOH HOH . G 6 HOH A 131 532 532 HOH HOH . G 6 HOH A 132 533 533 HOH HOH . G 6 HOH A 133 534 534 HOH HOH . G 6 HOH A 134 535 535 HOH HOH . G 6 HOH A 135 536 536 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 . . . E 4 22.318 21.971 72.246 1 23.81 ? PB ADP 317 A 1 HETATM 2 O O1B ADP . . . E 4 21.903 21.404 70.932 1 24.68 ? O1B ADP 317 A 1 HETATM 3 O O2B ADP . . . E 4 22.998 23.26 71.958 1 26.17 ? O2B ADP 317 A 1 HETATM 4 O O3B ADP . . . E 4 23.255 21.011 72.887 1 26.25 ? O3B ADP 317 A 1 HETATM 5 P PA ADP . . . E 4 20.728 21.578 74.624 1 23.79 ? PA ADP 317 A 1 HETATM 6 O O1A ADP . . . E 4 21.249 20.192 74.707 1 22.22 ? O1A ADP 317 A 1 HETATM 7 O O2A ADP . . . E 4 19.27 21.488 74.836 1 22.5 ? O2A ADP 317 A 1 HETATM 8 O O3A ADP . . . E 4 21.07 22.26 73.218 1 23.9 ? O3A ADP 317 A 1 HETATM 9 O O5' ADP . . . E 4 21.41 22.535 75.733 1 23.95 ? O5' ADP 317 A 1 HETATM 10 C C5' ADP . . . E 4 22.807 22.822 75.681 1 24.97 ? C5' ADP 317 A 1 HETATM 11 C C4' ADP . . . E 4 23.332 23.146 77.06 1 25.04 ? C4' ADP 317 A 1 HETATM 12 O O4' ADP . . . E 4 22.528 24.172 77.705 1 26.28 ? O4' ADP 317 A 1 HETATM 13 C C3' ADP . . . E 4 23.166 21.913 77.943 1 25.13 ? C3' ADP 317 A 1 HETATM 14 O O3' ADP . . . E 4 24.324 21.079 77.904 1 26.84 ? O3' ADP 317 A 1 HETATM 15 C C2' ADP . . . E 4 23.045 22.505 79.317 1 24.75 ? C2' ADP 317 A 1 HETATM 16 O O2' ADP . . . E 4 24.325 22.906 79.798 1 21.05 ? O2' ADP 317 A 1 HETATM 17 C C1' ADP . . . E 4 22.194 23.727 79.029 1 24.02 ? C1' ADP 317 A 1 HETATM 18 N N9 ADP . . . E 4 20.768 23.362 79.149 1 23.51 ? N9 ADP 317 A 1 HETATM 19 C C8 ADP . . . E 4 19.827 23.164 78.183 1 22.46 ? C8 ADP 317 A 1 HETATM 20 N N7 ADP . . . E 4 18.574 22.925 78.7 1 22.65 ? N7 ADP 317 A 1 HETATM 21 C C5 ADP . . . E 4 18.782 22.992 80.067 1 23.53 ? C5 ADP 317 A 1 HETATM 22 C C6 ADP . . . E 4 17.9 22.871 81.16 1 22.37 ? C6 ADP 317 A 1 HETATM 23 N N6 ADP . . . E 4 16.589 22.688 81.003 1 22.02 ? N6 ADP 317 A 1 HETATM 24 N N1 ADP . . . E 4 18.423 22.992 82.389 1 20.84 ? N1 ADP 317 A 1 HETATM 25 C C2 ADP . . . E 4 19.727 23.234 82.533 1 22.22 ? C2 ADP 317 A 1 HETATM 26 N N3 ADP . . . E 4 20.653 23.373 81.597 1 22.86 ? N3 ADP 317 A 1 HETATM 27 C C4 ADP . . . E 4 20.101 23.238 80.353 1 23.49 ? C4 ADP 317 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #