data_5HVG # _model_server_result.job_id fiAP1L8e9TERQjv7bXafrA _model_server_result.datetime_utc '2024-12-23 06:09:41' _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 5hvg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":506}' # _entry.id 5HVG # _exptl.entry_id 5HVG _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 90 _cell.angle_gamma 120 _cell.entry_id 5HVG _cell.length_a 193.266 _cell.length_b 193.266 _cell.length_c 111.767 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HVG _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,G,H,I,J,K 1 1 C,D,F,L,M,N 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 G N N ? 5 H N N ? 5 I N N ? 5 L N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 3 5 3 MAN BMA C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG 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 3 n E NAG 1 E 1 NAG A 422 NAG 3 n E NAG 2 E 2 NAG A 423 NAG 3 n E BMA 3 E 3 BMA A 424 BMA 3 n E MAN 4 E 4 MAN A 425 MAN 3 n E MAN 5 E 5 MAN A 426 MAN 4 n F NAG 1 F 1 NAG C 422 NAG 4 n F NAG 2 F 2 NAG C 423 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 156 A CYS 156 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 228 A CYS 228 1_555 A SG CYS 252 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf3 A SG CYS 243 A CYS 243 1_555 A SG CYS 257 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 B SG CYS 22 B CYS 22 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf5 C SG CYS 156 C CYS 156 1_555 C SG CYS 169 C CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 C SG CYS 228 C CYS 228 1_555 C SG CYS 252 C CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf7 C SG CYS 243 C CYS 243 1_555 C SG CYS 257 C CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 D SG CYS 22 D CYS 22 1_555 D SG CYS 95 D CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 22 A ASN 22 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale2 A ND2 ASN 51 A ASN 51 1_555 G C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale3 A ND2 ASN 63 A ASN 63 1_555 H C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 A ND2 ASN 86 A ASN 86 1_555 I C1 NAG . A NAG 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 C ND2 ASN 22 C ASN 22 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale6 C ND2 ASN 51 C ASN 51 1_555 L C1 NAG . C NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale8 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.42 ? covale ? covale9 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 E O6 BMA . E BMA 3 1_555 E C1 MAN . E MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale11 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? metalc ? metalc1 A ND1 HIS 159 A HIS 159 1_555 J ZN ZN . A ZN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? metalc ? metalc2 A OE1 GLU 162 A GLU 162 1_555 J ZN ZN . A ZN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc3 A OE2 GLU 162 A GLU 162 1_555 J ZN ZN . A ZN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc4 A ND1 HIS 288 A HIS 288 1_555 J ZN ZN . A ZN 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc5 J ZN ZN . A ZN 509 1_555 K OXT ACT . A ACT 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc6 C ND1 HIS 159 C HIS 159 1_555 M ZN ZN . C ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc7 C OE1 GLU 162 C GLU 162 1_555 M ZN ZN . C ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc8 C OE2 GLU 162 C GLU 162 1_555 M ZN ZN . C ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc9 C ND1 HIS 288 C HIS 288 1_555 M ZN ZN . C ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? # _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 289 n n C1 O1 NAG sing 290 n n C1 O5 NAG sing 291 n n C1 H1 NAG sing 292 n n C2 C3 NAG sing 293 n n C2 N2 NAG sing 294 n n C2 H2 NAG sing 295 n n C3 C4 NAG sing 296 n n C3 O3 NAG sing 297 n n C3 H3 NAG sing 298 n n C4 C5 NAG sing 299 n n C4 O4 NAG sing 300 n n C4 H4 NAG sing 301 n n C5 C6 NAG sing 302 n n C5 O5 NAG sing 303 n n C5 H5 NAG sing 304 n n C6 O6 NAG sing 305 n n C6 H61 NAG sing 306 n n C6 H62 NAG sing 307 n n C7 C8 NAG sing 308 n n C7 N2 NAG sing 309 n n C7 O7 NAG doub 310 n n C8 H81 NAG sing 311 n n C8 H82 NAG sing 312 n n C8 H83 NAG sing 313 n n N2 HN2 NAG sing 314 n n O1 HO1 NAG sing 315 n n O3 HO3 NAG sing 316 n n O4 HO4 NAG sing 317 n n O6 HO6 NAG sing 318 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 5HVG _atom_sites.fract_transf_matrix[1][1] 0.005174 _atom_sites.fract_transf_matrix[1][2] 0.002987 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005975 _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] 0.008947 _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 G 5 NAG A 1 506 451 NAG NAG . H 5 NAG A 1 507 463 NAG NAG . I 5 NAG A 1 508 486 NAG NAG . J 6 ZN A 1 509 501 ZN ZN . K 7 ACT A 1 510 1 ACT ACT . L 5 NAG C 1 503 451 NAG NAG . M 6 ZN C 1 504 501 ZN ZN . N 7 ACT C 1 505 2 ACT ACT . # 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 . . . G 5 96.904 24.3 -23.34 1 113.62 ? C1 NAG 506 A 1 HETATM 2 C C2 NAG . . . G 5 98.347 24.786 -23.518 1 114.89 ? C2 NAG 506 A 1 HETATM 3 C C3 NAG . . . G 5 98.536 26.308 -23.458 1 116.69 ? C3 NAG 506 A 1 HETATM 4 C C4 NAG . . . G 5 97.735 26.971 -22.328 1 117.25 ? C4 NAG 506 A 1 HETATM 5 C C5 NAG . . . G 5 96.474 26.2 -21.928 1 115.26 ? C5 NAG 506 A 1 HETATM 6 C C6 NAG . . . G 5 95.32 27.099 -21.541 1 112.69 ? C6 NAG 506 A 1 HETATM 7 C C7 NAG . . . G 5 100.09 23.103 -22.969 1 107.02 ? C7 NAG 506 A 1 HETATM 8 C C8 NAG . . . G 5 101.28 22.868 -22.084 1 103.72 ? C8 NAG 506 A 1 HETATM 9 N N2 NAG . . . G 5 99.285 24.127 -22.614 1 110.98 ? N2 NAG 506 A 1 HETATM 10 O O3 NAG . . . G 5 98.266 26.915 -24.72 1 115.18 ? O3 NAG 506 A 1 HETATM 11 O O4 NAG . . . G 5 98.553 27.235 -21.187 1 116.92 ? O4 NAG 506 A 1 HETATM 12 O O5 NAG . . . G 5 96.014 25.374 -23.013 1 114.52 ? O5 NAG 506 A 1 HETATM 13 O O6 NAG . . . G 5 94.124 26.355 -21.352 1 110.86 ? O6 NAG 506 A 1 HETATM 14 O O7 NAG . . . G 5 99.869 22.409 -23.962 1 106.35 ? O7 NAG 506 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #