data_5O4G # _model_server_result.job_id S7kPNb4VUhHaMR8oXqHY4w _model_server_result.datetime_utc '2024-11-21 18:50:47' _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 5o4g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":707}' # _entry.id 5O4G # _exptl.entry_id 5O4G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 101.92 _cell.angle_gamma 90 _cell.entry_id 5O4G _cell.length_a 62.79 _cell.length_b 113.5 _cell.length_c 113.49 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5O4G _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 4 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 4 6 3 MAN BMA C1 O1 . O3 HO3 . sing 6 ? 5 2 1 NAG 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 4 n D NAG 1 D 1 NAG C 1047 NAG 4 n D NAG 2 D 2 NAG C 1048 NAG 4 n D BMA 3 D 3 BMA C 1049 BMA 4 n D MAN 4 D 4 MAN C 1051 MAN 4 n D MAN 5 D 5 MAN C 1052 MAN 4 n D MAN 6 D 6 MAN C 1050 MAN 5 n E NAG 1 E 1 NAG C 1239 NAG 5 n E NAG 2 E 2 NAG C 1240 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 4 C CYS 4 1_555 A SG CYS 31 C CYS 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 140 C CYS 140 1_555 A SG CYS 170 C CYS 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 173 C CYS 173 1_555 A SG CYS 182 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 177 C CYS 177 1_555 A SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 198 C CYS 198 1_555 A SG CYS 205 C CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 202 C CYS 202 1_555 A SG CYS 213 C CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 214 C CYS 214 1_555 A SG CYS 222 C CYS 222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 A SG CYS 218 C CYS 218 1_555 A SG CYS 230 C CYS 230 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 A SG CYS 233 C CYS 233 1_555 A SG CYS 242 C CYS 242 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 A SG CYS 246 C CYS 246 1_555 A SG CYS 273 C CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf11 A SG CYS 277 C CYS 277 1_555 A SG CYS 289 C CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 A SG CYS 293 C CYS 293 1_555 A SG CYS 309 C CYS 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf13 A SG CYS 320 C CYS 320 1_555 A SG CYS 345 C CYS 345 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf14 A SG CYS 453 C CYS 453 1_555 A SG CYS 482 C CYS 482 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 A SG CYS 489 C CYS 489 1_555 A SG CYS 498 C CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 A SG CYS 493 C CYS 493 1_555 A SG CYS 506 C CYS 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf17 A SG CYS 509 C CYS 509 1_555 A SG CYS 518 C CYS 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf18 B SG CYS 23 A CYS 23 1_555 B SG CYS 88 A CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf19 B SG CYS 134 A CYS 134 1_555 B SG CYS 194 A CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf20 C SG CYS 42 B CYS 22 1_555 C SG CYS 116 B CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf21 C SG CYS 168 B CYS 148 1_555 C SG CYS 224 B CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 46 C ASN 46 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 A ND2 ASN 165 C ASN 165 1_555 F C1 NAG . C NAG 707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale3 A ND2 ASN 237 C ASN 237 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 D O6 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale7 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 D O3 MAN . D MAN 4 1_555 D C1 MAN . D MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NAG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-beta-D-glucopyranose _chem_comp.type 'd-saccharide, beta linking' _chem_comp.pdbx_synonyms N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE # 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 NAG sing 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 5O4G _atom_sites.fract_transf_matrix[1][1] 0.015926 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003362 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008811 _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] 0.009006 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id F _pdbx_nonpoly_scheme.entity_id 6 _pdbx_nonpoly_scheme.mon_id NAG _pdbx_nonpoly_scheme.pdb_strand_id C _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 707 _pdbx_nonpoly_scheme.auth_seq_num 1165 _pdbx_nonpoly_scheme.pdb_mon_id NAG _pdbx_nonpoly_scheme.auth_mon_id NAG _pdbx_nonpoly_scheme.pdb_ins_code . # 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 NAG . . . F 6 57.751 96.498 85.773 1 110.58 ? C1 NAG 707 C 1 HETATM 2 C C2 NAG . . . F 6 58.717 96.241 86.926 1 108.16 ? C2 NAG 707 C 1 HETATM 3 C C3 NAG . . . F 6 58.877 97.501 87.773 1 122.7 ? C3 NAG 707 C 1 HETATM 4 C C4 NAG . . . F 6 59.263 98.686 86.897 1 124.66 ? C4 NAG 707 C 1 HETATM 5 C C5 NAG . . . F 6 58.278 98.832 85.74 1 120.9 ? C5 NAG 707 C 1 HETATM 6 C C6 NAG . . . F 6 58.675 99.911 84.759 1 102.35 ? C6 NAG 707 C 1 HETATM 7 C C7 NAG . . . F 6 58.816 93.908 87.688 1 115.11 ? C7 NAG 707 C 1 HETATM 8 C C8 NAG . . . F 6 58.228 92.879 88.606 1 94.23 ? C8 NAG 707 C 1 HETATM 9 N N2 NAG . . . F 6 58.268 95.127 87.747 1 119.15 ? N2 NAG 707 C 1 HETATM 10 O O3 NAG . . . F 6 59.88 97.28 88.759 1 116.98 ? O3 NAG 707 C 1 HETATM 11 O O4 NAG . . . F 6 59.26 99.882 87.668 1 111.71 ? O4 NAG 707 C 1 HETATM 12 O O5 NAG . . . F 6 58.211 97.604 85 1 106.62 ? O5 NAG 707 C 1 HETATM 13 O O6 NAG . . . F 6 58.407 99.518 83.419 1 92.42 ? O6 NAG 707 C 1 HETATM 14 O O7 NAG . . . F 6 59.745 93.649 86.929 1 113.17 ? O7 NAG 707 C 1 # _model_server_stats.io_time_ms 134 _model_server_stats.parse_time_ms 40 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 1049 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 14 #