data_4DKD # _model_server_result.job_id PwUytilC26BcgG_N1Fortw _model_server_result.datetime_utc '2025-01-03 00:31:09' _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 4dkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":303}' # _entry.id 4DKD # _exptl.entry_id 4DKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 180.156 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description beta-D-mannopyranose _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 4DKD _cell.length_a 101.361 _cell.length_b 101.361 _cell.length_c 175.252 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DKD _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 ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,I,J,K,L,M,N _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 ? 4 F N N ? 4 G N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 NAG _pdbx_entity_branch_link.comp_id_2 NAG _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 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _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 3 n D NAG 1 D 1 NAG A 201 NAG 3 n D NAG 2 D 2 NAG A 202 NAG 3 n E NAG 1 E 1 NAG B 201 NAG 3 n E NAG 2 E 2 NAG B 202 NAG # 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 18 A CYS 35 1_555 A SG CYS 163 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 160 A CYS 177 1_555 A SG CYS 174 A CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 18 B CYS 35 1_555 B SG CYS 163 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 160 B CYS 177 1_555 B SG CYS 174 B CYS 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 C SG CYS 26 C CYS 42 1_555 C SG CYS 68 C CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? disulf ? disulf6 C SG CYS 111 C CYS 127 1_555 C SG CYS 161 C CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf7 C SG CYS 208 C CYS 224 1_555 C SG CYS 262 C CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 59 A ASN 76 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale2 B ND2 ASN 59 B ASN 76 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 C ND2 ASN 57 C ASN 73 1_555 H C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale4 C ND2 ASN 137 C ASN 153 1_555 I C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 C ND2 ASN 224 C ASN 240 1_555 J C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale6 C ND2 ASN 259 C ASN 275 1_555 K C1 NAG . C NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _chem_comp.formula 'C6 H12 O6' _chem_comp.formula_weight 180.156 _chem_comp.id BMA _chem_comp.mon_nstd_flag . _chem_comp.name beta-D-mannopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms beta-D-mannose;D-mannose;mannose # 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 BMA sing 70 n n C1 O1 BMA sing 71 n n C1 O5 BMA sing 72 n n C1 H1 BMA sing 73 n n C2 C3 BMA sing 74 n n C2 O2 BMA sing 75 n n C2 H2 BMA sing 76 n n C3 C4 BMA sing 77 n n C3 O3 BMA sing 78 n n C3 H3 BMA sing 79 n n C4 C5 BMA sing 80 n n C4 O4 BMA sing 81 n n C4 H4 BMA sing 82 n n C5 C6 BMA sing 83 n n C5 O5 BMA sing 84 n n C5 H5 BMA sing 85 n n C6 O6 BMA sing 86 n n C6 H61 BMA sing 87 n n C6 H62 BMA sing 88 n n O1 HO1 BMA sing 89 n n O2 HO2 BMA sing 90 n n O3 HO3 BMA sing 91 n n O4 HO4 BMA sing 92 n n O6 HO6 BMA sing 93 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 BMA DManpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 BMA b-D-mannopyranose 'COMMON NAME' GMML 1 BMA b-D-Manp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 BMA Man 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 4DKD _atom_sites.fract_transf_matrix[1][1] 0.009866 _atom_sites.fract_transf_matrix[1][2] 0.005696 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011392 _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] 0.005706 _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 4 BMA A 1 303 203 BMA BMA . G 4 BMA B 1 303 203 BMA BMA . H 5 NAG C 1 401 401 NAG NAG . I 5 NAG C 1 402 402 NAG NAG . J 5 NAG C 1 403 403 NAG NAG . K 5 NAG C 1 404 404 NAG NAG . L 6 HOH A 1 401 1 HOH HOH . L 6 HOH A 2 402 4 HOH HOH . L 6 HOH A 3 403 5 HOH HOH . L 6 HOH A 4 404 9 HOH HOH . M 6 HOH B 1 401 7 HOH HOH . M 6 HOH B 2 402 8 HOH HOH . M 6 HOH B 3 403 11 HOH HOH . M 6 HOH B 4 404 12 HOH HOH . M 6 HOH B 5 405 13 HOH HOH . M 6 HOH B 6 406 14 HOH HOH . M 6 HOH B 7 407 15 HOH HOH . M 6 HOH B 8 408 16 HOH HOH . N 6 HOH C 1 501 2 HOH HOH . N 6 HOH C 2 502 3 HOH HOH . N 6 HOH C 3 503 6 HOH HOH . N 6 HOH C 4 504 10 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 BMA . . . G 4 -77.911 21.461 60.106 1 124.14 ? C1 BMA 303 B 1 HETATM 2 C C2 BMA . . . G 4 -78.491 21.596 61.511 1 124.59 ? C2 BMA 303 B 1 HETATM 3 C C3 BMA . . . G 4 -79.605 20.578 61.739 1 126.97 ? C3 BMA 303 B 1 HETATM 4 C C4 BMA . . . G 4 -80.617 20.618 60.596 1 129.61 ? C4 BMA 303 B 1 HETATM 5 C C5 BMA . . . G 4 -79.918 20.527 59.239 1 129.14 ? C5 BMA 303 B 1 HETATM 6 C C6 BMA . . . G 4 -80.919 20.642 58.093 1 128.85 ? C6 BMA 303 B 1 HETATM 7 O O2 BMA . . . G 4 -78.999 22.922 61.696 1 118.71 ? O2 BMA 303 B 1 HETATM 8 O O3 BMA . . . G 4 -80.255 20.844 62.988 1 123.18 ? O3 BMA 303 B 1 HETATM 9 O O4 BMA . . . G 4 -81.546 19.536 60.737 1 132.7 ? O4 BMA 303 B 1 HETATM 10 O O5 BMA . . . G 4 -78.946 21.57 59.129 1 127.87 ? O5 BMA 303 B 1 HETATM 11 O O6 BMA . . . G 4 -80.35 20.102 56.894 1 125.97 ? O6 BMA 303 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 11 #