data_5GMG # _model_server_result.job_id iTPvq_PUk_n8yZtmk6eUWw _model_server_result.datetime_utc '2024-11-25 00:24:39' _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 5gmg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":905}' # _entry.id 5GMG # _exptl.entry_id 5GMG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 98.58 _cell.angle_gamma 90 _cell.entry_id 5GMG _cell.length_a 98.277 _cell.length_b 99.41 _cell.length_c 112.096 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GMG _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 ? _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,I,J,K,L,M,N,O,P,Q _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 G N N ? 4 H N N ? 4 I N N ? 4 L N N ? 4 M N N ? 4 N 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 E NAG 1 E 1 NAG A 904 NAG 3 n E NAG 2 E 2 NAG A 905 NAG 3 n F NAG 1 F 1 NAG B 903 NAG 3 n F NAG 2 F 2 NAG B 904 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 14 A CYS 36 1_555 A SG CYS 29 A CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf2 A SG CYS 76 A CYS 98 1_555 A SG CYS 453 A CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? disulf ? disulf3 A SG CYS 78 A CYS 100 1_555 A SG CYS 90 A CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 161 A CYS 183 1_555 A SG CYS 167 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 238 A CYS 260 1_555 A SG CYS 251 A CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf6 A SG CYS 241 A CYS 263 1_555 A SG CYS 248 A CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 A SG CYS 469 A CYS 491 1_555 A SG CYS 499 A CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf8 A SG CYS 765 A CYS 787 1_555 A SG CYS 792 A CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf9 A SG CYS 767 A CYS 789 1_555 A SG CYS 811 A CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? disulf ? disulf10 B SG CYS 14 B CYS 36 1_555 B SG CYS 29 B CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 B SG CYS 76 B CYS 98 1_555 B SG CYS 453 B CYS 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf12 B SG CYS 78 B CYS 100 1_555 B SG CYS 90 B CYS 112 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf13 B SG CYS 161 B CYS 183 1_555 B SG CYS 167 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf14 B SG CYS 238 B CYS 260 1_555 B SG CYS 251 B CYS 273 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf15 B SG CYS 241 B CYS 263 1_555 B SG CYS 248 B CYS 270 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf16 B SG CYS 469 B CYS 491 1_555 B SG CYS 499 B CYS 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf17 B SG CYS 765 B CYS 787 1_555 B SG CYS 792 B CYS 814 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf18 B SG CYS 767 B CYS 789 1_555 B SG CYS 811 B CYS 833 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? covale ? covale1 A ND2 ASN 47 A ASN 69 1_555 G C1 NAG . A NAG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale2 A ND2 ASN 193 A ASN 215 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale3 A ND2 ASN 501 A ASN 523 1_555 I C1 NAG . A NAG 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale4 A ND2 ASN 657 A ASN 679 1_555 H C1 NAG . A NAG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 B ND2 ASN 47 B ASN 69 1_555 N C1 NAG . B NAG 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.477 ? covale ? covale6 B ND2 ASN 193 B ASN 215 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 B ND2 ASN 501 B ASN 523 1_555 M C1 NAG . B NAG 906 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale8 B ND2 ASN 568 B ASN 590 1_555 L C1 NAG . B NAG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 5GMG _atom_sites.fract_transf_matrix[1][1] 0.010175 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001535 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010059 _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] 0.009022 _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 G 4 NAG A 1 901 902 NAG NAG . H 4 NAG A 1 904 906 NAG NAG . I 4 NAG A 1 905 907 NAG NAG . J 5 SDL B 1 901 901 SDL SDL . K 5 SDL B 1 902 901 SDL SDL . L 4 NAG B 1 903 902 NAG NAG . M 4 NAG B 1 906 905 NAG NAG . N 4 NAG B 1 907 906 NAG NAG . O 6 PO4 B 1 908 907 PO4 PO4 . P 7 HOH A 1 1001 1001 HOH HOH . P 7 HOH A 2 1002 1003 HOH HOH . P 7 HOH A 3 1003 1002 HOH HOH . P 7 HOH A 4 1004 1004 HOH HOH . P 7 HOH A 5 1005 1005 HOH HOH . P 7 HOH A 6 1006 1006 HOH HOH . P 7 HOH A 7 1007 1007 HOH HOH . P 7 HOH A 8 1008 1008 HOH HOH . P 7 HOH A 9 1009 1009 HOH HOH . P 7 HOH A 10 1010 1010 HOH HOH . P 7 HOH A 11 1011 1011 HOH HOH . P 7 HOH A 12 1012 1012 HOH HOH . P 7 HOH A 13 1013 1013 HOH HOH . P 7 HOH A 14 1014 1014 HOH HOH . P 7 HOH A 15 1015 1015 HOH HOH . P 7 HOH A 16 1016 1016 HOH HOH . Q 7 HOH B 1 1001 1001 HOH HOH . Q 7 HOH B 2 1002 1002 HOH HOH . Q 7 HOH B 3 1003 1003 HOH HOH . Q 7 HOH B 4 1004 1004 HOH HOH . Q 7 HOH B 5 1005 1005 HOH HOH . Q 7 HOH B 6 1006 1006 HOH HOH . Q 7 HOH B 7 1007 1008 HOH HOH . Q 7 HOH B 8 1008 1007 HOH HOH . Q 7 HOH B 9 1009 1009 HOH HOH . Q 7 HOH B 10 1010 1010 HOH HOH . Q 7 HOH B 11 1011 1011 HOH HOH . Q 7 HOH B 12 1012 1012 HOH HOH . Q 7 HOH B 13 1013 1013 HOH HOH . Q 7 HOH B 14 1014 1014 HOH HOH . Q 7 HOH B 15 1015 1015 HOH HOH . Q 7 HOH B 16 1016 1016 HOH HOH . Q 7 HOH B 17 1017 1017 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 NAG . . . I 4 7.407 -6.574 33.185 1 48.32 ? C1 NAG 905 A 1 HETATM 2 C C2 NAG . . . I 4 7.956 -5.741 32.035 1 48.67 ? C2 NAG 905 A 1 HETATM 3 C C3 NAG . . . I 4 9.313 -6.251 31.565 1 50.69 ? C3 NAG 905 A 1 HETATM 4 C C4 NAG . . . I 4 10.304 -6.315 32.701 1 49.55 ? C4 NAG 905 A 1 HETATM 5 C C5 NAG . . . I 4 9.705 -7.055 33.895 1 53.05 ? C5 NAG 905 A 1 HETATM 6 C C6 NAG . . . I 4 10.556 -6.692 35.115 1 52.72 ? C6 NAG 905 A 1 HETATM 7 C C7 NAG . . . I 4 6.52 -4.854 30.224 1 50.61 ? C7 NAG 905 A 1 HETATM 8 C C8 NAG . . . I 4 5.547 -5.321 29.177 1 48.82 ? C8 NAG 905 A 1 HETATM 9 N N2 NAG . . . I 4 6.998 -5.868 30.948 1 48.86 ? N2 NAG 905 A 1 HETATM 10 O O3 NAG . . . I 4 9.885 -5.437 30.527 1 44.4 ? O3 NAG 905 A 1 HETATM 11 O O4 NAG . . . I 4 11.501 -6.969 32.226 1 49.07 ? O4 NAG 905 A 1 HETATM 12 O O5 NAG . . . I 4 8.346 -6.72 34.238 1 50.83 ? O5 NAG 905 A 1 HETATM 13 O O6 NAG . . . I 4 10.49 -7.766 36.033 1 49.39 ? O6 NAG 905 A 1 HETATM 14 O O7 NAG . . . I 4 6.834 -3.664 30.349 1 45.68 ? O7 NAG 905 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #