data_1NIV # _model_server_result.job_id l2WWhoDURN8bFG1p5Mk7CQ _model_server_result.datetime_utc '2024-10-19 17:42:07' _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 1niv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":111}' # _entry.id 1NIV # _exptl.entry_id 1NIV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 194.182 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 'methyl alpha-D-mannopyranoside' _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 90 _cell.angle_gamma 90 _cell.entry_id 1NIV _cell.length_a 138.149 _cell.length_b 138.149 _cell.length_c 138.149 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NIV _symmetry.cell_setting ? _symmetry.Int_Tables_number 199 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 21 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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' 14_755 -x+2,-y+1/2,z -1 0 0 0 -1 0 0 0 1 276.298 69.0745 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 G N N ? 3 H N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 MAN _pdbx_entity_branch_link.comp_id_2 MMA _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O3 _pdbx_entity_branch_link.leaving_atom_id_2 HO3 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 MMA 1 B 1 MMA ? 2 MDM 2 n C MAN 2 B 2 MAN ? 2 MDM 2 n D MMA 1 D 1 MMA ? 3 MDM 2 n D MAN 2 D 2 MAN ? 3 MDM 2 n E MMA 1 E 1 MMA ? 6 MDM 2 n E MAN 2 E 2 MAN ? 6 MDM # 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 29 A CYS 29 1_555 A SG CYS 52 A CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 B SG CYS 29 C CYS 29 1_555 B SG CYS 52 C CYS 52 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 C O3 MMA . B MMA 1 1_555 C C1 MAN . B MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 sing covale ? covale2 D O3 MMA . D MMA 1 1_555 D C1 MAN . D MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 sing covale ? covale3 E O3 MMA . E MMA 1 1_555 E C1 MAN . E MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 sing # _chem_comp.formula 'C7 H14 O6' _chem_comp.formula_weight 194.182 _chem_comp.id MMA _chem_comp.mon_nstd_flag n _chem_comp.name 'methyl alpha-D-mannopyranoside' _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms 'O1-METHYL-MANNOSE;methyl alpha-D-mannoside;methyl D-mannoside;methyl mannoside' # 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 MMA sing 259 n n C1 O1 MMA sing 260 n n C1 O5 MMA sing 261 n n C1 H1 MMA sing 262 n n C2 C3 MMA sing 263 n n C2 O2 MMA sing 264 n n C2 H2 MMA sing 265 n n C3 C4 MMA sing 266 n n C3 O3 MMA sing 267 n n C3 H3 MMA sing 268 n n C4 C5 MMA sing 269 n n C4 O4 MMA sing 270 n n C4 H4 MMA sing 271 n n C5 C6 MMA sing 272 n n C5 O5 MMA sing 273 n n C5 H5 MMA sing 274 n n C6 O6 MMA sing 275 n n C6 H61 MMA sing 276 n n C6 H62 MMA sing 277 n n C7 O1 MMA sing 278 n n C7 H71 MMA sing 279 n n C7 H72 MMA sing 280 n n C7 H73 MMA sing 281 n n O2 HO2 MMA sing 282 n n O3 HO3 MMA sing 283 n n O4 HO4 MMA sing 284 n n O6 HO6 MMA sing 285 n n # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.identifier _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version MMA DManp[1Me]a 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 MMA 1-methyl-a-D-mannopyranose 'COMMON NAME' GMML 1 MMA o1-methyl-mannose 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 # _atom_sites.entry_id 1NIV _atom_sites.fract_transf_matrix[1][1] 0.007239 _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] 0.007239 _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] 0.007239 _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 F 3 MMA A 1 110 1 MMA MDM . G 3 MMA C 1 110 4 MMA MDM . H 3 MMA C 1 111 5 MMA MDM . # 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 MMA . . . H 3 137.902 3.694 115.853 1 50 ? C1 MMA 111 C 1 HETATM 2 C C2 MMA . . . H 3 136.971 4.221 116.937 1 50 ? C2 MMA 111 C 1 HETATM 3 C C3 MMA . . . H 3 135.611 4.485 116.318 1 50 ? C3 MMA 111 C 1 HETATM 4 C C4 MMA . . . H 3 135.779 5.517 115.21 1 50 ? C4 MMA 111 C 1 HETATM 5 C C5 MMA . . . H 3 136.817 5.04 114.185 1 50 ? C5 MMA 111 C 1 HETATM 6 C C6 MMA . . . H 3 137.157 6.102 113.159 1 50 ? C6 MMA 111 C 1 HETATM 7 C C7 MMA . . . H 3 138.114 1.927 114.227 1 50 ? C7 MMA 111 C 1 HETATM 8 O O1 MMA . . . H 3 137.353 2.558 115.276 1 50 ? O1 MMA 111 C 1 HETATM 9 O O2 MMA . . . H 3 137.497 5.439 117.44 1 50 ? O2 MMA 111 C 1 HETATM 10 O O3 MMA . . . H 3 134.715 4.973 117.304 1 50 ? O3 MMA 111 C 1 HETATM 11 O O4 MMA . . . H 3 134.531 5.726 114.567 1 50 ? O4 MMA 111 C 1 HETATM 12 O O5 MMA . . . H 3 138.061 4.686 114.834 1 50 ? O5 MMA 111 C 1 HETATM 13 O O6 MMA . . . H 3 138.351 5.774 112.465 1 50 ? O6 MMA 111 C 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 332 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #