data_5YR5 # _model_server_result.job_id w_GIFtyOCv4Xd2NLGG5Uig _model_server_result.datetime_utc '2024-11-30 13:55:22' _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 5yr5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5YR5 # _exptl.entry_id 5YR5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.933 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'COBALT (II) ION' _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 87.95 _cell.angle_gamma 90 _cell.entry_id 5YR5 _cell.length_a 47.392 _cell.length_b 77.339 _cell.length_c 47.464 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YR5 _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 author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D 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 A OE1 GLU 39 A GLU 128 1_555 D CO CO . A CO 403 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc2 A OE1 GLU 39 A GLU 128 1_555 D CO CO . A CO 403 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.818 ? metalc ? metalc3 A OH TYR 106 A TYR 195 1_555 D CO CO . A CO 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc4 A O ASN 118 A ASN 207 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc5 A O VAL 120 A VAL 209 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc6 A OD1 ASP 140 A ASP 229 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc7 A OD2 ASP 140 A ASP 229 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc8 A OD2 ASP 151 A ASP 240 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc9 A OD1 ASP 151 A ASP 240 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc10 A NE2 HIS 214 A HIS 303 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc11 A NE2 HIS 221 A HIS 310 1_555 D CO CO . A CO 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? metalc ? metalc12 A OE1 GLU 247 A GLU 336 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc13 A O SER 274 A SER 363 1_555 E NA NA . A NA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc14 A OE2 GLU 278 A GLU 367 1_555 B CO CO . A CO 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc15 A OE1 GLU 278 A GLU 367 1_555 C CO CO . A CO 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc16 B CO CO . A CO 401 1_555 G O HOH . A HOH 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc17 C CO CO . A CO 402 1_555 G O HOH . A HOH 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc18 C CO CO . A CO 402 1_555 G O HOH . A HOH 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc19 D CO CO . A CO 403 1_555 G O HOH . A HOH 612 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.313 ? metalc ? metalc20 D CO CO . A CO 403 1_555 G O HOH . A HOH 612 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.426 ? metalc ? metalc21 D CO CO . A CO 403 1_555 G O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? metalc ? metalc22 E NA NA . A NA 404 1_555 G O HOH . A HOH 440 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? # _chem_comp.formula 'Co 2' _chem_comp.formula_weight 58.933 _chem_comp.id CO _chem_comp.mon_nstd_flag . _chem_comp.name 'COBALT (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5YR5 _atom_sites.fract_transf_matrix[1][1] 0.021101 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] -0.000755 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01293 _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] 0.021082 _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 CO A 1 401 401 CO CO . C 2 CO A 1 402 402 CO CO . D 2 CO A 1 403 403 CO CO . E 3 NA A 1 404 404 NA NA . F 4 OVA A 1 405 405 OVA OVA . G 5 HOH A 1 411 411 HOH HOH . G 5 HOH A 2 412 412 HOH HOH . G 5 HOH A 3 413 413 HOH HOH . G 5 HOH A 4 414 414 HOH HOH . G 5 HOH A 5 415 415 HOH HOH . G 5 HOH A 6 416 416 HOH HOH . G 5 HOH A 7 417 417 HOH HOH . G 5 HOH A 8 418 418 HOH HOH . G 5 HOH A 9 419 419 HOH HOH . G 5 HOH A 10 420 420 HOH HOH . G 5 HOH A 11 421 421 HOH HOH . G 5 HOH A 12 422 422 HOH HOH . G 5 HOH A 13 423 423 HOH HOH . G 5 HOH A 14 424 424 HOH HOH . G 5 HOH A 15 425 425 HOH HOH . G 5 HOH A 16 426 426 HOH HOH . G 5 HOH A 17 427 427 HOH HOH . G 5 HOH A 18 428 428 HOH HOH . G 5 HOH A 19 429 429 HOH HOH . G 5 HOH A 20 430 430 HOH HOH . G 5 HOH A 21 431 431 HOH HOH . G 5 HOH A 22 432 432 HOH HOH . G 5 HOH A 23 433 433 HOH HOH . G 5 HOH A 24 434 434 HOH HOH . G 5 HOH A 25 435 435 HOH HOH . G 5 HOH A 26 436 436 HOH HOH . G 5 HOH A 27 437 437 HOH HOH . G 5 HOH A 28 438 438 HOH HOH . G 5 HOH A 29 439 439 HOH HOH . G 5 HOH A 30 440 440 HOH HOH . G 5 HOH A 31 441 441 HOH HOH . G 5 HOH A 32 442 442 HOH HOH . G 5 HOH A 33 443 443 HOH HOH . G 5 HOH A 34 444 444 HOH HOH . G 5 HOH A 35 445 445 HOH HOH . G 5 HOH A 36 446 446 HOH HOH . G 5 HOH A 37 447 447 HOH HOH . G 5 HOH A 38 448 448 HOH HOH . G 5 HOH A 39 449 449 HOH HOH . G 5 HOH A 40 450 450 HOH HOH . G 5 HOH A 41 451 451 HOH HOH . G 5 HOH A 42 452 452 HOH HOH . G 5 HOH A 43 453 453 HOH HOH . G 5 HOH A 44 454 454 HOH HOH . G 5 HOH A 45 455 455 HOH HOH . G 5 HOH A 46 456 456 HOH HOH . G 5 HOH A 47 457 457 HOH HOH . G 5 HOH A 48 458 458 HOH HOH . G 5 HOH A 49 459 459 HOH HOH . G 5 HOH A 50 460 460 HOH HOH . G 5 HOH A 51 461 461 HOH HOH . G 5 HOH A 52 462 462 HOH HOH . G 5 HOH A 53 463 463 HOH HOH . G 5 HOH A 54 464 464 HOH HOH . G 5 HOH A 55 465 465 HOH HOH . G 5 HOH A 56 466 466 HOH HOH . G 5 HOH A 57 467 467 HOH HOH . G 5 HOH A 58 468 468 HOH HOH . G 5 HOH A 59 469 469 HOH HOH . G 5 HOH A 60 470 470 HOH HOH . G 5 HOH A 61 471 471 HOH HOH . G 5 HOH A 62 472 472 HOH HOH . G 5 HOH A 63 473 473 HOH HOH . G 5 HOH A 64 474 474 HOH HOH . G 5 HOH A 65 475 475 HOH HOH . G 5 HOH A 66 476 476 HOH HOH . G 5 HOH A 67 477 477 HOH HOH . G 5 HOH A 68 478 478 HOH HOH . G 5 HOH A 69 479 479 HOH HOH . G 5 HOH A 70 480 480 HOH HOH . G 5 HOH A 71 481 481 HOH HOH . G 5 HOH A 72 482 482 HOH HOH . G 5 HOH A 73 483 483 HOH HOH . G 5 HOH A 74 484 484 HOH HOH . G 5 HOH A 75 485 485 HOH HOH . G 5 HOH A 76 486 486 HOH HOH . G 5 HOH A 77 487 487 HOH HOH . G 5 HOH A 78 488 488 HOH HOH . G 5 HOH A 79 489 489 HOH HOH . G 5 HOH A 80 490 490 HOH HOH . G 5 HOH A 81 491 491 HOH HOH . G 5 HOH A 82 492 492 HOH HOH . G 5 HOH A 83 493 493 HOH HOH . G 5 HOH A 84 494 494 HOH HOH . G 5 HOH A 85 495 495 HOH HOH . G 5 HOH A 86 496 496 HOH HOH . G 5 HOH A 87 497 497 HOH HOH . G 5 HOH A 88 498 498 HOH HOH . G 5 HOH A 89 499 499 HOH HOH . G 5 HOH A 90 500 500 HOH HOH . G 5 HOH A 91 501 501 HOH HOH . G 5 HOH A 92 502 502 HOH HOH . G 5 HOH A 93 503 503 HOH HOH . G 5 HOH A 94 504 504 HOH HOH . G 5 HOH A 95 505 505 HOH HOH . G 5 HOH A 96 506 506 HOH HOH . G 5 HOH A 97 507 507 HOH HOH . G 5 HOH A 98 508 508 HOH HOH . G 5 HOH A 99 509 509 HOH HOH . G 5 HOH A 100 510 510 HOH HOH . G 5 HOH A 101 511 511 HOH HOH . G 5 HOH A 102 512 512 HOH HOH . G 5 HOH A 103 513 513 HOH HOH . G 5 HOH A 104 514 514 HOH HOH . G 5 HOH A 105 515 515 HOH HOH . G 5 HOH A 106 516 516 HOH HOH . G 5 HOH A 107 517 517 HOH HOH . G 5 HOH A 108 518 518 HOH HOH . G 5 HOH A 109 519 519 HOH HOH . G 5 HOH A 110 520 520 HOH HOH . G 5 HOH A 111 521 521 HOH HOH . G 5 HOH A 112 522 522 HOH HOH . G 5 HOH A 113 523 523 HOH HOH . G 5 HOH A 114 524 524 HOH HOH . G 5 HOH A 115 525 525 HOH HOH . G 5 HOH A 116 526 526 HOH HOH . G 5 HOH A 117 527 527 HOH HOH . G 5 HOH A 118 528 528 HOH HOH . G 5 HOH A 119 529 529 HOH HOH . G 5 HOH A 120 530 530 HOH HOH . G 5 HOH A 121 531 531 HOH HOH . G 5 HOH A 122 532 532 HOH HOH . G 5 HOH A 123 533 533 HOH HOH . G 5 HOH A 124 534 534 HOH HOH . G 5 HOH A 125 535 535 HOH HOH . G 5 HOH A 126 536 536 HOH HOH . G 5 HOH A 127 537 537 HOH HOH . G 5 HOH A 128 538 538 HOH HOH . G 5 HOH A 129 539 539 HOH HOH . G 5 HOH A 130 540 540 HOH HOH . G 5 HOH A 131 541 541 HOH HOH . G 5 HOH A 132 542 542 HOH HOH . G 5 HOH A 133 543 543 HOH HOH . G 5 HOH A 134 544 544 HOH HOH . G 5 HOH A 135 545 545 HOH HOH . G 5 HOH A 136 546 546 HOH HOH . G 5 HOH A 137 547 547 HOH HOH . G 5 HOH A 138 548 548 HOH HOH . G 5 HOH A 139 549 549 HOH HOH . G 5 HOH A 140 550 550 HOH HOH . G 5 HOH A 141 551 551 HOH HOH . G 5 HOH A 142 552 552 HOH HOH . G 5 HOH A 143 553 553 HOH HOH . G 5 HOH A 144 554 554 HOH HOH . G 5 HOH A 145 555 555 HOH HOH . G 5 HOH A 146 556 556 HOH HOH . G 5 HOH A 147 557 557 HOH HOH . G 5 HOH A 148 558 558 HOH HOH . G 5 HOH A 149 559 559 HOH HOH . G 5 HOH A 150 560 560 HOH HOH . G 5 HOH A 151 561 561 HOH HOH . G 5 HOH A 152 562 562 HOH HOH . G 5 HOH A 153 563 563 HOH HOH . G 5 HOH A 154 564 564 HOH HOH . G 5 HOH A 155 565 565 HOH HOH . G 5 HOH A 156 566 566 HOH HOH . G 5 HOH A 157 567 567 HOH HOH . G 5 HOH A 158 568 568 HOH HOH . G 5 HOH A 159 569 569 HOH HOH . G 5 HOH A 160 570 570 HOH HOH . G 5 HOH A 161 571 571 HOH HOH . G 5 HOH A 162 572 572 HOH HOH . G 5 HOH A 163 573 573 HOH HOH . G 5 HOH A 164 574 574 HOH HOH . G 5 HOH A 165 575 575 HOH HOH . G 5 HOH A 166 576 576 HOH HOH . G 5 HOH A 167 577 577 HOH HOH . G 5 HOH A 168 578 578 HOH HOH . G 5 HOH A 169 579 579 HOH HOH . G 5 HOH A 170 580 580 HOH HOH . G 5 HOH A 171 581 581 HOH HOH . G 5 HOH A 172 582 582 HOH HOH . G 5 HOH A 173 583 583 HOH HOH . G 5 HOH A 174 584 584 HOH HOH . G 5 HOH A 175 585 585 HOH HOH . G 5 HOH A 176 586 586 HOH HOH . G 5 HOH A 177 587 587 HOH HOH . G 5 HOH A 178 588 588 HOH HOH . G 5 HOH A 179 589 589 HOH HOH . G 5 HOH A 180 590 590 HOH HOH . G 5 HOH A 181 591 591 HOH HOH . G 5 HOH A 182 592 592 HOH HOH . G 5 HOH A 183 593 593 HOH HOH . G 5 HOH A 184 594 594 HOH HOH . G 5 HOH A 185 595 595 HOH HOH . G 5 HOH A 186 596 596 HOH HOH . G 5 HOH A 187 597 597 HOH HOH . G 5 HOH A 188 598 598 HOH HOH . G 5 HOH A 189 599 599 HOH HOH . G 5 HOH A 190 600 600 HOH HOH . G 5 HOH A 191 601 601 HOH HOH . G 5 HOH A 192 602 602 HOH HOH . G 5 HOH A 193 603 603 HOH HOH . G 5 HOH A 194 604 604 HOH HOH . G 5 HOH A 195 605 605 HOH HOH . G 5 HOH A 196 606 606 HOH HOH . G 5 HOH A 197 607 607 HOH HOH . G 5 HOH A 198 608 608 HOH HOH . G 5 HOH A 199 609 609 HOH HOH . G 5 HOH A 200 610 610 HOH HOH . G 5 HOH A 201 611 611 HOH HOH . G 5 HOH A 202 612 612 HOH HOH . G 5 HOH A 203 613 613 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CO _atom_site.label_atom_id CO _atom_site.label_comp_id CO _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id B _atom_site.label_entity_id 2 _atom_site.Cartn_x 1.665 _atom_site.Cartn_y -0.559 _atom_site.Cartn_z 11.591 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 18.08 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CO _atom_site.auth_comp_id CO _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #