data_2BOP # _model_server_result.job_id YhIjIqrt1Mskek9QsZ0AxQ _model_server_result.datetime_utc '2025-01-28 15:59:45' _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 2bop # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":499}' # _entry.id 2BOP # _exptl.entry_id 2BOP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 173.04 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'YTTERBIUM (III) ION' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 61.8 _cell.angle_beta 61.8 _cell.angle_gamma 61.8 _cell.entry_id 2BOP _cell.length_a 64.6 _cell.length_b 64.6 _cell.length_c 64.6 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2BOP _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'R 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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' 4_776 -y+2,-x+2,-z+1 -0.472551 -0.881303 0 -0.881303 0.472551 0 0 0 -1 220.780338 132.134307 53.921113 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 C N N ? 3 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 C YB YB . B YB 500 1_555 E O HOH . B HOH 612 4_776 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc2 C YB YB . B YB 500 1_555 E O HOH . B HOH 613 4_776 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc3 C YB YB . B YB 500 1_555 E O HOH . B HOH 620 4_776 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc4 B OE1 GLU 29 A GLU 354 1_555 D YB YB . A YB 499 5_776 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc5 B OE2 GLU 29 A GLU 354 1_555 D YB YB . A YB 499 5_776 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc6 B OD1 ASP 40 A ASP 365 1_555 D YB YB . A YB 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc7 B OE1 GLU 44 A GLU 369 1_555 D YB YB . A YB 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc8 B OE2 GLU 44 A GLU 369 1_555 D YB YB . A YB 499 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? hydrog WATSON-CRICK hydrog1 A N3 DC 2 B DC 2 1_555 A N1 DG 17 B DG 17 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 2 B DC 2 1_555 A O6 DG 17 B DG 17 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 2 B DC 2 1_555 A N2 DG 17 B DG 17 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 3 B DG 3 1_555 A N3 DC 16 B DC 16 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 3 B DG 3 1_555 A O2 DC 16 B DC 16 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 3 B DG 3 1_555 A N4 DC 16 B DC 16 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DA 4 B DA 4 1_555 A N3 DT 15 B DT 15 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N6 DA 4 B DA 4 1_555 A O4 DT 15 B DT 15 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DC 5 B DC 5 1_555 A N1 DG 14 B DG 14 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 DC 5 B DC 5 1_555 A O6 DG 14 B DG 14 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 DC 5 B DC 5 1_555 A N2 DG 14 B DG 14 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 6 B DC 6 1_555 A N1 DG 13 B DG 13 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 6 B DC 6 1_555 A O6 DG 13 B DG 13 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 6 B DC 6 1_555 A N2 DG 13 B DG 13 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A N1 DG 7 B DG 7 1_555 A N3 DC 12 B DC 12 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N2 DG 7 B DG 7 1_555 A O2 DC 12 B DC 12 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A O6 DG 7 B DG 7 1_555 A N4 DC 12 B DC 12 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A N1 DA 8 B DA 8 1_555 A N3 DT 11 B DT 11 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N6 DA 8 B DA 8 1_555 A O4 DT 11 B DT 11 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A N3 DC 9 B DC 9 1_555 A N1 DG 10 B DG 10 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N4 DC 9 B DC 9 1_555 A O6 DG 10 B DG 10 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A O2 DC 9 B DC 9 1_555 A N2 DG 10 B DG 10 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N1 DG 10 B DG 10 1_555 A N3 DC 9 B DC 9 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A N2 DG 10 B DG 10 1_555 A O2 DC 9 B DC 9 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A O6 DG 10 B DG 10 1_555 A N4 DC 9 B DC 9 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N3 DT 11 B DT 11 1_555 A N1 DA 8 B DA 8 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O4 DT 11 B DT 11 1_555 A N6 DA 8 B DA 8 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 A N3 DC 12 B DC 12 1_555 A N1 DG 7 B DG 7 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 A N4 DC 12 B DC 12 1_555 A O6 DG 7 B DG 7 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 A O2 DC 12 B DC 12 1_555 A N2 DG 7 B DG 7 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 A N1 DG 13 B DG 13 1_555 A N3 DC 6 B DC 6 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 A N2 DG 13 B DG 13 1_555 A O2 DC 6 B DC 6 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 A O6 DG 13 B DG 13 1_555 A N4 DC 6 B DC 6 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 A N1 DG 14 B DG 14 1_555 A N3 DC 5 B DC 5 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 A N2 DG 14 B DG 14 1_555 A O2 DC 5 B DC 5 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 A O6 DG 14 B DG 14 1_555 A N4 DC 5 B DC 5 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 A N3 DT 15 B DT 15 1_555 A N1 DA 4 B DA 4 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 A O4 DT 15 B DT 15 1_555 A N6 DA 4 B DA 4 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 A N3 DC 16 B DC 16 1_555 A N1 DG 3 B DG 3 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 A N4 DC 16 B DC 16 1_555 A O6 DG 3 B DG 3 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 A O2 DC 16 B DC 16 1_555 A N2 DG 3 B DG 3 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 A N1 DG 17 B DG 17 1_555 A N3 DC 2 B DC 2 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 A N2 DG 17 B DG 17 1_555 A O2 DC 2 B DC 2 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 A O6 DG 17 B DG 17 1_555 A N4 DC 2 B DC 2 4_776 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'Yb 3' _chem_comp.formula_weight 173.04 _chem_comp.id YB _chem_comp.mon_nstd_flag . _chem_comp.name 'YTTERBIUM (III) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2BOP _atom_sites.fract_transf_matrix[1][1] 0.01548 _atom_sites.fract_transf_matrix[1][2] -0.0083 _atom_sites.fract_transf_matrix[1][3] -0.005951 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017565 _atom_sites.fract_transf_matrix[2][3] -0.005951 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.018546 _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 3 YB B 1 500 500 YB YB . D 3 YB A 1 499 499 YB YB . E 4 HOH B 1 502 502 HOH HOH . E 4 HOH B 2 503 503 HOH HOH . E 4 HOH B 3 504 504 HOH HOH . E 4 HOH B 4 506 506 HOH HOH . E 4 HOH B 5 507 507 HOH HOH . E 4 HOH B 6 508 508 HOH HOH . E 4 HOH B 7 511 511 HOH HOH . E 4 HOH B 8 513 513 HOH HOH . E 4 HOH B 9 514 514 HOH HOH . E 4 HOH B 10 515 515 HOH HOH . E 4 HOH B 11 516 516 HOH HOH . E 4 HOH B 12 517 517 HOH HOH . E 4 HOH B 13 518 518 HOH HOH . E 4 HOH B 14 521 521 HOH HOH . E 4 HOH B 15 522 522 HOH HOH . E 4 HOH B 16 525 525 HOH HOH . E 4 HOH B 17 529 529 HOH HOH . E 4 HOH B 18 532 532 HOH HOH . E 4 HOH B 19 537 537 HOH HOH . E 4 HOH B 20 543 543 HOH HOH . E 4 HOH B 21 544 544 HOH HOH . E 4 HOH B 22 553 553 HOH HOH . E 4 HOH B 23 563 563 HOH HOH . E 4 HOH B 24 564 564 HOH HOH . E 4 HOH B 25 566 566 HOH HOH . E 4 HOH B 26 567 567 HOH HOH . E 4 HOH B 27 575 575 HOH HOH . E 4 HOH B 28 576 576 HOH HOH . E 4 HOH B 29 577 577 HOH HOH . E 4 HOH B 30 578 578 HOH HOH . E 4 HOH B 31 579 579 HOH HOH . E 4 HOH B 32 585 585 HOH HOH . E 4 HOH B 33 589 589 HOH HOH . E 4 HOH B 34 597 597 HOH HOH . E 4 HOH B 35 601 601 HOH HOH . E 4 HOH B 36 602 602 HOH HOH . E 4 HOH B 37 603 603 HOH HOH . E 4 HOH B 38 604 604 HOH HOH . E 4 HOH B 39 605 605 HOH HOH . E 4 HOH B 40 606 606 HOH HOH . E 4 HOH B 41 607 607 HOH HOH . E 4 HOH B 42 608 608 HOH HOH . E 4 HOH B 43 609 609 HOH HOH . E 4 HOH B 44 610 610 HOH HOH . E 4 HOH B 45 611 611 HOH HOH . E 4 HOH B 46 612 612 HOH HOH . E 4 HOH B 47 613 613 HOH HOH . E 4 HOH B 48 615 615 HOH HOH . E 4 HOH B 49 617 617 HOH HOH . E 4 HOH B 50 618 618 HOH HOH . E 4 HOH B 51 620 620 HOH HOH . E 4 HOH B 52 621 621 HOH HOH . F 4 HOH A 1 501 501 HOH HOH . F 4 HOH A 2 505 505 HOH HOH . F 4 HOH A 3 509 509 HOH HOH . F 4 HOH A 4 510 510 HOH HOH . F 4 HOH A 5 512 512 HOH HOH . F 4 HOH A 6 519 519 HOH HOH . F 4 HOH A 7 520 520 HOH HOH . F 4 HOH A 8 523 523 HOH HOH . F 4 HOH A 9 524 524 HOH HOH . F 4 HOH A 10 526 526 HOH HOH . F 4 HOH A 11 527 527 HOH HOH . F 4 HOH A 12 528 528 HOH HOH . F 4 HOH A 13 530 530 HOH HOH . F 4 HOH A 14 531 531 HOH HOH . F 4 HOH A 15 533 533 HOH HOH . F 4 HOH A 16 534 534 HOH HOH . F 4 HOH A 17 535 535 HOH HOH . F 4 HOH A 18 536 536 HOH HOH . F 4 HOH A 19 538 538 HOH HOH . F 4 HOH A 20 539 539 HOH HOH . F 4 HOH A 21 540 540 HOH HOH . F 4 HOH A 22 541 541 HOH HOH . F 4 HOH A 23 542 542 HOH HOH . F 4 HOH A 24 545 545 HOH HOH . F 4 HOH A 25 546 546 HOH HOH . F 4 HOH A 26 547 547 HOH HOH . F 4 HOH A 27 548 548 HOH HOH . F 4 HOH A 28 549 549 HOH HOH . F 4 HOH A 29 550 550 HOH HOH . F 4 HOH A 30 551 551 HOH HOH . F 4 HOH A 31 552 552 HOH HOH . F 4 HOH A 32 554 554 HOH HOH . F 4 HOH A 33 555 555 HOH HOH . F 4 HOH A 34 556 556 HOH HOH . F 4 HOH A 35 557 557 HOH HOH . F 4 HOH A 36 558 558 HOH HOH . F 4 HOH A 37 559 559 HOH HOH . F 4 HOH A 38 560 560 HOH HOH . F 4 HOH A 39 561 561 HOH HOH . F 4 HOH A 40 562 562 HOH HOH . F 4 HOH A 41 565 565 HOH HOH . F 4 HOH A 42 568 568 HOH HOH . F 4 HOH A 43 569 569 HOH HOH . F 4 HOH A 44 570 570 HOH HOH . F 4 HOH A 45 571 571 HOH HOH . F 4 HOH A 46 572 572 HOH HOH . F 4 HOH A 47 573 573 HOH HOH . F 4 HOH A 48 574 574 HOH HOH . F 4 HOH A 49 580 580 HOH HOH . F 4 HOH A 50 581 581 HOH HOH . F 4 HOH A 51 582 582 HOH HOH . F 4 HOH A 52 583 583 HOH HOH . F 4 HOH A 53 584 584 HOH HOH . F 4 HOH A 54 586 586 HOH HOH . F 4 HOH A 55 587 587 HOH HOH . F 4 HOH A 56 588 588 HOH HOH . F 4 HOH A 57 590 590 HOH HOH . F 4 HOH A 58 591 591 HOH HOH . F 4 HOH A 59 592 592 HOH HOH . F 4 HOH A 60 593 593 HOH HOH . F 4 HOH A 61 594 594 HOH HOH . F 4 HOH A 62 595 595 HOH HOH . F 4 HOH A 63 596 596 HOH HOH . F 4 HOH A 64 598 598 HOH HOH . F 4 HOH A 65 599 599 HOH HOH . F 4 HOH A 66 600 600 HOH HOH . F 4 HOH A 67 614 614 HOH HOH . F 4 HOH A 68 616 616 HOH HOH . F 4 HOH A 69 619 619 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol YB _atom_site.label_atom_id YB _atom_site.label_comp_id YB _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 3 _atom_site.Cartn_x 119.193 _atom_site.Cartn_y 60.691 _atom_site.Cartn_z 45.87 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 20.2 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id YB _atom_site.auth_comp_id YB _atom_site.auth_seq_id 499 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 543 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #