data_6V49 # _model_server_result.job_id zPmSG-wBBviQ7gsYkm6qNw _model_server_result.datetime_utc '2024-11-25 01:29:31' _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 6v49 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":301}' # _entry.id 6V49 # _exptl.entry_id 6V49 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _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 90.74 _cell.angle_gamma 90 _cell.entry_id 6V49 _cell.length_a 108.667 _cell.length_b 101.38 _cell.length_c 163.27 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6V49 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 J N N ? 4 K N N ? 4 L 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 G NAG 1 G 1 NAG A 501 NAG 3 n G NAG 2 G 2 NAG A 502 NAG 3 n H NAG 1 H 1 NAG C 501 NAG 3 n H NAG 2 H 2 NAG C 502 NAG 3 n I NAG 1 I 1 NAG E 501 NAG 3 n I NAG 2 I 2 NAG E 502 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 5 A CYS 4 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf2 A SG CYS 43 A CYS 42 1_555 A SG CYS 279 A CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf3 A SG CYS 55 A CYS 54 1_555 A SG CYS 67 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? disulf ? disulf4 A SG CYS 88 A CYS 87 1_555 A SG CYS 130 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? disulf ? disulf5 A SG CYS 283 A CYS 282 1_555 A SG CYS 307 A CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? disulf ? disulf7 C SG CYS 5 C CYS 4 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? disulf ? disulf8 C SG CYS 43 C CYS 42 1_555 C SG CYS 279 C CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf9 C SG CYS 55 C CYS 54 1_555 C SG CYS 67 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf10 C SG CYS 88 C CYS 87 1_555 C SG CYS 130 C CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? disulf ? disulf11 C SG CYS 283 C CYS 282 1_555 C SG CYS 307 C CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? disulf ? disulf13 E SG CYS 5 E CYS 4 1_555 F SG CYS 137 F CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? disulf ? disulf14 E SG CYS 43 E CYS 42 1_555 E SG CYS 279 E CYS 278 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf15 E SG CYS 55 E CYS 54 1_555 E SG CYS 67 E CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf16 E SG CYS 88 E CYS 87 1_555 E SG CYS 130 E CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf17 E SG CYS 283 E CYS 282 1_555 E SG CYS 307 E CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf18 F SG CYS 144 F CYS 144 1_555 F SG CYS 148 F CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? covale ? covale1 A ND2 ASN 29 A ASN 28 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale2 B ND2 ASN 82 B ASN 82 1_555 J C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale3 C ND2 ASN 29 C ASN 28 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale4 D ND2 ASN 82 D ASN 82 1_555 K C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale5 E ND2 ASN 29 E ASN 28 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale6 F ND2 ASN 82 F ASN 82 1_555 L C1 NAG . F NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale8 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale9 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? # _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 235 n n C1 O1 NAG sing 236 n n C1 O5 NAG sing 237 n n C1 H1 NAG sing 238 n n C2 C3 NAG sing 239 n n C2 N2 NAG sing 240 n n C2 H2 NAG sing 241 n n C3 C4 NAG sing 242 n n C3 O3 NAG sing 243 n n C3 H3 NAG sing 244 n n C4 C5 NAG sing 245 n n C4 O4 NAG sing 246 n n C4 H4 NAG sing 247 n n C5 C6 NAG sing 248 n n C5 O5 NAG sing 249 n n C5 H5 NAG sing 250 n n C6 O6 NAG sing 251 n n C6 H61 NAG sing 252 n n C6 H62 NAG sing 253 n n C7 C8 NAG sing 254 n n C7 N2 NAG sing 255 n n C7 O7 NAG doub 256 n n C8 H81 NAG sing 257 n n C8 H82 NAG sing 258 n n C8 H83 NAG sing 259 n n N2 HN2 NAG sing 260 n n O1 HO1 NAG sing 261 n n O3 HO3 NAG sing 262 n n O4 HO4 NAG sing 263 n n O6 HO6 NAG sing 264 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 6V49 _atom_sites.fract_transf_matrix[1][1] 0.009202 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000119 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009864 _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] 0.006125 _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 J 4 NAG B 1 301 301 NAG NAG . K 4 NAG D 1 301 301 NAG NAG . L 4 NAG F 1 301 301 NAG NAG . # 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 . . . L 4 -11.094 -19.595 58.443 1 101.57 ? C1 NAG 301 F 1 HETATM 2 C C2 NAG . . . L 4 -9.727 -19.616 59.188 1 113.22 ? C2 NAG 301 F 1 HETATM 3 C C3 NAG . . . L 4 -9.642 -20.517 60.46 1 115.96 ? C3 NAG 301 F 1 HETATM 4 C C4 NAG . . . L 4 -10.964 -21.048 61.011 1 118.55 ? C4 NAG 301 F 1 HETATM 5 C C5 NAG . . . L 4 -11.966 -21.303 59.863 1 119.94 ? C5 NAG 301 F 1 HETATM 6 C C6 NAG . . . L 4 -13.325 -21.959 60.172 1 111.03 ? C6 NAG 301 F 1 HETATM 7 C C7 NAG . . . L 4 -7.901 -18.769 57.84 1 137.34 ? C7 NAG 301 F 1 HETATM 8 C C8 NAG . . . L 4 -6.45 -19.018 57.483 1 132.02 ? C8 NAG 301 F 1 HETATM 9 N N2 NAG . . . L 4 -8.599 -19.828 58.286 1 122.53 ? N2 NAG 301 F 1 HETATM 10 O O3 NAG . . . L 4 -9.086 -19.837 61.598 1 122.65 ? O3 NAG 301 F 1 HETATM 11 O O4 NAG . . . L 4 -10.648 -22.189 61.818 1 117.6 ? O4 NAG 301 F 1 HETATM 12 O O5 NAG . . . L 4 -12.207 -20.019 59.255 1 121.65 ? O5 NAG 301 F 1 HETATM 13 O O6 NAG . . . L 4 -14.252 -21.708 59.094 1 97.65 ? O6 NAG 301 F 1 HETATM 14 O O7 NAG . . . L 4 -8.424 -17.657 57.74 1 142.66 ? O7 NAG 301 F 1 # _model_server_stats.io_time_ms 112 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #