data_5JW1 # _model_server_result.job_id LkQFjA00Z8GPS_GV6CE2RQ _model_server_result.datetime_utc '2024-12-18 02:00:48' _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 5jw1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":604}' # _entry.id 5JW1 # _exptl.entry_id 5JW1 _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 4 _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 5JW1 _cell.length_a 120.362 _cell.length_b 132.198 _cell.length_c 180.392 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5JW1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _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,K,L,M,N,O _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 L N N ? 6 M 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 C NAG 1 C 1 NAG A 5 NAG 2 n C NAG 2 C 2 NAG A 6 NAG 2 n D NAG 1 D 1 NAG B 4 NAG 2 n D NAG 2 D 2 NAG B 5 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 4 A CYS 36 1_555 A SG CYS 15 A CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 5 A CYS 37 1_555 A SG CYS 128 A CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 9 A CYS 41 1_555 A SG CYS 25 A CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf4 A SG CYS 27 A CYS 59 1_555 A SG CYS 37 A CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf5 A SG CYS 538 A CYS 570 1_555 A SG CYS 544 A CYS 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 B SG CYS 4 B CYS 36 1_555 B SG CYS 15 B CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 5 B CYS 37 1_555 B SG CYS 128 B CYS 160 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf8 B SG CYS 9 B CYS 41 1_555 B SG CYS 25 B CYS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf9 B SG CYS 27 B CYS 59 1_555 B SG CYS 37 B CYS 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 B SG CYS 538 B CYS 570 1_555 B SG CYS 544 B CYS 576 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 36 A ASN 68 1_555 H C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 113 A ASN 145 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 A ND2 ASN 379 A ASN 411 1_555 I C1 NAG . A NAG 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale4 B ND2 ASN 36 B ASN 68 1_555 L C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 113 B ASN 145 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 B ND2 ASN 379 B ASN 411 1_555 M C1 NAG . B NAG 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D 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 409 n n C1 O1 NAG sing 410 n n C1 O5 NAG sing 411 n n C1 H1 NAG sing 412 n n C2 C3 NAG sing 413 n n C2 N2 NAG sing 414 n n C2 H2 NAG sing 415 n n C3 C4 NAG sing 416 n n C3 O3 NAG sing 417 n n C3 H3 NAG sing 418 n n C4 C5 NAG sing 419 n n C4 O4 NAG sing 420 n n C4 H4 NAG sing 421 n n C5 C6 NAG sing 422 n n C5 O5 NAG sing 423 n n C5 H5 NAG sing 424 n n C6 O6 NAG sing 425 n n C6 H61 NAG sing 426 n n C6 H62 NAG sing 427 n n C7 C8 NAG sing 428 n n C7 N2 NAG sing 429 n n C7 O7 NAG doub 430 n n C8 H81 NAG sing 431 n n C8 H82 NAG sing 432 n n C8 H83 NAG sing 433 n n N2 HN2 NAG sing 434 n n O1 HO1 NAG sing 435 n n O3 HO3 NAG sing 436 n n O4 HO4 NAG sing 437 n n O6 HO6 NAG sing 438 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 5JW1 _atom_sites.fract_transf_matrix[1][1] 0.008308 _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] 0.007564 _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] 0.005543 _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 3 COH A 1 601 1 COH COH . F 4 CEL A 1 602 2 CEL CEL . G 5 BOG A 1 603 3 BOG BOG . H 6 NAG A 1 604 4 NAG NAG . I 6 NAG A 1 607 7 NAG NAG . J 3 COH B 1 601 1 COH COH . K 4 CEL B 1 602 2 CEL CEL . L 6 NAG B 1 603 3 NAG NAG . M 6 NAG B 1 606 6 NAG NAG . N 7 HOH A 1 701 9 HOH HOH . N 7 HOH A 2 702 10 HOH HOH . N 7 HOH A 3 703 6 HOH HOH . N 7 HOH A 4 704 14 HOH HOH . N 7 HOH A 5 705 11 HOH HOH . O 7 HOH B 1 701 8 HOH HOH . O 7 HOH B 2 702 2 HOH HOH . O 7 HOH B 3 703 4 HOH HOH . O 7 HOH B 4 704 7 HOH HOH . O 7 HOH B 5 705 13 HOH HOH . O 7 HOH B 6 706 5 HOH HOH . O 7 HOH B 7 707 12 HOH HOH . O 7 HOH B 8 708 1 HOH HOH . O 7 HOH B 9 709 3 HOH HOH . O 7 HOH B 10 710 15 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 . . . H 6 115.521 170.787 66.112 1 51 ? C1 NAG 604 A 1 HETATM 2 C C2 NAG . . . H 6 114.178 170.728 66.849 1 53.07 ? C2 NAG 604 A 1 HETATM 3 C C3 NAG . . . H 6 113.877 172.061 67.53 1 56.35 ? C3 NAG 604 A 1 HETATM 4 C C4 NAG . . . H 6 115.044 172.489 68.408 1 70.96 ? C4 NAG 604 A 1 HETATM 5 C C5 NAG . . . H 6 116.319 172.52 67.576 1 53.67 ? C5 NAG 604 A 1 HETATM 6 C C6 NAG . . . H 6 117.547 172.861 68.385 1 53.57 ? C6 NAG 604 A 1 HETATM 7 C C7 NAG . . . H 6 112.651 169.119 65.8 1 63.06 ? C7 NAG 604 A 1 HETATM 8 C C8 NAG . . . H 6 111.531 168.931 64.822 1 50.66 ? C8 NAG 604 A 1 HETATM 9 N N2 NAG . . . H 6 113.1 170.37 65.941 1 53.41 ? N2 NAG 604 A 1 HETATM 10 O O3 NAG . . . H 6 112.704 171.922 68.323 1 64.03 ? O3 NAG 604 A 1 HETATM 11 O O4 NAG . . . H 6 114.8 173.779 68.959 1 64.98 ? O4 NAG 604 A 1 HETATM 12 O O5 NAG . . . H 6 116.545 171.222 67.01 1 51.19 ? O5 NAG 604 A 1 HETATM 13 O O6 NAG . . . H 6 118.462 173.642 67.629 1 60.75 ? O6 NAG 604 A 1 HETATM 14 O O7 NAG . . . H 6 113.129 168.18 66.43 1 58 ? O7 NAG 604 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 68 _model_server_stats.query_time_ms 458 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #