data_3C6E # _model_server_result.job_id IYHNZOD24ZSuZdvH5JwMZw _model_server_result.datetime_utc '2024-11-18 00:20:10' _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 3c6e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1396}' # _entry.id 3C6E # _exptl.entry_id 3C6E _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-alpha-D-glucopyranose _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 3C6E _cell.length_a 71.104 _cell.length_b 108.366 _cell.length_c 108.956 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3C6E _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NDG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NDG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN MAN C1 O1 . O3 HO3 . 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 C NAG 1 B 1 NAG A 1398 NAG 3 n C NDG 2 B 2 NDG A 1399 NDG 3 n C MAN 3 B 3 MAN A 1400 MAN 3 n C MAN 4 B 4 MAN A 1402 MAN # 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 11 A CYS 3 1_555 A SG CYS 38 A CYS 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf2 A SG CYS 68 A CYS 60 1_555 A SG CYS 129 A CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 82 A CYS 74 1_555 A SG CYS 113 A CYS 105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 A SG CYS 100 A CYS 92 1_555 A SG CYS 124 A CYS 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 A SG CYS 193 A CYS 185 1_555 A SG CYS 293 A CYS 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf6 A SG CYS 310 A CYS 302 1_555 A SG CYS 341 A CYS 333 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 B SG CYS 34 C CYS 34 1_555 B SG CYS 68 C CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf8 B SG CYS 45 C CYS 45 1_555 B SG CYS 80 C CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 B SG CYS 53 C CYS 53 1_555 B SG CYS 66 C CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 75 A ASN 67 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale2 C O4 NAG . B NAG 1 1_555 C C1 NDG . B NDG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.565 ? covale ? covale3 C O4 NDG . B NDG 2 1_555 C C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.658 ? covale ? covale4 C O3 MAN . B MAN 3 1_555 C C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.087 ? # _chem_comp.formula 'C8 H15 N O6' _chem_comp.formula_weight 221.208 _chem_comp.id NDG _chem_comp.mon_nstd_flag . _chem_comp.name 2-acetamido-2-deoxy-alpha-D-glucopyranose _chem_comp.type 'd-saccharide, alpha linking' _chem_comp.pdbx_synonyms N-acetyl-alpha-D-glucosamine;2-acetamido-2-deoxy-alpha-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE # 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 NDG sing 291 n n C1 O5 NDG sing 292 n n C1 O1 NDG sing 293 n n C1 H1 NDG sing 294 n n C2 C3 NDG sing 295 n n C2 N2 NDG sing 296 n n C2 H2 NDG sing 297 n n C3 C4 NDG sing 298 n n C3 O3 NDG sing 299 n n C3 H3 NDG sing 300 n n C4 C5 NDG sing 301 n n C4 O4 NDG sing 302 n n C4 H4 NDG sing 303 n n C5 C6 NDG sing 304 n n C5 O5 NDG sing 305 n n C5 H5 NDG sing 306 n n C6 O6 NDG sing 307 n n C6 H61 NDG sing 308 n n C6 H62 NDG sing 309 n n C7 C8 NDG sing 310 n n C7 O7 NDG doub 311 n n C7 N2 NDG sing 312 n n C8 H81 NDG sing 313 n n C8 H82 NDG sing 314 n n C8 H83 NDG sing 315 n n O3 HO3 NDG sing 316 n n O4 HO4 NDG sing 317 n n O6 HO6 NDG sing 318 n n N2 HN2 NDG sing 319 n n O1 HO1 NDG sing 320 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 NDG DGlcpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 NDG N-acetyl-a-D-glucopyranosamine 'COMMON NAME' GMML 1 NDG a-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 NDG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 # _atom_sites.entry_id 3C6E _atom_sites.fract_transf_matrix[1][1] 0.014064 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009228 _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] 0.009178 _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 D 4 NDG C 1 1396 1396 NDG NDG . E 5 NAG C 1 1397 1397 NAG NAG . F 6 HOH A 1 1399 1 HOH HOH . F 6 HOH A 2 1400 2 HOH HOH . F 6 HOH A 3 1401 3 HOH HOH . F 6 HOH A 4 1402 4 HOH HOH . F 6 HOH A 5 1403 6 HOH HOH . F 6 HOH A 6 1404 7 HOH HOH . F 6 HOH A 7 1405 8 HOH HOH . F 6 HOH A 8 1406 10 HOH HOH . F 6 HOH A 9 1407 11 HOH HOH . F 6 HOH A 10 1408 12 HOH HOH . F 6 HOH A 11 1409 13 HOH HOH . F 6 HOH A 12 1410 14 HOH HOH . F 6 HOH A 13 1411 15 HOH HOH . F 6 HOH A 14 1412 16 HOH HOH . F 6 HOH A 15 1413 18 HOH HOH . F 6 HOH A 16 1414 19 HOH HOH . F 6 HOH A 17 1415 20 HOH HOH . F 6 HOH A 18 1416 21 HOH HOH . F 6 HOH A 19 1417 22 HOH HOH . F 6 HOH A 20 1418 23 HOH HOH . F 6 HOH A 21 1419 24 HOH HOH . F 6 HOH A 22 1420 25 HOH HOH . F 6 HOH A 23 1421 27 HOH HOH . F 6 HOH A 24 1422 28 HOH HOH . F 6 HOH A 25 1423 31 HOH HOH . F 6 HOH A 26 1424 32 HOH HOH . F 6 HOH A 27 1425 33 HOH HOH . F 6 HOH A 28 1426 34 HOH HOH . F 6 HOH A 29 1427 35 HOH HOH . F 6 HOH A 30 1428 36 HOH HOH . F 6 HOH A 31 1429 37 HOH HOH . F 6 HOH A 32 1430 38 HOH HOH . F 6 HOH A 33 1431 43 HOH HOH . F 6 HOH A 34 1432 44 HOH HOH . F 6 HOH A 35 1433 45 HOH HOH . F 6 HOH A 36 1434 46 HOH HOH . F 6 HOH A 37 1435 47 HOH HOH . F 6 HOH A 38 1436 48 HOH HOH . G 6 HOH C 1 1403 17 HOH HOH . G 6 HOH C 2 1404 29 HOH HOH . G 6 HOH C 3 1405 30 HOH HOH . G 6 HOH C 4 1406 39 HOH HOH . G 6 HOH C 5 1407 40 HOH HOH . G 6 HOH C 6 1408 41 HOH HOH . G 6 HOH C 7 1409 42 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 NDG . . . D 4 5.67 8.706 -52.531 1 63.97 ? C1 NDG 1396 C 1 HETATM 2 C C2 NDG . . . D 4 6.088 9.462 -53.784 1 64.31 ? C2 NDG 1396 C 1 HETATM 3 C C3 NDG . . . D 4 5.462 10.858 -53.721 1 65.1 ? C3 NDG 1396 C 1 HETATM 4 C C4 NDG . . . D 4 3.935 10.776 -53.498 1 64.58 ? C4 NDG 1396 C 1 HETATM 5 C C5 NDG . . . D 4 3.596 9.853 -52.323 1 63.27 ? C5 NDG 1396 C 1 HETATM 6 C C6 NDG . . . D 4 2.112 9.586 -52.19 1 62.18 ? C6 NDG 1396 C 1 HETATM 7 C C7 NDG . . . D 4 8.283 8.488 -53.535 1 60.77 ? C7 NDG 1396 C 1 HETATM 8 C C8 NDG . . . D 4 9.74 8.73 -53.187 1 58.03 ? C8 NDG 1396 C 1 HETATM 9 O O5 NDG . . . D 4 4.245 8.578 -52.491 1 64.31 ? O5 NDG 1396 C 1 HETATM 10 O O3 NDG . . . D 4 5.724 11.539 -54.933 1 67.37 ? O3 NDG 1396 C 1 HETATM 11 O O4 NDG . . . D 4 3.425 12.07 -53.222 1 65.46 ? O4 NDG 1396 C 1 HETATM 12 O O6 NDG . . . D 4 1.385 10.199 -53.237 1 61.17 ? O6 NDG 1396 C 1 HETATM 13 O O7 NDG . . . D 4 7.834 7.34 -53.524 1 58.46 ? O7 NDG 1396 C 1 HETATM 14 N N2 NDG . . . D 4 7.538 9.552 -53.837 1 63.06 ? N2 NDG 1396 C 1 HETATM 15 O O1 NDG . . . D 4 6.047 9.452 -51.431 1 62.28 ? O1 NDG 1396 C 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 15 #