data_6JJP # _model_server_result.job_id 37bQbaEeHa9iwQ3zP4_4yQ _model_server_result.datetime_utc '2024-11-21 18:45:48' _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 6jjp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":306}' # _entry.id 6JJP # _exptl.entry_id 6JJP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 5 _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 113.92 _cell.angle_gamma 90 _cell.entry_id 6JJP _cell.length_a 102.61 _cell.length_b 54.219 _cell.length_c 126.082 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6JJP _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 2 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,G,I,J,M 1 1 D,E,F,H,K,L,N,O 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 ? 5 I N N ? 5 J N N ? 5 K N N ? 5 L N N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type 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 . O3 HO3 . sing 4 ? 4 5 1 FUC NAG C1 O1 . O6 HO6 . 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 G NAG 1 G 1 NAG C 301 NAG 4 n G NAG 2 G 2 NAG C 302 NAG 4 n G BMA 3 G 3 BMA C 304 BMA 4 n G MAN 4 G 4 MAN C 305 MAN 4 n G FUC 5 G 5 FUC C 303 FUC 4 n H NAG 1 H 1 NAG F 301 NAG 4 n H NAG 2 H 2 NAG F 302 NAG 4 n H BMA 3 H 3 BMA F 304 BMA 4 n H MAN 4 H 4 MAN F 305 MAN 4 n H FUC 5 H 5 FUC F 303 FUC # 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 22 A CYS 22 1_555 A SG CYS 96 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 A SG CYS 144 A CYS 144 1_555 A SG CYS 200 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 220 A CYS 220 1_555 B SG CYS 214 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 B SG CYS 23 B CYS 23 1_555 B SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 B SG CYS 134 B CYS 134 1_555 B SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 C SG CYS 34 C CYS 54 1_555 C SG CYS 103 C CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 D SG CYS 22 D CYS 22 1_555 D SG CYS 96 D CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf8 D SG CYS 144 D CYS 144 1_555 D SG CYS 200 D CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf9 E SG CYS 23 E CYS 23 1_555 E SG CYS 88 E CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf10 E SG CYS 134 E CYS 134 1_555 E SG CYS 194 E CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf11 F SG CYS 34 F CYS 54 1_555 F SG CYS 103 F CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 C ND2 ASN 29 C ASN 49 1_555 I C1 NAG . C NAG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 C ND2 ASN 38 C ASN 58 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 C ND2 ASN 96 C ASN 116 1_555 J C1 NAG . C NAG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 F ND2 ASN 29 F ASN 49 1_555 K C1 NAG . F NAG 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 F ND2 ASN 38 F ASN 58 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale6 F ND2 ASN 96 F ASN 116 1_555 L C1 NAG . F NAG 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 sing covale ? covale8 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 sing covale ? covale9 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 sing covale ? covale10 G O3 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.424 sing covale ? covale11 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 sing covale ? covale12 H O6 NAG . H NAG 1 1_555 H C1 FUC . H FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 sing covale ? covale13 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.4 sing covale ? covale14 H O3 BMA . H BMA 3 1_555 H C1 MAN . H MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 sing # _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 308 n n C1 O1 NAG sing 309 n n C1 O5 NAG sing 310 n n C1 H1 NAG sing 311 n n C2 C3 NAG sing 312 n n C2 N2 NAG sing 313 n n C2 H2 NAG sing 314 n n C3 C4 NAG sing 315 n n C3 O3 NAG sing 316 n n C3 H3 NAG sing 317 n n C4 C5 NAG sing 318 n n C4 O4 NAG sing 319 n n C4 H4 NAG sing 320 n n C5 C6 NAG sing 321 n n C5 O5 NAG sing 322 n n C5 H5 NAG sing 323 n n C6 O6 NAG sing 324 n n C6 H61 NAG sing 325 n n C6 H62 NAG sing 326 n n C7 C8 NAG sing 327 n n C7 N2 NAG sing 328 n n C7 O7 NAG doub 329 n n C8 H81 NAG sing 330 n n C8 H82 NAG sing 331 n n C8 H83 NAG sing 332 n n N2 HN2 NAG sing 333 n n O1 HO1 NAG sing 334 n n O3 HO3 NAG sing 335 n n O4 HO4 NAG sing 336 n n O6 HO6 NAG sing 337 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 6JJP _atom_sites.fract_transf_matrix[1][1] 0.009746 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004323 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018444 _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] 0.008677 _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 I 5 NAG C 1 306 401 NAG NAG . J 5 NAG C 1 307 501 NAG NAG . K 5 NAG F 1 306 401 NAG NAG . L 5 NAG F 1 307 501 NAG NAG . M 6 HOH A 1 301 1 HOH HOH . M 6 HOH A 2 302 5 HOH HOH . M 6 HOH A 3 303 3 HOH HOH . M 6 HOH A 4 304 8 HOH HOH . N 6 HOH D 1 301 6 HOH HOH . N 6 HOH D 2 302 7 HOH HOH . N 6 HOH D 3 303 2 HOH HOH . O 6 HOH E 1 301 4 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 5 -67.275 -20.33 -40.611 1 54.71 ? C1 NAG 306 C 1 HETATM 2 C C2 NAG . . . I 5 -68.714 -19.813 -40.502 1 58.86 ? C2 NAG 306 C 1 HETATM 3 C C3 NAG . . . I 5 -68.979 -18.745 -41.563 1 60.17 ? C3 NAG 306 C 1 HETATM 4 C C4 NAG . . . I 5 -67.937 -17.638 -41.475 1 59.97 ? C4 NAG 306 C 1 HETATM 5 C C5 NAG . . . I 5 -66.539 -18.237 -41.582 1 58.45 ? C5 NAG 306 C 1 HETATM 6 C C6 NAG . . . I 5 -65.437 -17.215 -41.414 1 64.92 ? C6 NAG 306 C 1 HETATM 7 C C7 NAG . . . I 5 -70.388 -21.366 -39.59 1 61.84 ? C7 NAG 306 C 1 HETATM 8 C C8 NAG . . . I 5 -71.326 -22.495 -39.898 1 61.22 ? C8 NAG 306 C 1 HETATM 9 N N2 NAG . . . I 5 -69.671 -20.902 -40.621 1 59.93 ? N2 NAG 306 C 1 HETATM 10 O O3 NAG . . . I 5 -70.283 -18.204 -41.384 1 48.51 ? O3 NAG 306 C 1 HETATM 11 O O4 NAG . . . I 5 -68.136 -16.685 -42.514 1 54.87 ? O4 NAG 306 C 1 HETATM 12 O O5 NAG . . . I 5 -66.354 -19.221 -40.553 1 56.91 ? O5 NAG 306 C 1 HETATM 13 O O6 NAG . . . I 5 -65.322 -16.773 -40.068 1 66.87 ? O6 NAG 306 C 1 HETATM 14 O O7 NAG . . . I 5 -70.284 -20.895 -38.461 1 61.09 ? O7 NAG 306 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 544 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 14 #