data_6DAZ # _model_server_result.job_id xgtP9HGkqAUy4y9WkVyMDA _model_server_result.datetime_utc '2024-11-28 23:06:25' _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 6daz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":403}' # _entry.id 6DAZ # _exptl.entry_id 6DAZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 204.227 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S)-N~6~-carbamimidoyl-3-hydroxy-L-lysine _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 109.6 _cell.angle_gamma 90 _cell.entry_id 6DAZ _cell.length_a 81.788 _cell.length_b 66.388 _cell.length_c 63.042 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DAZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 A NE2 HIS 146 A HIS 168 1_555 B FE FE2 . A FE2 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc2 A OE1 GLU 148 A GLU 170 1_555 B FE FE2 . A FE2 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc3 A NE2 HIS 294 A HIS 316 1_555 B FE FE2 . A FE2 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.251 ? metalc ? metalc4 B FE FE2 . A FE2 401 1_555 C O3 SIN . A SIN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc5 B FE FE2 . A FE2 401 1_555 C O4 SIN . A SIN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc6 B FE FE2 . A FE2 401 1_555 D O12 G3M . A G3M 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? # _chem_comp.formula 'C7 H16 N4 O3' _chem_comp.formula_weight 204.227 _chem_comp.id G3M _chem_comp.mon_nstd_flag n _chem_comp.name (3S)-N~6~-carbamimidoyl-3-hydroxy-L-lysine _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # 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 N11 C3 G3M sing 83 n n C3 C4 G3M sing 84 n n C3 C2 G3M sing 85 n n C4 O12 G3M sing 86 n n C4 C5 G3M sing 87 n n O1 C2 G3M doub 88 n n C2 O10 G3M sing 89 n n C6 C5 G3M sing 90 n n C6 C7 G3M sing 91 n n C7 N8 G3M sing 92 n n N8 C9 G3M sing 93 n n C9 N13 G3M doub 94 n n C9 N14 G3M sing 95 n n C3 H1 G3M sing 96 n n C4 H2 G3M sing 97 n n C7 H3 G3M sing 98 n n C7 H4 G3M sing 99 n n C6 H5 G3M sing 100 n n C6 H6 G3M sing 101 n n C5 H7 G3M sing 102 n n C5 H8 G3M sing 103 n n N8 H9 G3M sing 104 n n O10 H10 G3M sing 105 n n N11 H11 G3M sing 106 n n N11 H12 G3M sing 107 n n O12 H14 G3M sing 108 n n N13 H15 G3M sing 109 n n N14 H16 G3M sing 110 n n N14 H17 G3M sing 111 n n # _atom_sites.entry_id 6DAZ _atom_sites.fract_transf_matrix[1][1] 0.012227 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004353 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.015063 _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] 0.016838 _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 FE2 A 1 401 1 FE2 FE2 . C 3 SIN A 1 402 1 SIN SIN . D 4 G3M A 1 403 1 G3M OHH . E 5 HOH A 1 501 142 HOH HOH . E 5 HOH A 2 502 141 HOH HOH . E 5 HOH A 3 503 144 HOH HOH . E 5 HOH A 4 504 130 HOH HOH . E 5 HOH A 5 505 103 HOH HOH . E 5 HOH A 6 506 134 HOH HOH . E 5 HOH A 7 507 71 HOH HOH . E 5 HOH A 8 508 146 HOH HOH . E 5 HOH A 9 509 48 HOH HOH . E 5 HOH A 10 510 112 HOH HOH . E 5 HOH A 11 511 59 HOH HOH . E 5 HOH A 12 512 111 HOH HOH . E 5 HOH A 13 513 57 HOH HOH . E 5 HOH A 14 514 145 HOH HOH . E 5 HOH A 15 515 46 HOH HOH . E 5 HOH A 16 516 27 HOH HOH . E 5 HOH A 17 517 16 HOH HOH . E 5 HOH A 18 518 44 HOH HOH . E 5 HOH A 19 519 10 HOH HOH . E 5 HOH A 20 520 21 HOH HOH . E 5 HOH A 21 521 127 HOH HOH . E 5 HOH A 22 522 118 HOH HOH . E 5 HOH A 23 523 79 HOH HOH . E 5 HOH A 24 524 99 HOH HOH . E 5 HOH A 25 525 125 HOH HOH . E 5 HOH A 26 526 24 HOH HOH . E 5 HOH A 27 527 50 HOH HOH . E 5 HOH A 28 528 4 HOH HOH . E 5 HOH A 29 529 100 HOH HOH . E 5 HOH A 30 530 94 HOH HOH . E 5 HOH A 31 531 18 HOH HOH . E 5 HOH A 32 532 14 HOH HOH . E 5 HOH A 33 533 140 HOH HOH . E 5 HOH A 34 534 7 HOH HOH . E 5 HOH A 35 535 23 HOH HOH . E 5 HOH A 36 536 63 HOH HOH . E 5 HOH A 37 537 90 HOH HOH . E 5 HOH A 38 538 38 HOH HOH . E 5 HOH A 39 539 95 HOH HOH . E 5 HOH A 40 540 2 HOH HOH . E 5 HOH A 41 541 6 HOH HOH . E 5 HOH A 42 542 19 HOH HOH . E 5 HOH A 43 543 76 HOH HOH . E 5 HOH A 44 544 56 HOH HOH . E 5 HOH A 45 545 52 HOH HOH . E 5 HOH A 46 546 29 HOH HOH . E 5 HOH A 47 547 1 HOH HOH . E 5 HOH A 48 548 36 HOH HOH . E 5 HOH A 49 549 83 HOH HOH . E 5 HOH A 50 550 80 HOH HOH . E 5 HOH A 51 551 47 HOH HOH . E 5 HOH A 52 552 3 HOH HOH . E 5 HOH A 53 553 75 HOH HOH . E 5 HOH A 54 554 20 HOH HOH . E 5 HOH A 55 555 39 HOH HOH . E 5 HOH A 56 556 42 HOH HOH . E 5 HOH A 57 557 26 HOH HOH . E 5 HOH A 58 558 5 HOH HOH . E 5 HOH A 59 559 87 HOH HOH . E 5 HOH A 60 560 28 HOH HOH . E 5 HOH A 61 561 113 HOH HOH . E 5 HOH A 62 562 49 HOH HOH . E 5 HOH A 63 563 120 HOH HOH . E 5 HOH A 64 564 143 HOH HOH . E 5 HOH A 65 565 13 HOH HOH . E 5 HOH A 66 566 70 HOH HOH . E 5 HOH A 67 567 121 HOH HOH . E 5 HOH A 68 568 8 HOH HOH . E 5 HOH A 69 569 54 HOH HOH . E 5 HOH A 70 570 135 HOH HOH . E 5 HOH A 71 571 116 HOH HOH . E 5 HOH A 72 572 25 HOH HOH . E 5 HOH A 73 573 9 HOH HOH . E 5 HOH A 74 574 102 HOH HOH . E 5 HOH A 75 575 89 HOH HOH . E 5 HOH A 76 576 65 HOH HOH . E 5 HOH A 77 577 30 HOH HOH . E 5 HOH A 78 578 84 HOH HOH . E 5 HOH A 79 579 123 HOH HOH . E 5 HOH A 80 580 11 HOH HOH . E 5 HOH A 81 581 131 HOH HOH . E 5 HOH A 82 582 61 HOH HOH . E 5 HOH A 83 583 22 HOH HOH . E 5 HOH A 84 584 119 HOH HOH . E 5 HOH A 85 585 114 HOH HOH . E 5 HOH A 86 586 17 HOH HOH . E 5 HOH A 87 587 58 HOH HOH . E 5 HOH A 88 588 136 HOH HOH . E 5 HOH A 89 589 35 HOH HOH . E 5 HOH A 90 590 69 HOH HOH . E 5 HOH A 91 591 137 HOH HOH . E 5 HOH A 92 592 12 HOH HOH . E 5 HOH A 93 593 15 HOH HOH . E 5 HOH A 94 594 104 HOH HOH . E 5 HOH A 95 595 72 HOH HOH . E 5 HOH A 96 596 86 HOH HOH . E 5 HOH A 97 597 115 HOH HOH . E 5 HOH A 98 598 91 HOH HOH . E 5 HOH A 99 599 31 HOH HOH . E 5 HOH A 100 600 85 HOH HOH . E 5 HOH A 101 601 55 HOH HOH . E 5 HOH A 102 602 64 HOH HOH . E 5 HOH A 103 603 88 HOH HOH . E 5 HOH A 104 604 41 HOH HOH . E 5 HOH A 105 605 68 HOH HOH . E 5 HOH A 106 606 37 HOH HOH . E 5 HOH A 107 607 66 HOH HOH . E 5 HOH A 108 608 40 HOH HOH . E 5 HOH A 109 609 73 HOH HOH . E 5 HOH A 110 610 96 HOH HOH . E 5 HOH A 111 611 126 HOH HOH . E 5 HOH A 112 612 51 HOH HOH . E 5 HOH A 113 613 132 HOH HOH . E 5 HOH A 114 614 129 HOH HOH . E 5 HOH A 115 615 107 HOH HOH . E 5 HOH A 116 616 122 HOH HOH . E 5 HOH A 117 617 147 HOH HOH . E 5 HOH A 118 618 74 HOH HOH . E 5 HOH A 119 619 67 HOH HOH . E 5 HOH A 120 620 53 HOH HOH . E 5 HOH A 121 621 110 HOH HOH . E 5 HOH A 122 622 108 HOH HOH . E 5 HOH A 123 623 93 HOH HOH . E 5 HOH A 124 624 32 HOH HOH . E 5 HOH A 125 625 33 HOH HOH . E 5 HOH A 126 626 60 HOH HOH . E 5 HOH A 127 627 77 HOH HOH . E 5 HOH A 128 628 82 HOH HOH . E 5 HOH A 129 629 105 HOH HOH . E 5 HOH A 130 630 149 HOH HOH . E 5 HOH A 131 631 148 HOH HOH . E 5 HOH A 132 632 106 HOH HOH . E 5 HOH A 133 633 101 HOH HOH . E 5 HOH A 134 634 138 HOH HOH . E 5 HOH A 135 635 81 HOH HOH . E 5 HOH A 136 636 78 HOH HOH . E 5 HOH A 137 637 109 HOH HOH . E 5 HOH A 138 638 139 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 O O1 G3M . . . D 4 12.555 4.603 19.442 1 19.86 ? O1 G3M 403 A 1 HETATM 2 C C9 G3M . . . D 4 8.342 11.277 22.455 1 22.12 ? C9 G3M 403 A 1 HETATM 3 C C2 G3M . . . D 4 12.389 5.824 19.643 1 19.96 ? C2 G3M 403 A 1 HETATM 4 C C3 G3M . . . D 4 11.595 6.627 18.646 1 19.88 ? C3 G3M 403 A 1 HETATM 5 C C4 G3M . . . D 4 10.12 6.785 19.046 1 20.36 ? C4 G3M 403 A 1 HETATM 6 C C7 G3M . . . D 4 9.915 10.039 21.088 1 22.1 ? C7 G3M 403 A 1 HETATM 7 C C6 G3M . . . D 4 9.89 9.149 19.858 1 21.68 ? C6 G3M 403 A 1 HETATM 8 C C5 G3M . . . D 4 9.931 7.681 20.266 1 21.15 ? C5 G3M 403 A 1 HETATM 9 N N8 G3M . . . D 4 8.713 10.823 21.258 1 22.23 ? N8 G3M 403 A 1 HETATM 10 O O10 G3M . . . D 4 12.881 6.407 20.632 1 19.69 ? O10 G3M 403 A 1 HETATM 11 N N11 G3M . . . D 4 11.682 6.013 17.295 1 19.71 ? N11 G3M 403 A 1 HETATM 12 O O12 G3M . . . D 4 9.517 5.511 19.316 1 20.15 ? O12 G3M 403 A 1 HETATM 13 N N13 G3M . . . D 4 7.133 12.008 22.574 1 22.23 ? N13 G3M 403 A 1 HETATM 14 N N14 G3M . . . D 4 9.049 11.056 23.48 1 21.9 ? N14 G3M 403 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #