data_7EFM # _model_server_result.job_id t1LK3-E8SYpvuTJoFhcf8Q _model_server_result.datetime_utc '2024-11-15 15:46:10' _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 7efm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":303}' # _entry.id 7EFM # _exptl.entry_id 7EFM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method syn _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 _cell.angle_gamma 120 _cell.entry_id 7EFM _cell.length_a 104.69 _cell.length_b 104.69 _cell.length_c 368.02 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EFM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 6 H N N ? 6 I N N ? 6 J N N # 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 B SG CYS 102 B CYS 131 1_555 B SG CYS 123 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 B SG CYS 172 B CYS 201 1_555 B SG CYS 233 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A C SER 338 A SER 384 1_555 A N BFD 339 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale2 A C BFD 339 A BFD 385 1_555 A N LYS 340 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale3 B ND2 ASN 70 B ASN 99 1_555 H C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale4 B ND2 ASN 101 B ASN 130 1_555 I C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale5 B ND2 ASN 132 B ASN 161 1_555 J C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? metalc ? metalc1 A O ASP 137 A ASP 183 1_555 E RB RB . A RB 1103 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 3.067 ? metalc ? metalc2 A OD1 ASP 139 A ASP 185 1_555 E RB RB . A RB 1103 6_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.877 ? metalc ? metalc3 A O VAL 295 A VAL 341 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? metalc ? metalc4 A OE1 GLU 297 A GLU 343 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.036 ? metalc ? metalc5 A OD2 BFD 339 A BFD 385 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc6 A O THR 341 A THR 387 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc7 A O SER 362 A SER 408 1_555 E RB RB . A RB 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc8 A O GLN 372 A GLN 418 1_555 E RB RB . A RB 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? metalc ? metalc9 A OD1 ASP 680 A ASP 726 1_555 C MG MG . A MG 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc10 A O LEU 688 A LEU 734 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.137 ? metalc ? metalc11 A O LYS 689 A LYS 735 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc12 A O ALA 691 A ALA 737 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.819 ? metalc ? metalc13 A OD2 ASP 710 A ASP 756 1_555 D RB RB . A RB 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc14 A OD1 ASN 746 A ASN 792 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.895 ? metalc ? metalc15 A OE1 GLU 749 A GLU 795 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.122 ? metalc ? metalc16 A OD2 ASP 774 A ASP 820 1_555 G RB RB . A RB 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? # _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 298 n n C1 O1 NAG sing 299 n n C1 O5 NAG sing 300 n n C1 H1 NAG sing 301 n n C2 C3 NAG sing 302 n n C2 N2 NAG sing 303 n n C2 H2 NAG sing 304 n n C3 C4 NAG sing 305 n n C3 O3 NAG sing 306 n n C3 H3 NAG sing 307 n n C4 C5 NAG sing 308 n n C4 O4 NAG sing 309 n n C4 H4 NAG sing 310 n n C5 C6 NAG sing 311 n n C5 O5 NAG sing 312 n n C5 H5 NAG sing 313 n n C6 O6 NAG sing 314 n n C6 H61 NAG sing 315 n n C6 H62 NAG sing 316 n n C7 C8 NAG sing 317 n n C7 N2 NAG sing 318 n n C7 O7 NAG doub 319 n n C8 H81 NAG sing 320 n n C8 H82 NAG sing 321 n n C8 H83 NAG sing 322 n n N2 HN2 NAG sing 323 n n O1 HO1 NAG sing 324 n n O3 HO3 NAG sing 325 n n O4 HO4 NAG sing 326 n n O6 HO6 NAG sing 327 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 7EFM _atom_sites.fract_transf_matrix[1][1] 0.009552 _atom_sites.fract_transf_matrix[1][2] 0.005515 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01103 _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] 0.002717 _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 C 3 MG A 1 1101 1102 MG MG . D 4 RB A 1 1102 1105 RB RB . E 4 RB A 1 1103 1106 RB RB . F 5 J3C A 1 1104 1 J3C BYK . G 4 RB A 1 1105 1 RB RB . H 6 NAG B 1 301 301 NAG NAG . I 6 NAG B 1 302 302 NAG NAG . J 6 NAG B 1 303 303 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 . . . J 6 57.256 -16.311 -60.174 1 152.3 ? C1 NAG 303 B 1 HETATM 2 C C2 NAG . . . J 6 58.124 -17.527 -60.399 1 154.27 ? C2 NAG 303 B 1 HETATM 3 C C3 NAG . . . J 6 58.967 -17.312 -61.646 1 155.65 ? C3 NAG 303 B 1 HETATM 4 C C4 NAG . . . J 6 58.061 -17.011 -62.837 1 157.34 ? C4 NAG 303 B 1 HETATM 5 C C5 NAG . . . J 6 57.031 -15.917 -62.517 1 155.4 ? C5 NAG 303 B 1 HETATM 6 C C6 NAG . . . J 6 55.942 -15.81 -63.556 1 152.99 ? C6 NAG 303 B 1 HETATM 7 C C7 NAG . . . J 6 59.142 -19.051 -58.782 1 153.75 ? C7 NAG 303 B 1 HETATM 8 C C8 NAG . . . J 6 60.039 -19.175 -57.594 1 153.38 ? C8 NAG 303 B 1 HETATM 9 N N2 NAG . . . J 6 58.962 -17.813 -59.249 1 153.76 ? N2 NAG 303 B 1 HETATM 10 O O3 NAG . . . J 6 59.768 -18.465 -61.885 1 154.19 ? O3 NAG 303 B 1 HETATM 11 O O4 NAG . . . J 6 58.844 -16.572 -63.942 1 158.64 ? O4 NAG 303 B 1 HETATM 12 O O5 NAG . . . J 6 56.363 -16.164 -61.268 1 153.64 ? O5 NAG 303 B 1 HETATM 13 O O6 NAG . . . J 6 54.677 -16.148 -63.003 1 149.35 ? O6 NAG 303 B 1 HETATM 14 O O7 NAG . . . J 6 58.606 -20.027 -59.299 1 154.86 ? O7 NAG 303 B 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #