data_4XP9 # _model_server_result.job_id KDt89fE2-wGBIRPN57zNBw _model_server_result.datetime_utc '2024-11-06 03:38:00' _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 4xp9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":702}' # _entry.id 4XP9 # _exptl.entry_id 4XP9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-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 4XP9 _cell.length_a 97.348 _cell.length_b 140.748 _cell.length_c 166.76 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XP9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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,M,N,O,P,Q _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 6 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _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 GLC _pdbx_entity_branch_link.comp_id_2 GLC _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 4 n D GLC 1 A 1 GLC C 603 MAL 4 n D GLC 2 A 2 GLC C 603 MAL # 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 124 C CYS 148 1_555 A SG CYS 133 C CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf2 B SG CYS 23 L CYS 23 1_555 B SG CYS 89 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? disulf ? disulf3 B SG CYS 135 L CYS 135 1_555 B SG CYS 195 L CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 C SG CYS 22 H CYS 22 1_555 C SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf5 C SG CYS 146 H CYS 146 1_555 C SG CYS 201 H CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? covale ? covale1 A ND2 ASN 117 C ASN 141 1_555 F C1 NAG . C NAG 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale2 D O4 GLC . A GLC 1 1_555 D C1 GLC . A GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 sing metalc ? metalc1 A O GLY 18 C GLY 42 1_555 M NA NA . C NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc2 A O ALA 20 C ALA 44 1_555 L NA NA . C NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? metalc ? metalc3 A O VAL 21 C VAL 45 1_555 M NA NA . C NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc4 A OD1 ASN 25 C ASN 49 1_555 L NA NA . C NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc5 A O SER 255 C SER 320 1_555 L NA NA . C NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc6 A OG SER 255 C SER 320 1_555 L NA NA . C NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc7 A OD1 ASN 287 C ASN 352 1_555 L NA NA . C NA 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc8 A O LEU 352 C LEU 417 1_555 M NA NA . C NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc9 A OD2 ASP 355 C ASP 420 1_555 M NA NA . C NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? metalc ? metalc10 A OG SER 356 C SER 421 1_555 M NA NA . C NA 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc11 L NA NA . C NA 709 1_555 O O HOH . C HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.715 ? # _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 389 n n C1 O1 NAG sing 390 n n C1 O5 NAG sing 391 n n C1 H1 NAG sing 392 n n C2 C3 NAG sing 393 n n C2 N2 NAG sing 394 n n C2 H2 NAG sing 395 n n C3 C4 NAG sing 396 n n C3 O3 NAG sing 397 n n C3 H3 NAG sing 398 n n C4 C5 NAG sing 399 n n C4 O4 NAG sing 400 n n C4 H4 NAG sing 401 n n C5 C6 NAG sing 402 n n C5 O5 NAG sing 403 n n C5 H5 NAG sing 404 n n C6 O6 NAG sing 405 n n C6 H61 NAG sing 406 n n C6 H62 NAG sing 407 n n C7 C8 NAG sing 408 n n C7 N2 NAG sing 409 n n C7 O7 NAG doub 410 n n C8 H81 NAG sing 411 n n C8 H82 NAG sing 412 n n C8 H83 NAG sing 413 n n N2 HN2 NAG sing 414 n n O1 HO1 NAG sing 415 n n O3 HO3 NAG sing 416 n n O4 HO4 NAG sing 417 n n O6 HO6 NAG sing 418 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 4XP9 _atom_sites.fract_transf_matrix[1][1] 0.010272 _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] 0.007105 _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] 0.005997 _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 E 5 Y01 C 1 701 601 Y01 Y01 . F 6 NAG C 1 702 602 NAG NAG . G 7 MPO C 1 704 604 MPO MPO . H 8 CLR C 1 705 605 CLR CLR . I 9 1WE C 1 706 606 1WE 1WE . J 10 P4G C 1 707 607 P4G P4G . K 10 P4G C 1 708 608 P4G P4G . L 11 NA C 1 709 609 NA NA . M 11 NA C 1 710 610 NA NA . N 12 CL C 1 711 611 CL CL . O 13 HOH C 1 801 701 HOH HOH . O 13 HOH C 2 802 702 HOH HOH . O 13 HOH C 3 803 703 HOH HOH . O 13 HOH C 4 804 704 HOH HOH . O 13 HOH C 5 805 705 HOH HOH . O 13 HOH C 6 806 706 HOH HOH . O 13 HOH C 7 807 707 HOH HOH . O 13 HOH C 8 808 708 HOH HOH . O 13 HOH C 9 809 709 HOH HOH . O 13 HOH C 10 810 710 HOH HOH . O 13 HOH C 11 811 711 HOH HOH . O 13 HOH C 12 812 712 HOH HOH . O 13 HOH C 13 813 713 HOH HOH . O 13 HOH C 14 814 714 HOH HOH . O 13 HOH C 15 815 715 HOH HOH . O 13 HOH C 16 816 716 HOH HOH . P 13 HOH L 1 301 301 HOH HOH . P 13 HOH L 2 302 302 HOH HOH . P 13 HOH L 3 303 303 HOH HOH . P 13 HOH L 4 304 304 HOH HOH . P 13 HOH L 5 305 305 HOH HOH . P 13 HOH L 6 306 306 HOH HOH . P 13 HOH L 7 307 307 HOH HOH . P 13 HOH L 8 308 308 HOH HOH . P 13 HOH L 9 309 309 HOH HOH . Q 13 HOH H 1 301 301 HOH HOH . Q 13 HOH H 2 302 302 HOH HOH . Q 13 HOH H 3 303 303 HOH HOH . Q 13 HOH H 4 304 304 HOH HOH . Q 13 HOH H 5 305 305 HOH HOH . Q 13 HOH H 6 306 306 HOH HOH . Q 13 HOH H 7 307 307 HOH HOH . Q 13 HOH H 8 308 308 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 . . . F 6 -132.711 -144.476 165.758 1 120.11 ? C1 NAG 702 C 1 HETATM 2 C C2 NAG . . . F 6 -133.543 -144.284 164.48 1 114.63 ? C2 NAG 702 C 1 HETATM 3 C C3 NAG . . . F 6 -134.885 -145.009 164.587 1 114.64 ? C3 NAG 702 C 1 HETATM 4 C C4 NAG . . . F 6 -134.688 -146.473 164.983 1 118.09 ? C4 NAG 702 C 1 HETATM 5 C C5 NAG . . . F 6 -133.766 -146.588 166.201 1 118.52 ? C5 NAG 702 C 1 HETATM 6 C C6 NAG . . . F 6 -133.442 -148.009 166.592 1 119.33 ? C6 NAG 702 C 1 HETATM 7 C C7 NAG . . . F 6 -133.484 -142.336 163.002 1 122.86 ? C7 NAG 702 C 1 HETATM 8 C C8 NAG . . . F 6 -133.719 -140.863 162.862 1 120.61 ? C8 NAG 702 C 1 HETATM 9 N N2 NAG . . . F 6 -133.747 -142.858 164.199 1 118.59 ? N2 NAG 702 C 1 HETATM 10 O O3 NAG . . . F 6 -135.602 -144.956 163.36 1 115.5 ? O3 NAG 702 C 1 HETATM 11 O O4 NAG . . . F 6 -135.923 -147.102 165.327 1 116.45 ? O4 NAG 702 C 1 HETATM 12 O O5 NAG . . . F 6 -132.512 -145.928 165.973 1 121.32 ? O5 NAG 702 C 1 HETATM 13 O O6 NAG . . . F 6 -133.323 -148.146 168.003 1 115.97 ? O6 NAG 702 C 1 HETATM 14 O O7 NAG . . . F 6 -133.092 -143.02 162.059 1 122.68 ? O7 NAG 702 C 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 362 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 14 #