data_3RJR # _model_server_result.job_id x6Lkvhd3Zu0hdFlGWwL-mQ _model_server_result.datetime_utc '2024-11-05 10:27:52' _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 3rjr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":3053}' # _entry.id 3RJR # _exptl.entry_id 3RJR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.72 _cell.angle_gamma 90 _cell.entry_id 3RJR _cell.length_a 54.69 _cell.length_b 126.94 _cell.length_c 137.93 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RJR _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G 1 1 C,D,F,H,I,J 2 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 ? 3 G N N ? 3 H N N ? 3 I N N ? 3 J 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 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 2 n E NAG 1 E 1 NAG B 3053 NAG 2 n E NAG 2 E 2 NAG B 3054 NAG 2 n F NAG 1 F 1 NAG C 3053 NAG 2 n F NAG 2 F 2 NAG C 3054 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 196 A CYS 194 1_555 B SG CYS 198 B CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 198 A CYS 196 1_555 B SG CYS 196 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 258 A CYS 256 1_555 A SG CYS 267 A CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 266 A CYS 264 1_555 A SG CYS 329 A CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 295 A CYS 293 1_555 A SG CYS 360 A CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 299 A CYS 297 1_555 A SG CYS 362 A CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf7 A SG CYS 328 A CYS 326 1_555 B SG CYS 328 B CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 B SG CYS 258 B CYS 256 1_555 B SG CYS 267 B CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 B SG CYS 266 B CYS 264 1_555 B SG CYS 329 B CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf10 B SG CYS 295 B CYS 293 1_555 B SG CYS 360 B CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 B SG CYS 299 B CYS 297 1_555 B SG CYS 362 B CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 C SG CYS 196 C CYS 194 1_555 D SG CYS 198 D CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 C SG CYS 198 C CYS 196 1_555 D SG CYS 196 D CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf14 C SG CYS 258 C CYS 256 1_555 C SG CYS 267 C CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 C SG CYS 266 C CYS 264 1_555 C SG CYS 329 C CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf16 C SG CYS 295 C CYS 293 1_555 C SG CYS 360 C CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf17 C SG CYS 299 C CYS 297 1_555 C SG CYS 362 C CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 C SG CYS 328 C CYS 326 1_555 D SG CYS 328 D CYS 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 D SG CYS 258 D CYS 256 1_555 D SG CYS 267 D CYS 265 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf20 D SG CYS 266 D CYS 264 1_555 D SG CYS 329 D CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf21 D SG CYS 295 D CYS 293 1_555 D SG CYS 360 D CYS 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf22 D SG CYS 299 D CYS 297 1_555 D SG CYS 362 D CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 55 A ASN 53 1_555 G C1 NAG . A NAG 3053 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 55 B ASN 53 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 C ND2 ASN 55 C ASN 53 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale4 C ND2 ASN 109 C ASN 107 1_555 H C1 NAG . C NAG 3107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale5 D ND2 ASN 55 D ASN 53 1_555 I C1 NAG . D NAG 3053 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 D ND2 ASN 109 D ASN 107 1_555 J C1 NAG . D NAG 3107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? # _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 3RJR _atom_sites.fract_transf_matrix[1][1] 0.018285 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002154 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007878 _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] 0.0073 _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 3 NAG A 1 3053 3053 NAG NAG . H 3 NAG C 1 3107 3107 NAG NAG . I 3 NAG D 1 3053 3053 NAG NAG . J 3 NAG D 1 3107 3107 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 . . . I 3 -60.915 6.785 53.636 1 234.24 ? C1 NAG 3053 D 1 HETATM 2 C C2 NAG . . . I 3 -61.425 5.744 52.642 1 228.55 ? C2 NAG 3053 D 1 HETATM 3 C C3 NAG . . . I 3 -60.856 4.36 52.925 1 225.82 ? C3 NAG 3053 D 1 HETATM 4 C C4 NAG . . . I 3 -59.349 4.432 53.114 1 235.6 ? C4 NAG 3053 D 1 HETATM 5 C C5 NAG . . . I 3 -58.998 5.491 54.149 1 230.7 ? C5 NAG 3053 D 1 HETATM 6 C C6 NAG . . . I 3 -57.487 5.578 54.331 1 254.14 ? C6 NAG 3053 D 1 HETATM 7 C C7 NAG . . . I 3 -63.597 5.851 51.567 1 183.33 ? C7 NAG 3053 D 1 HETATM 8 C C8 NAG . . . I 3 -65.087 5.828 51.733 1 183.52 ? C8 NAG 3053 D 1 HETATM 9 N N2 NAG . . . I 3 -62.875 5.694 52.672 1 137.01 ? N2 NAG 3053 D 1 HETATM 10 O O3 NAG . . . I 3 -61.156 3.496 51.852 1 220.07 ? O3 NAG 3053 D 1 HETATM 11 O O4 NAG . . . I 3 -58.867 3.178 53.541 1 267.34 ? O4 NAG 3053 D 1 HETATM 12 O O5 NAG . . . I 3 -59.505 6.747 53.744 1 236.07 ? O5 NAG 3053 D 1 HETATM 13 O O6 NAG . . . I 3 -57.193 5.967 55.654 1 252.28 ? O6 NAG 3053 D 1 HETATM 14 O O7 NAG . . . I 3 -63.094 6.006 50.455 1 213.63 ? O7 NAG 3053 D 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #