data_5SXH # _model_server_result.job_id 8gZYoBPFnFx0EUIHCGC-SQ _model_server_result.datetime_utc '2024-11-26 16:13:49' _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 5sxh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 5SXH # _exptl.entry_id 5SXH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 62.068 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1,2-ETHANEDIOL _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 101.96 _cell.angle_gamma 90 _cell.entry_id 5SXH _cell.length_a 44.39 _cell.length_b 50.99 _cell.length_c 77.41 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SXH _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # 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 monomeric 1 author_and_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,H,I 1 1 A,B,C,D,E,F,G,H,I 2 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 ? 3 D N N ? 3 E N N ? 3 G 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 ND1 HIS 60 A HIS 253 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc2 A SG CYS 91 A CYS 284 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc3 A SG CYS 96 A CYS 289 1_555 C ZN ZN . A ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc4 C ZN ZN . A ZN 401 1_555 H O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc5 B ND1 HIS 60 B HIS 253 1_555 F ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc6 B SG CYS 91 B CYS 284 1_555 F ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc7 B SG CYS 96 B CYS 289 1_555 F ZN ZN . B ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc8 F ZN ZN . B ZN 401 1_555 I O HOH . B HOH 570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? # _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 83 n n C1 C2 EDO sing 84 n n C1 H11 EDO sing 85 n n C1 H12 EDO sing 86 n n O1 HO1 EDO sing 87 n n C2 O2 EDO sing 88 n n C2 H21 EDO sing 89 n n C2 H22 EDO sing 90 n n O2 HO2 EDO sing 91 n n # _atom_sites.entry_id 5SXH _atom_sites.fract_transf_matrix[1][1] 0.022528 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004772 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019612 _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] 0.013205 _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 2 ZN A 1 401 401 ZN ZN . D 3 EDO A 1 402 402 EDO EDO . E 3 EDO A 1 403 403 EDO EDO . F 2 ZN B 1 401 401 ZN ZN . G 3 EDO B 1 402 402 EDO EDO . H 4 HOH A 1 501 501 HOH HOH . H 4 HOH A 2 502 503 HOH HOH . H 4 HOH A 3 503 504 HOH HOH . H 4 HOH A 4 504 507 HOH HOH . H 4 HOH A 5 505 505 HOH HOH . H 4 HOH A 6 506 502 HOH HOH . H 4 HOH A 7 507 506 HOH HOH . H 4 HOH A 8 508 511 HOH HOH . H 4 HOH A 9 509 513 HOH HOH . H 4 HOH A 10 510 521 HOH HOH . H 4 HOH A 11 511 526 HOH HOH . H 4 HOH A 12 512 509 HOH HOH . H 4 HOH A 13 513 545 HOH HOH . H 4 HOH A 14 514 523 HOH HOH . H 4 HOH A 15 515 514 HOH HOH . H 4 HOH A 16 516 512 HOH HOH . H 4 HOH A 17 517 508 HOH HOH . H 4 HOH A 18 518 515 HOH HOH . H 4 HOH A 19 519 525 HOH HOH . H 4 HOH A 20 520 529 HOH HOH . H 4 HOH A 21 521 518 HOH HOH . H 4 HOH A 22 522 510 HOH HOH . H 4 HOH A 23 523 547 HOH HOH . H 4 HOH A 24 524 519 HOH HOH . H 4 HOH A 25 525 520 HOH HOH . H 4 HOH A 26 526 528 HOH HOH . H 4 HOH A 27 527 516 HOH HOH . H 4 HOH A 28 528 527 HOH HOH . H 4 HOH A 29 529 538 HOH HOH . H 4 HOH A 30 530 532 HOH HOH . H 4 HOH A 31 531 531 HOH HOH . H 4 HOH A 32 532 517 HOH HOH . H 4 HOH A 33 533 524 HOH HOH . H 4 HOH A 34 534 533 HOH HOH . H 4 HOH A 35 535 539 HOH HOH . H 4 HOH A 36 536 550 HOH HOH . H 4 HOH A 37 537 535 HOH HOH . H 4 HOH A 38 538 522 HOH HOH . H 4 HOH A 39 539 534 HOH HOH . H 4 HOH A 40 540 537 HOH HOH . H 4 HOH A 41 541 546 HOH HOH . H 4 HOH A 42 542 530 HOH HOH . H 4 HOH A 43 543 536 HOH HOH . H 4 HOH A 44 544 548 HOH HOH . H 4 HOH A 45 545 544 HOH HOH . H 4 HOH A 46 546 551 HOH HOH . H 4 HOH A 47 547 558 HOH HOH . H 4 HOH A 48 548 556 HOH HOH . H 4 HOH A 49 549 542 HOH HOH . H 4 HOH A 50 550 540 HOH HOH . H 4 HOH A 51 551 549 HOH HOH . H 4 HOH A 52 552 555 HOH HOH . H 4 HOH A 53 553 574 HOH HOH . H 4 HOH A 54 554 554 HOH HOH . H 4 HOH A 55 555 553 HOH HOH . H 4 HOH A 56 556 559 HOH HOH . H 4 HOH A 57 557 588 HOH HOH . H 4 HOH A 58 558 566 HOH HOH . H 4 HOH A 59 559 563 HOH HOH . H 4 HOH A 60 560 557 HOH HOH . H 4 HOH A 61 561 586 HOH HOH . H 4 HOH A 62 562 564 HOH HOH . H 4 HOH A 63 563 543 HOH HOH . H 4 HOH A 64 564 560 HOH HOH . H 4 HOH A 65 565 541 HOH HOH . H 4 HOH A 66 566 565 HOH HOH . H 4 HOH A 67 567 561 HOH HOH . H 4 HOH A 68 568 571 HOH HOH . H 4 HOH A 69 569 569 HOH HOH . H 4 HOH A 70 570 552 HOH HOH . H 4 HOH A 71 571 579 HOH HOH . H 4 HOH A 72 572 578 HOH HOH . H 4 HOH A 73 573 572 HOH HOH . H 4 HOH A 74 574 567 HOH HOH . H 4 HOH A 75 575 570 HOH HOH . H 4 HOH A 76 576 595 HOH HOH . H 4 HOH A 77 577 568 HOH HOH . H 4 HOH A 78 578 581 HOH HOH . H 4 HOH A 79 579 582 HOH HOH . H 4 HOH A 80 580 575 HOH HOH . H 4 HOH A 81 581 562 HOH HOH . H 4 HOH A 82 582 573 HOH HOH . H 4 HOH A 83 583 594 HOH HOH . H 4 HOH A 84 584 577 HOH HOH . H 4 HOH A 85 585 583 HOH HOH . H 4 HOH A 86 586 576 HOH HOH . H 4 HOH A 87 587 587 HOH HOH . H 4 HOH A 88 588 585 HOH HOH . H 4 HOH A 89 589 580 HOH HOH . H 4 HOH A 90 590 584 HOH HOH . H 4 HOH A 91 591 591 HOH HOH . H 4 HOH A 92 592 592 HOH HOH . H 4 HOH A 93 593 593 HOH HOH . H 4 HOH A 94 594 596 HOH HOH . H 4 HOH A 95 595 589 HOH HOH . H 4 HOH A 96 596 590 HOH HOH . H 4 HOH A 97 597 597 HOH HOH . H 4 HOH A 98 598 601 HOH HOH . H 4 HOH A 99 599 598 HOH HOH . H 4 HOH A 100 600 599 HOH HOH . H 4 HOH A 101 601 605 HOH HOH . H 4 HOH A 102 602 600 HOH HOH . H 4 HOH A 103 603 602 HOH HOH . H 4 HOH A 104 604 606 HOH HOH . H 4 HOH A 105 605 604 HOH HOH . H 4 HOH A 106 606 608 HOH HOH . H 4 HOH A 107 607 607 HOH HOH . H 4 HOH A 108 608 592 HOH HOH . H 4 HOH A 109 609 609 HOH HOH . H 4 HOH A 110 610 610 HOH HOH . H 4 HOH A 111 611 612 HOH HOH . H 4 HOH A 112 612 611 HOH HOH . I 4 HOH B 1 501 504 HOH HOH . I 4 HOH B 2 502 502 HOH HOH . I 4 HOH B 3 503 501 HOH HOH . I 4 HOH B 4 504 505 HOH HOH . I 4 HOH B 5 505 506 HOH HOH . I 4 HOH B 6 506 503 HOH HOH . I 4 HOH B 7 507 508 HOH HOH . I 4 HOH B 8 508 511 HOH HOH . I 4 HOH B 9 509 507 HOH HOH . I 4 HOH B 10 510 510 HOH HOH . I 4 HOH B 11 511 513 HOH HOH . I 4 HOH B 12 512 512 HOH HOH . I 4 HOH B 13 513 515 HOH HOH . I 4 HOH B 14 514 517 HOH HOH . I 4 HOH B 15 515 519 HOH HOH . I 4 HOH B 16 516 509 HOH HOH . I 4 HOH B 17 517 518 HOH HOH . I 4 HOH B 18 518 516 HOH HOH . I 4 HOH B 19 519 581 HOH HOH . I 4 HOH B 20 520 521 HOH HOH . I 4 HOH B 21 521 544 HOH HOH . I 4 HOH B 22 522 523 HOH HOH . I 4 HOH B 23 523 531 HOH HOH . I 4 HOH B 24 524 525 HOH HOH . I 4 HOH B 25 525 524 HOH HOH . I 4 HOH B 26 526 520 HOH HOH . I 4 HOH B 27 527 537 HOH HOH . I 4 HOH B 28 528 529 HOH HOH . I 4 HOH B 29 529 526 HOH HOH . I 4 HOH B 30 530 533 HOH HOH . I 4 HOH B 31 531 540 HOH HOH . I 4 HOH B 32 532 539 HOH HOH . I 4 HOH B 33 533 528 HOH HOH . I 4 HOH B 34 534 541 HOH HOH . I 4 HOH B 35 535 535 HOH HOH . I 4 HOH B 36 536 538 HOH HOH . I 4 HOH B 37 537 522 HOH HOH . I 4 HOH B 38 538 514 HOH HOH . I 4 HOH B 39 539 546 HOH HOH . I 4 HOH B 40 540 530 HOH HOH . I 4 HOH B 41 541 547 HOH HOH . I 4 HOH B 42 542 545 HOH HOH . I 4 HOH B 43 543 543 HOH HOH . I 4 HOH B 44 544 534 HOH HOH . I 4 HOH B 45 545 527 HOH HOH . I 4 HOH B 46 546 548 HOH HOH . I 4 HOH B 47 547 554 HOH HOH . I 4 HOH B 48 548 569 HOH HOH . I 4 HOH B 49 549 551 HOH HOH . I 4 HOH B 50 550 532 HOH HOH . I 4 HOH B 51 551 555 HOH HOH . I 4 HOH B 52 552 550 HOH HOH . I 4 HOH B 53 553 562 HOH HOH . I 4 HOH B 54 554 542 HOH HOH . I 4 HOH B 55 555 564 HOH HOH . I 4 HOH B 56 556 556 HOH HOH . I 4 HOH B 57 557 565 HOH HOH . I 4 HOH B 58 558 553 HOH HOH . I 4 HOH B 59 559 563 HOH HOH . I 4 HOH B 60 560 536 HOH HOH . I 4 HOH B 61 561 567 HOH HOH . I 4 HOH B 62 562 552 HOH HOH . I 4 HOH B 63 563 557 HOH HOH . I 4 HOH B 64 564 566 HOH HOH . I 4 HOH B 65 565 560 HOH HOH . I 4 HOH B 66 566 570 HOH HOH . I 4 HOH B 67 567 561 HOH HOH . I 4 HOH B 68 568 574 HOH HOH . I 4 HOH B 69 569 549 HOH HOH . I 4 HOH B 70 570 558 HOH HOH . I 4 HOH B 71 571 576 HOH HOH . I 4 HOH B 72 572 568 HOH HOH . I 4 HOH B 73 573 573 HOH HOH . I 4 HOH B 74 574 559 HOH HOH . I 4 HOH B 75 575 572 HOH HOH . I 4 HOH B 76 576 580 HOH HOH . I 4 HOH B 77 577 577 HOH HOH . I 4 HOH B 78 578 571 HOH HOH . I 4 HOH B 79 579 575 HOH HOH . I 4 HOH B 80 580 579 HOH HOH . I 4 HOH B 81 581 578 HOH HOH . I 4 HOH B 82 582 583 HOH HOH . I 4 HOH B 83 583 590 HOH HOH . I 4 HOH B 84 584 584 HOH HOH . I 4 HOH B 85 585 582 HOH HOH . I 4 HOH B 86 586 585 HOH HOH . I 4 HOH B 87 587 587 HOH HOH . I 4 HOH B 88 588 603 HOH HOH . I 4 HOH B 89 589 589 HOH HOH . I 4 HOH B 90 590 586 HOH HOH . I 4 HOH B 91 591 588 HOH HOH . I 4 HOH B 92 592 591 HOH HOH . I 4 HOH B 93 593 593 HOH HOH . I 4 HOH B 94 594 594 HOH HOH . I 4 HOH B 95 595 595 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 3 13.75 24.186 -15.226 1 50.14 ? C1 EDO 402 A 1 HETATM 2 O O1 EDO . . . D 3 14.794 24.546 -14.314 1 55.9 ? O1 EDO 402 A 1 HETATM 3 C C2 EDO . . . D 3 12.464 23.902 -14.457 1 45.67 ? C2 EDO 402 A 1 HETATM 4 O O2 EDO . . . D 3 11.389 23.71 -15.384 1 53.41 ? O2 EDO 402 A 1 HETATM 5 H H11 EDO . . . D 3 13.584 24.999 -15.936 1 60.17 ? H11 EDO 402 A 1 HETATM 6 H H12 EDO . . . D 3 14.045 23.3 -15.793 1 60.17 ? H12 EDO 402 A 1 HETATM 7 H HO1 EDO . . . D 3 15.63 24.619 -14.795 1 67.08 ? HO1 EDO 402 A 1 HETATM 8 H H21 EDO . . . D 3 12.236 24.737 -13.792 1 54.81 ? H21 EDO 402 A 1 HETATM 9 H H22 EDO . . . D 3 12.589 23.008 -13.842 1 54.81 ? H22 EDO 402 A 1 HETATM 10 H HO2 EDO . . . D 3 10.575 23.519 -14.898 1 64.09 ? HO2 EDO 402 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 35 _model_server_stats.query_time_ms 518 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 10 #