data_4YN2 # _model_server_result.job_id SJZw0RRrZcMhRIQ1SWV2Jg _model_server_result.datetime_utc '2024-11-25 10:20:22' _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 4yn2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":405}' # _entry.id 4YN2 # _exptl.entry_id 4YN2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _entity.pdbx_number_of_molecules 2 _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 4YN2 _cell.length_a 68.182 _cell.length_b 68.182 _cell.length_c 128.058 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YN2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 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 PISA 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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 68.182 68.182 64.029 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 D N N ? 4 E N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 2 n B NAG 1 B 1 NAG A 401 NAG 2 n B NAG 2 B 2 NAG A 402 NAG 2 n B BMA 3 B 3 BMA A 403 BMA # 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 disulf ? disulf1 A SG CYS 14 A CYS 14 1_555 A SG CYS 33 A CYS 33 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? disulf ? disulf2 A SG CYS 80 A CYS 80 1_555 A SG CYS 255 A CYS 255 1_565 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 92 A CYS 92 1_555 A SG CYS 225 A CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 A SG CYS 137 A CYS 137 1_555 A SG CYS 187 A CYS 187 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? covale ? covale1 A ND2 ASN 173 A ASN 173 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? metalc ? metalc1 A N HIS 1 A HIS 1 1_555 C ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc2 A ND1 HIS 1 A HIS 1 1_555 C ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc3 A NE2 HIS 142 A HIS 142 1_555 C ZN ZN . A ZN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc4 A OE2 GLU 239 A GLU 239 1_555 C ZN ZN . A ZN 404 6_465 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? # _chem_comp.formula 'C2 H6 O2' _chem_comp.formula_weight 62.068 _chem_comp.id EDO _chem_comp.mon_nstd_flag . _chem_comp.name 1,2-ETHANEDIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'ETHYLENE GLYCOL' # 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 C1 O1 EDO sing 107 n n C1 C2 EDO sing 108 n n C1 H11 EDO sing 109 n n C1 H12 EDO sing 110 n n O1 HO1 EDO sing 111 n n C2 O2 EDO sing 112 n n C2 H21 EDO sing 113 n n C2 H22 EDO sing 114 n n O2 HO2 EDO sing 115 n n # _atom_sites.entry_id 4YN2 _atom_sites.fract_transf_matrix[1][1] 0.014667 _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] 0.014667 _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] 0.007809 _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 ZN A 1 404 404 ZN ZN . D 4 EDO A 1 405 405 EDO EDO . E 4 EDO A 1 406 406 EDO EDO . F 5 HOH A 1 501 551 HOH HOH . F 5 HOH A 2 502 517 HOH HOH . F 5 HOH A 3 503 610 HOH HOH . F 5 HOH A 4 504 560 HOH HOH . F 5 HOH A 5 505 515 HOH HOH . F 5 HOH A 6 506 516 HOH HOH . F 5 HOH A 7 507 525 HOH HOH . F 5 HOH A 8 508 564 HOH HOH . F 5 HOH A 9 509 600 HOH HOH . F 5 HOH A 10 510 662 HOH HOH . F 5 HOH A 11 511 535 HOH HOH . F 5 HOH A 12 512 509 HOH HOH . F 5 HOH A 13 513 543 HOH HOH . F 5 HOH A 14 514 538 HOH HOH . F 5 HOH A 15 515 532 HOH HOH . F 5 HOH A 16 516 527 HOH HOH . F 5 HOH A 17 517 544 HOH HOH . F 5 HOH A 18 518 545 HOH HOH . F 5 HOH A 19 519 582 HOH HOH . F 5 HOH A 20 520 565 HOH HOH . F 5 HOH A 21 521 511 HOH HOH . F 5 HOH A 22 522 519 HOH HOH . F 5 HOH A 23 523 539 HOH HOH . F 5 HOH A 24 524 557 HOH HOH . F 5 HOH A 25 525 619 HOH HOH . F 5 HOH A 26 526 531 HOH HOH . F 5 HOH A 27 527 635 HOH HOH . F 5 HOH A 28 528 660 HOH HOH . F 5 HOH A 29 529 568 HOH HOH . F 5 HOH A 30 530 521 HOH HOH . F 5 HOH A 31 531 670 HOH HOH . F 5 HOH A 32 532 522 HOH HOH . F 5 HOH A 33 533 657 HOH HOH . F 5 HOH A 34 534 528 HOH HOH . F 5 HOH A 35 535 573 HOH HOH . F 5 HOH A 36 536 597 HOH HOH . F 5 HOH A 37 537 542 HOH HOH . F 5 HOH A 38 538 570 HOH HOH . F 5 HOH A 39 539 566 HOH HOH . F 5 HOH A 40 540 629 HOH HOH . F 5 HOH A 41 541 590 HOH HOH . F 5 HOH A 42 542 614 HOH HOH . F 5 HOH A 43 543 529 HOH HOH . F 5 HOH A 44 544 547 HOH HOH . F 5 HOH A 45 545 623 HOH HOH . F 5 HOH A 46 546 644 HOH HOH . F 5 HOH A 47 547 589 HOH HOH . F 5 HOH A 48 548 599 HOH HOH . F 5 HOH A 49 549 631 HOH HOH . F 5 HOH A 50 550 667 HOH HOH . F 5 HOH A 51 551 567 HOH HOH . F 5 HOH A 52 552 533 HOH HOH . F 5 HOH A 53 553 507 HOH HOH . F 5 HOH A 54 554 558 HOH HOH . F 5 HOH A 55 555 503 HOH HOH . F 5 HOH A 56 556 584 HOH HOH . F 5 HOH A 57 557 669 HOH HOH . F 5 HOH A 58 558 574 HOH HOH . F 5 HOH A 59 559 504 HOH HOH . F 5 HOH A 60 560 575 HOH HOH . F 5 HOH A 61 561 553 HOH HOH . F 5 HOH A 62 562 627 HOH HOH . F 5 HOH A 63 563 550 HOH HOH . F 5 HOH A 64 564 634 HOH HOH . F 5 HOH A 65 565 611 HOH HOH . F 5 HOH A 66 566 609 HOH HOH . F 5 HOH A 67 567 588 HOH HOH . F 5 HOH A 68 568 621 HOH HOH . F 5 HOH A 69 569 526 HOH HOH . F 5 HOH A 70 570 624 HOH HOH . F 5 HOH A 71 571 579 HOH HOH . F 5 HOH A 72 572 664 HOH HOH . F 5 HOH A 73 573 571 HOH HOH . F 5 HOH A 74 574 586 HOH HOH . F 5 HOH A 75 575 628 HOH HOH . F 5 HOH A 76 576 612 HOH HOH . F 5 HOH A 77 577 534 HOH HOH . F 5 HOH A 78 578 661 HOH HOH . F 5 HOH A 79 579 646 HOH HOH . F 5 HOH A 80 580 663 HOH HOH . F 5 HOH A 81 581 523 HOH HOH . F 5 HOH A 82 582 563 HOH HOH . F 5 HOH A 83 583 648 HOH HOH . F 5 HOH A 84 584 585 HOH HOH . F 5 HOH A 85 585 626 HOH HOH . F 5 HOH A 86 586 603 HOH HOH . F 5 HOH A 87 587 653 HOH HOH . F 5 HOH A 88 588 540 HOH HOH . F 5 HOH A 89 589 616 HOH HOH . F 5 HOH A 90 590 505 HOH HOH . F 5 HOH A 91 591 541 HOH HOH . F 5 HOH A 92 592 654 HOH HOH . F 5 HOH A 93 593 569 HOH HOH . F 5 HOH A 94 594 572 HOH HOH . F 5 HOH A 95 595 594 HOH HOH . F 5 HOH A 96 596 546 HOH HOH . F 5 HOH A 97 597 602 HOH HOH . F 5 HOH A 98 598 548 HOH HOH . F 5 HOH A 99 599 501 HOH HOH . F 5 HOH A 100 600 613 HOH HOH . F 5 HOH A 101 601 632 HOH HOH . F 5 HOH A 102 602 559 HOH HOH . F 5 HOH A 103 603 668 HOH HOH . F 5 HOH A 104 604 502 HOH HOH . F 5 HOH A 105 605 562 HOH HOH . F 5 HOH A 106 606 518 HOH HOH . F 5 HOH A 107 607 625 HOH HOH . F 5 HOH A 108 608 580 HOH HOH . F 5 HOH A 109 609 536 HOH HOH . F 5 HOH A 110 610 556 HOH HOH . F 5 HOH A 111 611 596 HOH HOH . F 5 HOH A 112 612 617 HOH HOH . F 5 HOH A 113 613 512 HOH HOH . F 5 HOH A 114 614 593 HOH HOH . F 5 HOH A 115 615 639 HOH HOH . F 5 HOH A 116 616 578 HOH HOH . F 5 HOH A 117 617 642 HOH HOH . F 5 HOH A 118 618 641 HOH HOH . F 5 HOH A 119 619 655 HOH HOH . F 5 HOH A 120 620 656 HOH HOH . F 5 HOH A 121 621 549 HOH HOH . F 5 HOH A 122 622 658 HOH HOH . F 5 HOH A 123 623 598 HOH HOH . F 5 HOH A 124 624 513 HOH HOH . F 5 HOH A 125 625 620 HOH HOH . F 5 HOH A 126 626 659 HOH HOH . F 5 HOH A 127 627 638 HOH HOH . F 5 HOH A 128 628 606 HOH HOH . F 5 HOH A 129 629 530 HOH HOH . F 5 HOH A 130 630 577 HOH HOH . F 5 HOH A 131 631 555 HOH HOH . F 5 HOH A 132 632 645 HOH HOH . F 5 HOH A 133 633 665 HOH HOH . F 5 HOH A 134 634 561 HOH HOH . F 5 HOH A 135 635 601 HOH HOH . F 5 HOH A 136 636 581 HOH HOH . F 5 HOH A 137 637 650 HOH HOH . F 5 HOH A 138 638 524 HOH HOH . F 5 HOH A 139 639 647 HOH HOH . F 5 HOH A 140 640 651 HOH HOH . F 5 HOH A 141 641 554 HOH HOH . F 5 HOH A 142 642 583 HOH HOH . F 5 HOH A 143 643 508 HOH HOH . F 5 HOH A 144 644 506 HOH HOH . F 5 HOH A 145 645 640 HOH HOH . F 5 HOH A 146 646 537 HOH HOH . F 5 HOH A 147 647 618 HOH HOH . F 5 HOH A 148 648 666 HOH HOH . F 5 HOH A 149 649 520 HOH HOH . F 5 HOH A 150 650 630 HOH HOH . F 5 HOH A 151 651 576 HOH HOH . F 5 HOH A 152 652 633 HOH HOH . F 5 HOH A 153 653 592 HOH HOH . F 5 HOH A 154 654 652 HOH HOH . F 5 HOH A 155 655 649 HOH HOH . F 5 HOH A 156 656 510 HOH HOH . F 5 HOH A 157 657 643 HOH HOH . F 5 HOH A 158 658 636 HOH HOH . F 5 HOH A 159 659 587 HOH HOH . F 5 HOH A 160 660 552 HOH HOH . F 5 HOH A 161 661 637 HOH HOH . F 5 HOH A 162 662 591 HOH HOH . F 5 HOH A 163 663 608 HOH HOH . F 5 HOH A 164 664 605 HOH HOH . F 5 HOH A 165 665 604 HOH HOH . F 5 HOH A 166 666 622 HOH HOH . F 5 HOH A 167 667 607 HOH HOH . F 5 HOH A 168 668 615 HOH HOH . F 5 HOH A 169 669 595 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 C C1 EDO . . . D 4 31.207 50.415 59.706 1 22.19 ? C1 EDO 405 A 1 HETATM 2 O O1 EDO . . . D 4 31.239 49.707 58.462 1 23.27 ? O1 EDO 405 A 1 HETATM 3 C C2 EDO . . . D 4 30.649 51.849 59.515 1 22.34 ? C2 EDO 405 A 1 HETATM 4 O O2 EDO . . . D 4 29.624 51.869 58.518 1 18.29 ? O2 EDO 405 A 1 HETATM 5 H H11 EDO . . . D 4 32.176 50.437 60.202 1 21.32 ? H11 EDO 405 A 1 HETATM 6 H H12 EDO . . . D 4 30.543 49.823 60.335 1 22.19 ? H12 EDO 405 A 1 HETATM 7 H HO1 EDO . . . D 4 31.719 48.854 58.628 1 23.17 ? HO1 EDO 405 A 1 HETATM 8 H H21 EDO . . . D 4 31.417 52.533 59.159 1 22.23 ? H21 EDO 405 A 1 HETATM 9 H H22 EDO . . . D 4 30.309 52.263 60.462 1 22.78 ? H22 EDO 405 A 1 HETATM 10 H HO2 EDO . . . D 4 28.862 51.34 58.872 1 18.4 ? HO2 EDO 405 A 1 # _model_server_stats.io_time_ms 64 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 10 #