data_3GXT # _model_server_result.job_id oNGcuLGAZ_PAJ4jTtXaJfQ _model_server_result.datetime_utc '2024-11-07 16:37:05' _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 3gxt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":639}' # _entry.id 3GXT # _exptl.entry_id 3GXT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _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 120 _cell.entry_id 3GXT _cell.length_a 89.61 _cell.length_b 89.61 _cell.length_c 216.64 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3GXT _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 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,K,L,M,N,O,P,Q,R _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 8 _struct_asym.id M _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 2 1 MAN MAN C1 O1 . O3 HO3 . sing 3 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 5 ? 4 4 3 MAN MAN C1 O1 . O3 HO3 . sing 6 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 7 ? 5 3 2 MAN NAG C1 O1 . O4 HO4 . 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 D 639 NAG 2 n C NAG 2 C 2 NAG D 640 NAG 2 n D NAG 1 D 1 NAG E 692 NAG 2 n D NAG 2 D 2 NAG E 693 NAG 3 n E MAN 1 E 1 MAN E 694 MAN 3 n E MAN 2 E 2 MAN E 696 MAN 2 n F NAG 1 F 1 NAG H 715 NAG 2 n F NAG 2 F 2 NAG H 716 NAG 4 n G NAG 1 G 1 NAG J 692 NAG 4 n G NAG 2 G 2 NAG J 693 NAG 4 n G MAN 3 G 3 MAN J 694 MAN 4 n G MAN 4 G 4 MAN J 695 MAN 5 n H NAG 1 H 1 NAG K 715 NAG 5 n H NAG 2 H 2 NAG K 716 NAG 5 n H MAN 3 H 3 MAN K 717 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 21 A CYS 52 1_555 A SG CYS 63 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf2 A SG CYS 25 A CYS 56 1_555 A SG CYS 32 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? disulf ? disulf3 A SG CYS 111 A CYS 142 1_555 A SG CYS 141 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? disulf ? disulf4 A SG CYS 171 A CYS 202 1_555 A SG CYS 192 A CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf5 A SG CYS 347 A CYS 378 1_555 A SG CYS 351 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 21 B CYS 52 1_555 B SG CYS 63 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf7 B SG CYS 25 B CYS 56 1_555 B SG CYS 32 B CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf8 B SG CYS 111 B CYS 142 1_555 B SG CYS 141 B CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf9 B SG CYS 171 B CYS 202 1_555 B SG CYS 192 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf10 B SG CYS 347 B CYS 378 1_555 B SG CYS 351 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? covale ? covale1 A ND2 ASN 108 A ASN 139 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale2 A ND2 ASN 161 A ASN 192 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 A ND2 ASN 184 A ASN 215 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale4 B ND2 ASN 161 B ASN 192 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 E O3 MAN . E MAN 1 1_555 E C1 MAN . E MAN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale8 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale10 G O4 NAG . G NAG 2 1_555 G C1 MAN . G MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale11 G O3 MAN . G MAN 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale13 H O4 NAG . H NAG 2 1_555 H C1 MAN . H MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 3GXT _atom_sites.fract_transf_matrix[1][1] 0.011159 _atom_sites.fract_transf_matrix[1][2] 0.006443 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012886 _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] 0.004616 _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 6 SO4 A 1 1 1 SO4 SO4 . J 6 SO4 A 1 2 2 SO4 SO4 . K 6 SO4 A 1 5 5 SO4 SO4 . L 7 NOJ A 1 430 1 NOJ NOJ . M 8 NAG B 1 639 639 NAG NAG . N 6 SO4 B 1 3 3 SO4 SO4 . O 6 SO4 B 1 4 4 SO4 SO4 . P 7 NOJ B 1 1 1 NOJ NOJ . Q 9 HOH A 1 3 3 HOH HOH . Q 9 HOH A 2 4 4 HOH HOH . Q 9 HOH A 3 8 8 HOH HOH . Q 9 HOH A 4 9 9 HOH HOH . Q 9 HOH A 5 11 11 HOH HOH . Q 9 HOH A 6 12 12 HOH HOH . Q 9 HOH A 7 15 15 HOH HOH . Q 9 HOH A 8 16 16 HOH HOH . Q 9 HOH A 9 18 18 HOH HOH . Q 9 HOH A 10 19 19 HOH HOH . Q 9 HOH A 11 23 23 HOH HOH . Q 9 HOH A 12 25 25 HOH HOH . Q 9 HOH A 13 26 26 HOH HOH . Q 9 HOH A 14 30 30 HOH HOH . Q 9 HOH A 15 431 5 HOH HOH . Q 9 HOH A 16 432 32 HOH HOH . Q 9 HOH A 17 433 34 HOH HOH . Q 9 HOH A 18 434 36 HOH HOH . Q 9 HOH A 19 435 41 HOH HOH . Q 9 HOH A 20 436 42 HOH HOH . Q 9 HOH A 21 437 44 HOH HOH . Q 9 HOH A 22 438 48 HOH HOH . Q 9 HOH A 23 439 49 HOH HOH . Q 9 HOH A 24 440 51 HOH HOH . Q 9 HOH A 25 441 52 HOH HOH . Q 9 HOH A 26 442 53 HOH HOH . Q 9 HOH A 27 443 54 HOH HOH . Q 9 HOH A 28 444 55 HOH HOH . Q 9 HOH A 29 445 62 HOH HOH . Q 9 HOH A 30 446 63 HOH HOH . Q 9 HOH A 31 447 64 HOH HOH . Q 9 HOH A 32 448 67 HOH HOH . Q 9 HOH A 33 449 70 HOH HOH . Q 9 HOH A 34 450 74 HOH HOH . Q 9 HOH A 35 451 78 HOH HOH . Q 9 HOH A 36 452 79 HOH HOH . R 9 HOH B 1 6 6 HOH HOH . R 9 HOH B 2 7 7 HOH HOH . R 9 HOH B 3 10 10 HOH HOH . R 9 HOH B 4 13 13 HOH HOH . R 9 HOH B 5 14 14 HOH HOH . R 9 HOH B 6 17 17 HOH HOH . R 9 HOH B 7 21 21 HOH HOH . R 9 HOH B 8 24 24 HOH HOH . R 9 HOH B 9 27 27 HOH HOH . R 9 HOH B 10 28 28 HOH HOH . R 9 HOH B 11 31 31 HOH HOH . R 9 HOH B 12 430 37 HOH HOH . R 9 HOH B 13 431 38 HOH HOH . R 9 HOH B 14 432 40 HOH HOH . R 9 HOH B 15 433 43 HOH HOH . R 9 HOH B 16 434 45 HOH HOH . R 9 HOH B 17 435 47 HOH HOH . R 9 HOH B 18 436 50 HOH HOH . R 9 HOH B 19 437 56 HOH HOH . R 9 HOH B 20 438 57 HOH HOH . R 9 HOH B 21 439 59 HOH HOH . R 9 HOH B 22 440 60 HOH HOH . R 9 HOH B 23 441 65 HOH HOH . R 9 HOH B 24 442 66 HOH HOH . R 9 HOH B 25 443 72 HOH HOH . R 9 HOH B 26 444 73 HOH HOH . R 9 HOH B 27 445 75 HOH HOH . R 9 HOH B 28 446 77 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 . . . M 8 33.892 84.005 84.714 1 110.32 ? C1 NAG 639 B 1 HETATM 2 C C2 NAG . . . M 8 32.473 84.573 84.59 1 109.87 ? C2 NAG 639 B 1 HETATM 3 C C3 NAG . . . M 8 32.534 86.014 84.059 1 109.53 ? C3 NAG 639 B 1 HETATM 4 C C4 NAG . . . M 8 33.518 86.909 84.804 1 109.65 ? C4 NAG 639 B 1 HETATM 5 C C5 NAG . . . M 8 34.652 86.184 85.595 1 110.39 ? C5 NAG 639 B 1 HETATM 6 C C6 NAG . . . M 8 34.663 86.675 87.054 1 110.19 ? C6 NAG 639 B 1 HETATM 7 C C7 NAG . . . M 8 30.33 83.71 83.576 1 108.57 ? C7 NAG 639 B 1 HETATM 8 C C8 NAG . . . M 8 29.708 82.781 82.577 1 107.8 ? C8 NAG 639 B 1 HETATM 9 N N2 NAG . . . M 8 31.667 83.678 83.749 1 109.22 ? N2 NAG 639 B 1 HETATM 10 O O3 NAG . . . M 8 31.292 86.669 84.18 1 109.87 ? O3 NAG 639 B 1 HETATM 11 O O4 NAG . . . M 8 33.985 87.875 83.868 1 107.89 ? O4 NAG 639 B 1 HETATM 12 O O5 NAG . . . M 8 34.679 84.746 85.634 1 110.58 ? O5 NAG 639 B 1 HETATM 13 O O6 NAG . . . M 8 33.446 86.389 87.724 1 109.58 ? O6 NAG 639 B 1 HETATM 14 O O7 NAG . . . M 8 29.576 84.452 84.187 1 108.29 ? O7 NAG 639 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 14 #