data_1TUV # _model_server_result.job_id bFoGDerX1Bp6eTkcaVCQvg _model_server_result.datetime_utc '2025-02-05 04:51:54' _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 1tuv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":4558}' # _entry.id 1TUV # _exptl.entry_id 1TUV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 172.18 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description MENADIONE _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 90 _cell.angle_gamma 90 _cell.entry_id 1TUV _cell.length_a 102.562 _cell.length_b 102.562 _cell.length_c 102.562 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TUV _symmetry.cell_setting ? _symmetry.Int_Tables_number 213 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 3 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 ? dimeric 2 author_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PQS monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1,2 A,B,C 2 1,3 A,B,C 3 1 # 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' 7_454 -z-1/2,-x,y-1/2 0 0 -1 -1 0 0 0 1 0 -51.281 0 -51.281 3 'crystal symmetry operation' 22_554 z+1/4,-y+1/4,x-1/4 0 0 1 0 -1 0 1 0 0 25.6405 25.6405 -25.6405 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C11 H8 O2' _chem_comp.formula_weight 172.18 _chem_comp.id VK3 _chem_comp.mon_nstd_flag . _chem_comp.name MENADIONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN K3;2-METHYL-1,4-NAPHTHALENEDIONE' # 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 C1K O1K VK3 doub 376 n n C1K C2K VK3 sing 377 n n C1K C10 VK3 sing 378 n n C2K C3K VK3 doub 379 n n C2K H2K1 VK3 sing 380 n n C3K C4K VK3 sing 381 n n C3K C11 VK3 sing 382 n n C4K O4K VK3 doub 383 n n C4K C5K VK3 sing 384 n n C5K C6K VK3 doub 385 n y C5K C10 VK3 sing 386 n y C6K C7K VK3 sing 387 n y C6K H6K1 VK3 sing 388 n n C7K C8K VK3 doub 389 n y C7K H7K1 VK3 sing 390 n n C8K C9K VK3 sing 391 n y C8K H8K1 VK3 sing 392 n n C9K C10 VK3 doub 393 n y C9K H9K1 VK3 sing 394 n n C11 H111 VK3 sing 395 n n C11 H112 VK3 sing 396 n n C11 H113 VK3 sing 397 n n # _atom_sites.entry_id 1TUV _atom_sites.fract_transf_matrix[1][1] 0.00975 _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] 0.00975 _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] 0.00975 _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 VK3 A 1 4558 4558 VK3 VK3 . C 3 HOH A 1 4559 1 HOH HOH . C 3 HOH A 2 4560 2 HOH HOH . C 3 HOH A 3 4561 3 HOH HOH . C 3 HOH A 4 4562 4 HOH HOH . C 3 HOH A 5 4563 5 HOH HOH . C 3 HOH A 6 4564 6 HOH HOH . C 3 HOH A 7 4565 7 HOH HOH . C 3 HOH A 8 4566 8 HOH HOH . C 3 HOH A 9 4567 9 HOH HOH . C 3 HOH A 10 4568 10 HOH HOH . C 3 HOH A 11 4569 12 HOH HOH . C 3 HOH A 12 4570 13 HOH HOH . C 3 HOH A 13 4571 14 HOH HOH . C 3 HOH A 14 4572 15 HOH HOH . C 3 HOH A 15 4573 16 HOH HOH . C 3 HOH A 16 4574 17 HOH HOH . C 3 HOH A 17 4575 18 HOH HOH . C 3 HOH A 18 4576 19 HOH HOH . C 3 HOH A 19 4577 20 HOH HOH . C 3 HOH A 20 4578 21 HOH HOH . C 3 HOH A 21 4579 22 HOH HOH . C 3 HOH A 22 4580 23 HOH HOH . C 3 HOH A 23 4581 24 HOH HOH . C 3 HOH A 24 4582 25 HOH HOH . C 3 HOH A 25 4583 26 HOH HOH . C 3 HOH A 26 4584 27 HOH HOH . C 3 HOH A 27 4585 28 HOH HOH . C 3 HOH A 28 4586 29 HOH HOH . C 3 HOH A 29 4587 30 HOH HOH . C 3 HOH A 30 4588 31 HOH HOH . C 3 HOH A 31 4589 32 HOH HOH . C 3 HOH A 32 4590 33 HOH HOH . C 3 HOH A 33 4591 34 HOH HOH . C 3 HOH A 34 4592 35 HOH HOH . C 3 HOH A 35 4593 36 HOH HOH . C 3 HOH A 36 4594 37 HOH HOH . C 3 HOH A 37 4595 38 HOH HOH . C 3 HOH A 38 4596 39 HOH HOH . C 3 HOH A 39 4597 40 HOH HOH . C 3 HOH A 40 4598 41 HOH HOH . C 3 HOH A 41 4599 42 HOH HOH . C 3 HOH A 42 4600 43 HOH HOH . C 3 HOH A 43 4601 44 HOH HOH . C 3 HOH A 44 4602 45 HOH HOH . C 3 HOH A 45 4603 46 HOH HOH . C 3 HOH A 46 4604 47 HOH HOH . C 3 HOH A 47 4605 48 HOH HOH . C 3 HOH A 48 4606 49 HOH HOH . C 3 HOH A 49 4607 50 HOH HOH . C 3 HOH A 50 4608 51 HOH HOH . C 3 HOH A 51 4609 52 HOH HOH . C 3 HOH A 52 4610 53 HOH HOH . C 3 HOH A 53 4611 54 HOH HOH . C 3 HOH A 54 4612 55 HOH HOH . C 3 HOH A 55 4613 56 HOH HOH . C 3 HOH A 56 4614 57 HOH HOH . C 3 HOH A 57 4615 58 HOH HOH . C 3 HOH A 58 4616 59 HOH HOH . C 3 HOH A 59 4617 60 HOH HOH . C 3 HOH A 60 4618 61 HOH HOH . C 3 HOH A 61 4619 62 HOH HOH . C 3 HOH A 62 4620 63 HOH HOH . C 3 HOH A 63 4621 64 HOH HOH . C 3 HOH A 64 4622 65 HOH HOH . C 3 HOH A 65 4623 66 HOH HOH . C 3 HOH A 66 4624 67 HOH HOH . C 3 HOH A 67 4625 68 HOH HOH . C 3 HOH A 68 4626 69 HOH HOH . C 3 HOH A 69 4627 70 HOH HOH . C 3 HOH A 70 4628 71 HOH HOH . C 3 HOH A 71 4629 72 HOH HOH . C 3 HOH A 72 4630 73 HOH HOH . C 3 HOH A 73 4631 74 HOH HOH . C 3 HOH A 74 4632 75 HOH HOH . C 3 HOH A 75 4633 76 HOH HOH . C 3 HOH A 76 4634 77 HOH HOH . C 3 HOH A 77 4635 78 HOH HOH . C 3 HOH A 78 4636 79 HOH HOH . C 3 HOH A 79 4637 80 HOH HOH . C 3 HOH A 80 4638 81 HOH HOH . C 3 HOH A 81 4639 82 HOH HOH . C 3 HOH A 82 4640 83 HOH HOH . C 3 HOH A 83 4641 84 HOH HOH . C 3 HOH A 84 4642 85 HOH HOH . C 3 HOH A 85 4643 86 HOH HOH . C 3 HOH A 86 4644 87 HOH HOH . C 3 HOH A 87 4645 88 HOH HOH . C 3 HOH A 88 4646 89 HOH HOH . C 3 HOH A 89 4647 90 HOH HOH . C 3 HOH A 90 4648 91 HOH HOH . C 3 HOH A 91 4649 92 HOH HOH . C 3 HOH A 92 4650 93 HOH HOH . C 3 HOH A 93 4651 94 HOH HOH . C 3 HOH A 94 4652 95 HOH HOH . C 3 HOH A 95 4653 96 HOH HOH . C 3 HOH A 96 4654 97 HOH HOH . C 3 HOH A 97 4655 98 HOH HOH . C 3 HOH A 98 4656 99 HOH HOH . C 3 HOH A 99 4657 100 HOH HOH . C 3 HOH A 100 4658 101 HOH HOH . C 3 HOH A 101 4659 103 HOH HOH . C 3 HOH A 102 4660 104 HOH HOH . C 3 HOH A 103 4661 105 HOH HOH . C 3 HOH A 104 4662 106 HOH HOH . C 3 HOH A 105 4663 107 HOH HOH . C 3 HOH A 106 4664 108 HOH HOH . C 3 HOH A 107 4665 109 HOH HOH . C 3 HOH A 108 4666 110 HOH HOH . C 3 HOH A 109 4667 111 HOH HOH . C 3 HOH A 110 4668 112 HOH HOH . C 3 HOH A 111 4669 113 HOH HOH . C 3 HOH A 112 4670 114 HOH HOH . C 3 HOH A 113 4671 115 HOH HOH . C 3 HOH A 114 4672 116 HOH HOH . C 3 HOH A 115 4673 117 HOH HOH . C 3 HOH A 116 4674 118 HOH HOH . C 3 HOH A 117 4675 119 HOH HOH . C 3 HOH A 118 4676 120 HOH HOH . C 3 HOH A 119 4677 121 HOH HOH . C 3 HOH A 120 4678 122 HOH HOH . C 3 HOH A 121 4679 123 HOH HOH . C 3 HOH A 122 4680 124 HOH HOH . C 3 HOH A 123 4681 125 HOH HOH . C 3 HOH A 124 4682 126 HOH HOH . C 3 HOH A 125 4683 127 HOH HOH . C 3 HOH A 126 4684 128 HOH HOH . C 3 HOH A 127 4685 129 HOH HOH . C 3 HOH A 128 4686 130 HOH HOH . C 3 HOH A 129 4687 131 HOH HOH . C 3 HOH A 130 4688 132 HOH HOH . C 3 HOH A 131 4689 133 HOH HOH . C 3 HOH A 132 4690 134 HOH HOH . C 3 HOH A 133 4691 135 HOH HOH . C 3 HOH A 134 4692 136 HOH HOH . C 3 HOH A 135 4693 137 HOH HOH . C 3 HOH A 136 4694 138 HOH HOH . C 3 HOH A 137 4695 139 HOH HOH . C 3 HOH A 138 4696 140 HOH HOH . C 3 HOH A 139 4697 141 HOH HOH . C 3 HOH A 140 4698 142 HOH HOH . C 3 HOH A 141 4699 143 HOH HOH . C 3 HOH A 142 4700 144 HOH HOH . C 3 HOH A 143 4701 145 HOH HOH . C 3 HOH A 144 4702 146 HOH HOH . C 3 HOH A 145 4703 148 HOH HOH . C 3 HOH A 146 4704 149 HOH HOH . C 3 HOH A 147 4705 150 HOH HOH . C 3 HOH A 148 4706 151 HOH HOH . C 3 HOH A 149 4707 152 HOH HOH . C 3 HOH A 150 4708 153 HOH HOH . C 3 HOH A 151 4709 154 HOH HOH . C 3 HOH A 152 4710 155 HOH HOH . C 3 HOH A 153 4711 157 HOH HOH . C 3 HOH A 154 4712 158 HOH HOH . C 3 HOH A 155 4713 159 HOH HOH . C 3 HOH A 156 4714 160 HOH HOH . C 3 HOH A 157 4715 161 HOH HOH . C 3 HOH A 158 4716 162 HOH HOH . C 3 HOH A 159 4717 163 HOH HOH . C 3 HOH A 160 4718 164 HOH HOH . C 3 HOH A 161 4719 165 HOH HOH . C 3 HOH A 162 4720 166 HOH HOH . C 3 HOH A 163 4721 167 HOH HOH . C 3 HOH A 164 4722 168 HOH HOH . C 3 HOH A 165 4723 170 HOH HOH . C 3 HOH A 166 4724 171 HOH HOH . C 3 HOH A 167 4725 172 HOH HOH . C 3 HOH A 168 4726 173 HOH HOH . C 3 HOH A 169 4727 174 HOH HOH . C 3 HOH A 170 4728 175 HOH HOH . C 3 HOH A 171 4729 176 HOH HOH . C 3 HOH A 172 4730 177 HOH HOH . C 3 HOH A 173 4731 178 HOH HOH . C 3 HOH A 174 4732 179 HOH HOH . C 3 HOH A 175 4733 180 HOH HOH . C 3 HOH A 176 4734 181 HOH HOH . C 3 HOH A 177 4735 182 HOH HOH . C 3 HOH A 178 4736 183 HOH HOH . C 3 HOH A 179 4737 184 HOH HOH . C 3 HOH A 180 4738 185 HOH HOH . C 3 HOH A 181 4739 186 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 C1K VK3 . . . B 2 -10.861 4.461 -18.237 1 48.91 ? C1K VK3 4558 A 1 HETATM 2 O O1K VK3 . . . B 2 -11.538 5.003 -17.366 1 51.69 ? O1K VK3 4558 A 1 HETATM 3 C C2K VK3 . . . B 2 -11.495 3.541 -19.058 1 51.93 ? C2K VK3 4558 A 1 HETATM 4 C C3K VK3 . . . B 2 -10.829 2.893 -20.078 1 52.18 ? C3K VK3 4558 A 1 HETATM 5 C C4K VK3 . . . B 2 -9.396 3.12 -20.338 1 50.32 ? C4K VK3 4558 A 1 HETATM 6 O O4K VK3 . . . B 2 -8.816 2.484 -21.243 1 52.27 ? O4K VK3 4558 A 1 HETATM 7 C C5K VK3 . . . B 2 -8.668 4.057 -19.469 1 49.27 ? C5K VK3 4558 A 1 HETATM 8 C C6K VK3 . . . B 2 -7.316 4.313 -19.603 1 47.64 ? C6K VK3 4558 A 1 HETATM 9 C C7K VK3 . . . B 2 -6.711 5.214 -18.72 1 38.41 ? C7K VK3 4558 A 1 HETATM 10 C C8K VK3 . . . B 2 -7.425 5.81 -17.73 1 24.61 ? C8K VK3 4558 A 1 HETATM 11 C C9K VK3 . . . B 2 -8.73 5.611 -17.555 1 44.98 ? C9K VK3 4558 A 1 HETATM 12 C C10 VK3 . . . B 2 -9.419 4.754 -18.395 1 49.69 ? C10 VK3 4558 A 1 HETATM 13 C C11 VK3 . . . B 2 -11.56 1.915 -20.947 1 53.92 ? C11 VK3 4558 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #