data_3GXT # _model_server_result.job_id rzpFkmkvTeJSt3-RjGSAjg _model_server_result.datetime_utc '2024-11-07 16:40:09' _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 3gxt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":430}' # _entry.id 3GXT # _exptl.entry_id 3GXT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 163.172 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-DEOXYNOJIRIMYCIN _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 120 _cell.entry_id 3GXT _cell.length_a 89.61 _cell.length_b 89.61 _cell.length_c 216.64 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GXT _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 7 L N N ? 7 P N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 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 ? 3 2 1 MAN MAN C1 O1 . O3 HO3 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 5 ? 4 4 3 MAN MAN C1 O1 . O3 HO3 . sing 6 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 5 3 2 MAN 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 C NAG 1 C 1 NAG D 639 NAG 2 n C NAG 2 C 2 NAG D 640 NAG 2 n D NAG 1 D 1 NAG E 692 NAG 2 n D NAG 2 D 2 NAG E 693 NAG 3 n E MAN 1 E 1 MAN E 694 MAN 3 n E MAN 2 E 2 MAN E 696 MAN 2 n F NAG 1 F 1 NAG H 715 NAG 2 n F NAG 2 F 2 NAG H 716 NAG 4 n G NAG 1 G 1 NAG J 692 NAG 4 n G NAG 2 G 2 NAG J 693 NAG 4 n G MAN 3 G 3 MAN J 694 MAN 4 n G MAN 4 G 4 MAN J 695 MAN 5 n H NAG 1 H 1 NAG K 715 NAG 5 n H NAG 2 H 2 NAG K 716 NAG 5 n H MAN 3 H 3 MAN K 717 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 21 A CYS 52 1_555 A SG CYS 63 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf2 A SG CYS 25 A CYS 56 1_555 A SG CYS 32 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf3 A SG CYS 111 A CYS 142 1_555 A SG CYS 141 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? disulf ? disulf4 A SG CYS 171 A CYS 202 1_555 A SG CYS 192 A CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf5 A SG CYS 347 A CYS 378 1_555 A SG CYS 351 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 21 B CYS 52 1_555 B SG CYS 63 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf7 B SG CYS 25 B CYS 56 1_555 B SG CYS 32 B CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf8 B SG CYS 111 B CYS 142 1_555 B SG CYS 141 B CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf9 B SG CYS 171 B CYS 202 1_555 B SG CYS 192 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf10 B SG CYS 347 B CYS 378 1_555 B SG CYS 351 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? covale ? covale1 A ND2 ASN 108 A ASN 139 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale2 A ND2 ASN 161 A ASN 192 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 A ND2 ASN 184 A ASN 215 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale4 B ND2 ASN 161 B ASN 192 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 E O3 MAN . E MAN 1 1_555 E C1 MAN . E MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale10 G O4 NAG . G NAG 2 1_555 G C1 MAN . G MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale11 G O3 MAN . G MAN 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale13 H O4 NAG . H NAG 2 1_555 H C1 MAN . H MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _chem_comp.formula 'C6 H13 N O4' _chem_comp.formula_weight 163.172 _chem_comp.id NOJ _chem_comp.mon_nstd_flag . _chem_comp.name 1-DEOXYNOJIRIMYCIN _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms MORANOLINE # 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 C2 NOJ sing 291 n n C1 N5 NOJ sing 292 n n C1 H11 NOJ sing 293 n n C1 H12 NOJ sing 294 n n C2 O2 NOJ sing 295 n n C2 C3 NOJ sing 296 n n C2 H2 NOJ sing 297 n n O2 HO2 NOJ sing 298 n n C3 O3 NOJ sing 299 n n C3 C4 NOJ sing 300 n n C3 H3 NOJ sing 301 n n O3 HO3 NOJ sing 302 n n C4 O4 NOJ sing 303 n n C4 C5 NOJ sing 304 n n C4 H4 NOJ sing 305 n n O4 HO4 NOJ sing 306 n n C5 N5 NOJ sing 307 n n C5 C6 NOJ sing 308 n n C5 H5 NOJ sing 309 n n N5 HN5 NOJ sing 310 n n C6 O6 NOJ sing 311 n n C6 H61 NOJ sing 312 n n C6 H62 NOJ sing 313 n n O6 HO6 NOJ sing 314 n n # _atom_sites.entry_id 3GXT _atom_sites.fract_transf_matrix[1][1] 0.011159 _atom_sites.fract_transf_matrix[1][2] 0.006443 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012886 _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] 0.004616 _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 I 6 SO4 A 1 1 1 SO4 SO4 . J 6 SO4 A 1 2 2 SO4 SO4 . K 6 SO4 A 1 5 5 SO4 SO4 . L 7 NOJ A 1 430 1 NOJ NOJ . M 8 NAG B 1 639 639 NAG NAG . N 6 SO4 B 1 3 3 SO4 SO4 . O 6 SO4 B 1 4 4 SO4 SO4 . P 7 NOJ B 1 1 1 NOJ NOJ . Q 9 HOH A 1 3 3 HOH HOH . Q 9 HOH A 2 4 4 HOH HOH . Q 9 HOH A 3 8 8 HOH HOH . Q 9 HOH A 4 9 9 HOH HOH . Q 9 HOH A 5 11 11 HOH HOH . Q 9 HOH A 6 12 12 HOH HOH . Q 9 HOH A 7 15 15 HOH HOH . Q 9 HOH A 8 16 16 HOH HOH . Q 9 HOH A 9 18 18 HOH HOH . Q 9 HOH A 10 19 19 HOH HOH . Q 9 HOH A 11 23 23 HOH HOH . Q 9 HOH A 12 25 25 HOH HOH . Q 9 HOH A 13 26 26 HOH HOH . Q 9 HOH A 14 30 30 HOH HOH . Q 9 HOH A 15 431 5 HOH HOH . Q 9 HOH A 16 432 32 HOH HOH . Q 9 HOH A 17 433 34 HOH HOH . Q 9 HOH A 18 434 36 HOH HOH . Q 9 HOH A 19 435 41 HOH HOH . Q 9 HOH A 20 436 42 HOH HOH . Q 9 HOH A 21 437 44 HOH HOH . Q 9 HOH A 22 438 48 HOH HOH . Q 9 HOH A 23 439 49 HOH HOH . Q 9 HOH A 24 440 51 HOH HOH . Q 9 HOH A 25 441 52 HOH HOH . Q 9 HOH A 26 442 53 HOH HOH . Q 9 HOH A 27 443 54 HOH HOH . Q 9 HOH A 28 444 55 HOH HOH . Q 9 HOH A 29 445 62 HOH HOH . Q 9 HOH A 30 446 63 HOH HOH . Q 9 HOH A 31 447 64 HOH HOH . Q 9 HOH A 32 448 67 HOH HOH . Q 9 HOH A 33 449 70 HOH HOH . Q 9 HOH A 34 450 74 HOH HOH . Q 9 HOH A 35 451 78 HOH HOH . Q 9 HOH A 36 452 79 HOH HOH . R 9 HOH B 1 6 6 HOH HOH . R 9 HOH B 2 7 7 HOH HOH . R 9 HOH B 3 10 10 HOH HOH . R 9 HOH B 4 13 13 HOH HOH . R 9 HOH B 5 14 14 HOH HOH . R 9 HOH B 6 17 17 HOH HOH . R 9 HOH B 7 21 21 HOH HOH . R 9 HOH B 8 24 24 HOH HOH . R 9 HOH B 9 27 27 HOH HOH . R 9 HOH B 10 28 28 HOH HOH . R 9 HOH B 11 31 31 HOH HOH . R 9 HOH B 12 430 37 HOH HOH . R 9 HOH B 13 431 38 HOH HOH . R 9 HOH B 14 432 40 HOH HOH . R 9 HOH B 15 433 43 HOH HOH . R 9 HOH B 16 434 45 HOH HOH . R 9 HOH B 17 435 47 HOH HOH . R 9 HOH B 18 436 50 HOH HOH . R 9 HOH B 19 437 56 HOH HOH . R 9 HOH B 20 438 57 HOH HOH . R 9 HOH B 21 439 59 HOH HOH . R 9 HOH B 22 440 60 HOH HOH . R 9 HOH B 23 441 65 HOH HOH . R 9 HOH B 24 442 66 HOH HOH . R 9 HOH B 25 443 72 HOH HOH . R 9 HOH B 26 444 73 HOH HOH . R 9 HOH B 27 445 75 HOH HOH . R 9 HOH B 28 446 77 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 NOJ . . . L 7 -17.167 61.343 105.691 1 57.12 ? C1 NOJ 430 A 1 HETATM 2 C C2 NOJ . . . L 7 -16.551 60.228 106.558 1 58.47 ? C2 NOJ 430 A 1 HETATM 3 O O2 NOJ . . . L 7 -15.257 60.58 107.086 1 59.34 ? O2 NOJ 430 A 1 HETATM 4 C C3 NOJ . . . L 7 -16.572 58.934 105.721 1 57.67 ? C3 NOJ 430 A 1 HETATM 5 O O3 NOJ . . . L 7 -15.734 57.855 106.194 1 56.18 ? O3 NOJ 430 A 1 HETATM 6 C C4 NOJ . . . L 7 -18.054 58.606 105.775 1 57.05 ? C4 NOJ 430 A 1 HETATM 7 O O4 NOJ . . . L 7 -18.293 57.27 105.38 1 55.32 ? O4 NOJ 430 A 1 HETATM 8 C C5 NOJ . . . L 7 -18.692 59.629 104.838 1 57.19 ? C5 NOJ 430 A 1 HETATM 9 N N5 NOJ . . . L 7 -18.555 60.997 105.372 1 56.29 ? N5 NOJ 430 A 1 HETATM 10 C C6 NOJ . . . L 7 -20.152 59.386 104.642 1 58.28 ? C6 NOJ 430 A 1 HETATM 11 O O6 NOJ . . . L 7 -20.586 60.398 103.742 1 62.29 ? O6 NOJ 430 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 223 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 11 #