data_5DLP # _model_server_result.job_id PILOvRXZ0NnWvFSNTCmjVA _model_server_result.datetime_utc '2024-10-14 10:20:30' _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 5dlp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 5DLP # _exptl.entry_id 5DLP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.399 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM _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 120 _cell.entry_id 5DLP _cell.length_a 111.059 _cell.length_b 111.059 _cell.length_c 137.172 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DLP _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U _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' 6_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 45.724 # _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_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 FUC NAG C1 O1 . O6 HO6 . sing 2 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 3 5 4 MAN MAN C1 O1 . O2 HO2 . 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 1536 NAG 2 n B FUC 2 B 2 FUC A 2106 FUC 3 n C NAG 1 C 1 NAG A 1539 NAG 3 n C NAG 2 C 2 NAG A 2107 NAG 3 n C BMA 3 C 3 BMA A 2108 BMA 3 n C MAN 4 C 4 MAN A 2109 MAN 3 n C MAN 5 C 5 MAN A 2110 MAN # 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 67 A CYS 67 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 254 A CYS 254 1_555 A SG CYS 265 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf3 A SG CYS 402 A CYS 402 1_555 A SG CYS 521 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 59 A ASN 59 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale2 A ND2 ASN 416 A ASN 416 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale3 A ND2 ASN 457 A ASN 457 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale4 B O6 NAG . B NAG 1 1_555 B C1 FUC . B FUC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale8 C O2 MAN . C MAN 4 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? # _chem_comp.formula 'C16 H18 N3 S 1' _chem_comp.formula_weight 284.399 _chem_comp.id MBT _chem_comp.mon_nstd_flag . _chem_comp.name 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'METHYLENE BLUE' # 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 C14 MBT sing 289 n y C1 N6 MBT doub 290 n y C1 C2 MBT sing 291 n y C2 S3 MBT doub 292 n y C2 C11 MBT sing 293 n y S3 C4 MBT sing 294 n y C4 C7 MBT doub 295 n y C4 C5 MBT sing 296 n y C5 N6 MBT sing 297 n y C5 C10 MBT doub 298 n y C7 C8 MBT sing 299 n y C7 H7 MBT sing 300 n n C8 C9 MBT doub 301 n y C8 N15 MBT sing 302 n n C9 C10 MBT sing 303 n y C9 H9 MBT sing 304 n n C10 H10 MBT sing 305 n n C11 C12 MBT doub 306 n y C11 H11 MBT sing 307 n n C12 N18 MBT sing 308 n n C12 C13 MBT sing 309 n y C13 C14 MBT doub 310 n y C13 H13 MBT sing 311 n n C14 H14 MBT sing 312 n n N15 C16 MBT sing 313 n n N15 C17 MBT sing 314 n n C16 H161 MBT sing 315 n n C16 H162 MBT sing 316 n n C16 H163 MBT sing 317 n n C17 H171 MBT sing 318 n n C17 H172 MBT sing 319 n n C17 H173 MBT sing 320 n n N18 C19 MBT sing 321 n n N18 C20 MBT sing 322 n n C19 H191 MBT sing 323 n n C19 H192 MBT sing 324 n n C19 H193 MBT sing 325 n n C20 H201 MBT sing 326 n n C20 H202 MBT sing 327 n n C20 H203 MBT sing 328 n n # _atom_sites.entry_id 5DLP _atom_sites.fract_transf_matrix[1][1] 0.009004 _atom_sites.fract_transf_matrix[1][2] 0.005199 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010397 _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] 0.00729 _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 D 4 MBT A 1 601 1540 MBT MBT . E 5 NAG A 1 602 1537 NAG NAG . F 6 SO4 A 1 603 701 SO4 SO4 . G 6 SO4 A 1 604 702 SO4 SO4 . H 6 SO4 A 1 605 703 SO4 SO4 . I 6 SO4 A 1 606 704 SO4 SO4 . J 6 SO4 A 1 607 705 SO4 SO4 . K 6 SO4 A 1 608 706 SO4 SO4 . L 6 SO4 A 1 609 707 SO4 SO4 . M 6 SO4 A 1 610 708 SO4 SO4 . N 6 SO4 A 1 611 709 SO4 SO4 . O 6 SO4 A 1 612 710 SO4 SO4 . P 6 SO4 A 1 613 711 SO4 SO4 . Q 6 SO4 A 1 614 712 SO4 SO4 . R 6 SO4 A 1 615 713 SO4 SO4 . S 6 SO4 A 1 616 714 SO4 SO4 . T 6 SO4 A 1 617 715 SO4 SO4 . U 7 HOH A 1 701 611 HOH HOH . U 7 HOH A 2 702 603 HOH HOH . U 7 HOH A 3 703 606 HOH HOH . U 7 HOH A 4 704 614 HOH HOH . U 7 HOH A 5 705 605 HOH HOH . U 7 HOH A 6 706 607 HOH HOH . U 7 HOH A 7 707 604 HOH HOH . U 7 HOH A 8 708 608 HOH HOH . U 7 HOH A 9 709 613 HOH HOH . U 7 HOH A 10 710 609 HOH HOH . U 7 HOH A 11 711 615 HOH HOH . U 7 HOH A 12 712 602 HOH HOH . U 7 HOH A 13 713 610 HOH HOH . U 7 HOH A 14 714 612 HOH HOH . U 7 HOH A 15 715 601 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 MBT . . . D 4 -53.562 34.096 23.751 1 73.89 ? C1 MBT 601 A 1 HETATM 2 C C2 MBT . . . D 4 -54.992 33.718 23.898 1 76.65 ? C2 MBT 601 A 1 HETATM 3 S S3 MBT . . . D 4 -55.396 32.416 24.727 1 84.79 ? S3 MBT 601 A 1 HETATM 4 C C4 MBT . . . D 4 -54.107 31.688 25.333 1 75.87 ? C4 MBT 601 A 1 HETATM 5 C C5 MBT . . . D 4 -52.761 32.24 25.067 1 75.01 ? C5 MBT 601 A 1 HETATM 6 N N6 MBT . . . D 4 -52.568 33.366 24.322 1 75.33 ? N6 MBT 601 A 1 HETATM 7 C C7 MBT . . . D 4 -54.223 30.522 26.098 1 76.41 ? C7 MBT 601 A 1 HETATM 8 C C8 MBT . . . D 4 -53.117 29.844 26.65 1 74 ? C8 MBT 601 A 1 HETATM 9 C C9 MBT . . . D 4 -51.849 30.391 26.385 1 74.3 ? C9 MBT 601 A 1 HETATM 10 C C10 MBT . . . D 4 -51.688 31.548 25.616 1 75.88 ? C10 MBT 601 A 1 HETATM 11 C C11 MBT . . . D 4 -55.979 34.495 23.291 1 73.51 ? C11 MBT 601 A 1 HETATM 12 C C12 MBT . . . D 4 -55.651 35.648 22.546 1 72.06 ? C12 MBT 601 A 1 HETATM 13 C C13 MBT . . . D 4 -54.288 35.99 22.421 1 71.16 ? C13 MBT 601 A 1 HETATM 14 C C14 MBT . . . D 4 -53.27 35.231 23.009 1 74.3 ? C14 MBT 601 A 1 HETATM 15 N N15 MBT . . . D 4 -53.256 28.653 27.439 1 74.58 ? N15 MBT 601 A 1 HETATM 16 C C16 MBT . . . D 4 -54.551 28.038 27.747 1 72.72 ? C16 MBT 601 A 1 HETATM 17 C C17 MBT . . . D 4 -52.08 27.972 27.99 1 74.23 ? C17 MBT 601 A 1 HETATM 18 N N18 MBT . . . D 4 -56.672 36.441 21.937 1 70.1 ? N18 MBT 601 A 1 HETATM 19 C C19 MBT . . . D 4 -58.089 36.089 22.06 1 70.62 ? C19 MBT 601 A 1 HETATM 20 C C20 MBT . . . D 4 -56.337 37.641 21.173 1 71.12 ? C20 MBT 601 A 1 # _model_server_stats.io_time_ms 185 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #