data_3EQD # _model_server_result.job_id rnheGJxqqv7t9P03ysQmoQ _model_server_result.datetime_utc '2024-11-28 18:16:44' _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 3eqd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2}' # _entry.id 3EQD # _exptl.entry_id 3EQD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 3EQD _cell.length_a 77.01 _cell.length_b 77.01 _cell.length_c 222.37 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3EQD _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 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 monomeric 1 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 1 1 A,B,C,D,E,F 2 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' 11_555 -x+y,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 111.185 # _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 B O1B AGS . A AGS 2 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc2 B O2A AGS . A AGS 2 1_555 C MG MG . A MG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.464 ? metalc ? metalc3 C MG MG . A MG 3 1_555 A OD1 ASN 162 A ASN 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc4 C MG MG . A MG 3 1_555 A OD2 ASP 175 A ASP 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.974 ? metalc ? metalc5 C MG MG . A MG 3 1_555 F O HOH . A HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc6 C MG MG . A MG 3 1_555 F O HOH . A HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc7 D CA CA . A CA 5 1_555 A OD1 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 4.655 ? metalc ? metalc8 D CA CA . A CA 5 1_555 A OD2 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc9 D CA CA . A CA 5 1_555 A OD1 ASP 33 A ASP 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc10 D CA CA . A CA 5 1_555 F O HOH . A HOH 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc11 E NA NA . A NA 6 1_555 A OD1 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc12 E NA NA . A NA 6 1_555 A OD2 ASP 32 A ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc13 E NA NA . A NA 6 1_555 F O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc14 E NA NA . A NA 6 1_555 F O HOH . A HOH 441 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc15 E NA NA . A NA 6 1_555 F O HOH . A HOH 470 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc16 E NA NA . A NA 6 1_555 F O HOH . A HOH 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 PG S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 3EQD _atom_sites.fract_transf_matrix[1][1] 0.012985 _atom_sites.fract_transf_matrix[1][2] 0.007497 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014994 _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] 0.004497 _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 AGS A 1 2 2 AGS AGS . C 3 MG A 1 3 3 MG MG . D 4 CA A 1 5 5 CA CA . E 5 NA A 1 6 6 NA NA . F 6 HOH A 1 394 394 HOH HOH . F 6 HOH A 2 395 395 HOH HOH . F 6 HOH A 3 396 396 HOH HOH . F 6 HOH A 4 397 397 HOH HOH . F 6 HOH A 5 398 398 HOH HOH . F 6 HOH A 6 399 399 HOH HOH . F 6 HOH A 7 400 400 HOH HOH . F 6 HOH A 8 401 401 HOH HOH . F 6 HOH A 9 402 402 HOH HOH . F 6 HOH A 10 403 403 HOH HOH . F 6 HOH A 11 404 404 HOH HOH . F 6 HOH A 12 405 405 HOH HOH . F 6 HOH A 13 406 406 HOH HOH . F 6 HOH A 14 407 407 HOH HOH . F 6 HOH A 15 408 408 HOH HOH . F 6 HOH A 16 409 409 HOH HOH . F 6 HOH A 17 410 410 HOH HOH . F 6 HOH A 18 411 411 HOH HOH . F 6 HOH A 19 412 412 HOH HOH . F 6 HOH A 20 413 413 HOH HOH . F 6 HOH A 21 414 414 HOH HOH . F 6 HOH A 22 415 415 HOH HOH . F 6 HOH A 23 416 416 HOH HOH . F 6 HOH A 24 417 417 HOH HOH . F 6 HOH A 25 418 418 HOH HOH . F 6 HOH A 26 419 419 HOH HOH . F 6 HOH A 27 420 420 HOH HOH . F 6 HOH A 28 421 421 HOH HOH . F 6 HOH A 29 422 422 HOH HOH . F 6 HOH A 30 423 423 HOH HOH . F 6 HOH A 31 424 424 HOH HOH . F 6 HOH A 32 425 425 HOH HOH . F 6 HOH A 33 426 426 HOH HOH . F 6 HOH A 34 427 427 HOH HOH . F 6 HOH A 35 428 428 HOH HOH . F 6 HOH A 36 429 429 HOH HOH . F 6 HOH A 37 430 430 HOH HOH . F 6 HOH A 38 431 431 HOH HOH . F 6 HOH A 39 432 432 HOH HOH . F 6 HOH A 40 433 433 HOH HOH . F 6 HOH A 41 434 434 HOH HOH . F 6 HOH A 42 435 435 HOH HOH . F 6 HOH A 43 436 436 HOH HOH . F 6 HOH A 44 437 437 HOH HOH . F 6 HOH A 45 438 438 HOH HOH . F 6 HOH A 46 439 439 HOH HOH . F 6 HOH A 47 440 440 HOH HOH . F 6 HOH A 48 441 441 HOH HOH . F 6 HOH A 49 442 442 HOH HOH . F 6 HOH A 50 443 443 HOH HOH . F 6 HOH A 51 444 444 HOH HOH . F 6 HOH A 52 445 445 HOH HOH . F 6 HOH A 53 446 446 HOH HOH . F 6 HOH A 54 447 447 HOH HOH . F 6 HOH A 55 448 448 HOH HOH . F 6 HOH A 56 449 449 HOH HOH . F 6 HOH A 57 450 450 HOH HOH . F 6 HOH A 58 451 451 HOH HOH . F 6 HOH A 59 452 452 HOH HOH . F 6 HOH A 60 453 453 HOH HOH . F 6 HOH A 61 454 454 HOH HOH . F 6 HOH A 62 455 455 HOH HOH . F 6 HOH A 63 456 456 HOH HOH . F 6 HOH A 64 457 457 HOH HOH . F 6 HOH A 65 458 458 HOH HOH . F 6 HOH A 66 459 459 HOH HOH . F 6 HOH A 67 460 460 HOH HOH . F 6 HOH A 68 461 461 HOH HOH . F 6 HOH A 69 462 462 HOH HOH . F 6 HOH A 70 463 463 HOH HOH . F 6 HOH A 71 464 464 HOH HOH . F 6 HOH A 72 465 465 HOH HOH . F 6 HOH A 73 466 466 HOH HOH . F 6 HOH A 74 467 467 HOH HOH . F 6 HOH A 75 468 468 HOH HOH . F 6 HOH A 76 469 469 HOH HOH . F 6 HOH A 77 470 470 HOH HOH . F 6 HOH A 78 471 471 HOH HOH . F 6 HOH A 79 472 472 HOH HOH . F 6 HOH A 80 473 473 HOH HOH . F 6 HOH A 81 474 474 HOH HOH . F 6 HOH A 82 475 475 HOH HOH . F 6 HOH A 83 476 476 HOH HOH . F 6 HOH A 84 477 477 HOH HOH . F 6 HOH A 85 478 478 HOH HOH . F 6 HOH A 86 479 479 HOH HOH . F 6 HOH A 87 480 480 HOH HOH . F 6 HOH A 88 481 481 HOH HOH . F 6 HOH A 89 482 482 HOH HOH . F 6 HOH A 90 483 483 HOH HOH . F 6 HOH A 91 484 484 HOH HOH . F 6 HOH A 92 485 485 HOH HOH . F 6 HOH A 93 486 486 HOH HOH . F 6 HOH A 94 487 487 HOH HOH . F 6 HOH A 95 488 488 HOH HOH . F 6 HOH A 96 489 489 HOH HOH . F 6 HOH A 97 490 490 HOH HOH . F 6 HOH A 98 491 491 HOH HOH . F 6 HOH A 99 492 492 HOH HOH . F 6 HOH A 100 493 493 HOH HOH . F 6 HOH A 101 494 494 HOH HOH . F 6 HOH A 102 495 495 HOH HOH . F 6 HOH A 103 496 496 HOH HOH . F 6 HOH A 104 497 497 HOH HOH . F 6 HOH A 105 498 498 HOH HOH . F 6 HOH A 106 499 499 HOH HOH . F 6 HOH A 107 500 500 HOH HOH . F 6 HOH A 108 501 501 HOH HOH . F 6 HOH A 109 502 502 HOH HOH . F 6 HOH A 110 503 503 HOH HOH . F 6 HOH A 111 504 504 HOH HOH . F 6 HOH A 112 505 505 HOH HOH . F 6 HOH A 113 506 506 HOH HOH . F 6 HOH A 114 507 507 HOH HOH . F 6 HOH A 115 508 508 HOH HOH . F 6 HOH A 116 509 509 HOH HOH . F 6 HOH A 117 510 510 HOH HOH . F 6 HOH A 118 511 511 HOH HOH . F 6 HOH A 119 512 512 HOH HOH . F 6 HOH A 120 513 513 HOH HOH . F 6 HOH A 121 514 514 HOH HOH . F 6 HOH A 122 515 515 HOH HOH . F 6 HOH A 123 516 516 HOH HOH . F 6 HOH A 124 517 517 HOH HOH . F 6 HOH A 125 518 518 HOH HOH . F 6 HOH A 126 519 519 HOH HOH . F 6 HOH A 127 520 520 HOH HOH . F 6 HOH A 128 521 521 HOH HOH . F 6 HOH A 129 522 522 HOH HOH . F 6 HOH A 130 523 523 HOH HOH . F 6 HOH A 131 524 524 HOH HOH . F 6 HOH A 132 525 393 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 PG AGS . . . B 2 -10.573 60.726 33.107 1 76.45 ? PG AGS 2 A 1 HETATM 2 S S1G AGS . . . B 2 -11.994 59.87 32.845 1 79.34 ? S1G AGS 2 A 1 HETATM 3 O O2G AGS . . . B 2 -9.502 60.281 32.12 1 76.01 ? O2G AGS 2 A 1 HETATM 4 O O3G AGS . . . B 2 -10.056 60.56 34.617 1 76.14 ? O3G AGS 2 A 1 HETATM 5 P PB AGS . . . B 2 -9.938 63.524 32.977 1 67.79 ? PB AGS 2 A 1 HETATM 6 O O1B AGS . . . B 2 -8.744 63.384 32.053 1 66.25 ? O1B AGS 2 A 1 HETATM 7 O O2B AGS . . . B 2 -10.651 64.808 32.643 1 67.9 ? O2B AGS 2 A 1 HETATM 8 O O3B AGS . . . B 2 -10.922 62.272 32.876 1 72.64 ? O3B AGS 2 A 1 HETATM 9 P PA AGS . . . B 2 -8.124 64.007 35.204 1 62.76 ? PA AGS 2 A 1 HETATM 10 O O1A AGS . . . B 2 -8.097 63.752 36.693 1 63.68 ? O1A AGS 2 A 1 HETATM 11 O O2A AGS . . . B 2 -6.903 63.383 34.619 1 62.77 ? O2A AGS 2 A 1 HETATM 12 O O3A AGS . . . B 2 -9.489 63.574 34.525 1 65.66 ? O3A AGS 2 A 1 HETATM 13 O O5' AGS . . . B 2 -8.037 65.57 34.956 1 59.99 ? O5' AGS 2 A 1 HETATM 14 C C5' AGS . . . B 2 -9.202 66.393 35.231 1 57.21 ? C5' AGS 2 A 1 HETATM 15 C C4' AGS . . . B 2 -8.952 67.758 34.574 1 55.15 ? C4' AGS 2 A 1 HETATM 16 O O4' AGS . . . B 2 -7.851 68.451 35.224 1 52.35 ? O4' AGS 2 A 1 HETATM 17 C C3' AGS . . . B 2 -8.505 67.742 33.121 1 55.32 ? C3' AGS 2 A 1 HETATM 18 O O3' AGS . . . B 2 -9.619 67.463 32.277 1 56.9 ? O3' AGS 2 A 1 HETATM 19 C C2' AGS . . . B 2 -7.872 69.139 33.011 1 53.42 ? C2' AGS 2 A 1 HETATM 20 O O2' AGS . . . B 2 -8.883 70.128 32.854 1 55.29 ? O2' AGS 2 A 1 HETATM 21 C C1' AGS . . . B 2 -7.235 69.373 34.387 1 50.61 ? C1' AGS 2 A 1 HETATM 22 N N9 AGS . . . B 2 -5.775 69.168 34.42 1 46.38 ? N9 AGS 2 A 1 HETATM 23 C C8 AGS . . . B 2 -5.086 67.986 34.512 1 45.42 ? C8 AGS 2 A 1 HETATM 24 N N7 AGS . . . B 2 -3.727 68.142 34.494 1 44.75 ? N7 AGS 2 A 1 HETATM 25 C C5 AGS . . . B 2 -3.525 69.517 34.38 1 42.91 ? C5 AGS 2 A 1 HETATM 26 C C6 AGS . . . B 2 -2.331 70.281 34.319 1 41.17 ? C6 AGS 2 A 1 HETATM 27 N N6 AGS . . . B 2 -1.118 69.902 34.328 1 39.27 ? N6 AGS 2 A 1 HETATM 28 N N1 AGS . . . B 2 -2.624 71.624 34.223 1 41.56 ? N1 AGS 2 A 1 HETATM 29 C C2 AGS . . . B 2 -3.881 72.201 34.162 1 43.41 ? C2 AGS 2 A 1 HETATM 30 N N3 AGS . . . B 2 -4.999 71.504 34.211 1 44.31 ? N3 AGS 2 A 1 HETATM 31 C C4 AGS . . . B 2 -4.788 70.163 34.328 1 44.12 ? C4 AGS 2 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #