data_5HVF # _model_server_result.job_id 8j_uGk3eNsZgJJzfRb7qIw _model_server_result.datetime_utc '2024-11-02 20:26:28' _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 5hvf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":505}' # _entry.id 5HVF # _exptl.entry_id 5HVF _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-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 5HVF _cell.length_a 51.29 _cell.length_b 69.978 _cell.length_c 165.337 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HVF _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 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 _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 ? 4 D N N ? 4 E N N ? 4 F N 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 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 # 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 C 1 NAG A 522 NAG 3 n C NAG 2 C 2 NAG A 523 NAG 3 n C BMA 3 C 3 BMA A 524 BMA 3 n C MAN 4 C 4 MAN A 525 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 156 A CYS 156 1_555 A SG CYS 169 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 228 A CYS 228 1_555 A SG CYS 252 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 243 A CYS 243 1_555 A SG CYS 257 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf4 B SG CYS 22 B CYS 22 1_555 B SG CYS 94 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? covale ? covale1 A ND2 ASN 22 A ASN 22 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale2 A ND2 ASN 51 A ASN 51 1_555 D C1 NAG . A NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A ND2 ASN 63 A ASN 63 1_555 E C1 NAG . A NAG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale4 A ND2 ASN 86 A ASN 86 1_555 F C1 NAG . A NAG 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale5 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale6 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.418 ? covale ? covale7 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? metalc ? metalc1 A ND1 HIS 159 A HIS 159 1_555 G ZN ZN . A ZN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc2 A OE1 GLU 162 A GLU 162 1_555 G ZN ZN . A ZN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc3 A OE2 GLU 162 A GLU 162 1_555 G ZN ZN . A ZN 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc4 G ZN ZN . A ZN 508 1_555 H OA1 FLC . A FLC 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? # _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 302 n n C1 O1 NAG sing 303 n n C1 O5 NAG sing 304 n n C1 H1 NAG sing 305 n n C2 C3 NAG sing 306 n n C2 N2 NAG sing 307 n n C2 H2 NAG sing 308 n n C3 C4 NAG sing 309 n n C3 O3 NAG sing 310 n n C3 H3 NAG sing 311 n n C4 C5 NAG sing 312 n n C4 O4 NAG sing 313 n n C4 H4 NAG sing 314 n n C5 C6 NAG sing 315 n n C5 O5 NAG sing 316 n n C5 H5 NAG sing 317 n n C6 O6 NAG sing 318 n n C6 H61 NAG sing 319 n n C6 H62 NAG sing 320 n n C7 C8 NAG sing 321 n n C7 N2 NAG sing 322 n n C7 O7 NAG doub 323 n n C8 H81 NAG sing 324 n n C8 H82 NAG sing 325 n n C8 H83 NAG sing 326 n n N2 HN2 NAG sing 327 n n O1 HO1 NAG sing 328 n n O3 HO3 NAG sing 329 n n O4 HO4 NAG sing 330 n n O6 HO6 NAG sing 331 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 5HVF _atom_sites.fract_transf_matrix[1][1] 0.019497 _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] 0.01429 _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] 0.006048 _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 NAG A 1 505 551 NAG NAG . E 4 NAG A 1 506 563 NAG NAG . F 4 NAG A 1 507 586 NAG NAG . G 5 ZN A 1 508 1 ZN ZN . H 6 FLC A 1 509 1 FLC FLC . I 7 HOH A 1 601 9 HOH HOH . I 7 HOH A 2 602 13 HOH HOH . I 7 HOH A 3 603 2 HOH HOH . I 7 HOH A 4 604 4 HOH HOH . I 7 HOH A 5 605 5 HOH HOH . I 7 HOH A 6 606 30 HOH HOH . I 7 HOH A 7 607 15 HOH HOH . I 7 HOH A 8 608 10 HOH HOH . I 7 HOH A 9 609 33 HOH HOH . I 7 HOH A 10 610 19 HOH HOH . I 7 HOH A 11 611 7 HOH HOH . I 7 HOH A 12 612 16 HOH HOH . I 7 HOH A 13 613 21 HOH HOH . I 7 HOH A 14 614 26 HOH HOH . I 7 HOH A 15 615 24 HOH HOH . I 7 HOH A 16 616 14 HOH HOH . I 7 HOH A 17 617 20 HOH HOH . I 7 HOH A 18 618 27 HOH HOH . I 7 HOH A 19 619 8 HOH HOH . I 7 HOH A 20 620 29 HOH HOH . J 7 HOH B 1 201 1 HOH HOH . J 7 HOH B 2 202 22 HOH HOH . J 7 HOH B 3 203 6 HOH HOH . J 7 HOH B 4 204 11 HOH HOH . J 7 HOH B 5 205 17 HOH HOH . J 7 HOH B 6 206 32 HOH HOH . J 7 HOH B 7 207 18 HOH HOH . J 7 HOH B 8 208 12 HOH HOH . J 7 HOH B 9 209 25 HOH HOH . J 7 HOH B 10 210 28 HOH HOH . J 7 HOH B 11 211 23 HOH HOH . J 7 HOH B 12 212 3 HOH HOH . J 7 HOH B 13 213 31 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 . . . D 4 -23.601 -16.616 27.292 1 118.77 ? C1 NAG 505 A 1 HETATM 2 C C2 NAG . . . D 4 -23.308 -17.917 26.541 1 121.98 ? C2 NAG 505 A 1 HETATM 3 C C3 NAG . . . D 4 -24.666 -18.389 26.008 1 122.87 ? C3 NAG 505 A 1 HETATM 4 C C4 NAG . . . D 4 -25.695 -18.511 27.131 1 125.01 ? C4 NAG 505 A 1 HETATM 5 C C5 NAG . . . D 4 -25.813 -17.196 27.908 1 123.82 ? C5 NAG 505 A 1 HETATM 6 C C6 NAG . . . D 4 -26.721 -17.268 29.12 1 123.34 ? C6 NAG 505 A 1 HETATM 7 C C7 NAG . . . D 4 -21.681 -18.501 24.749 1 124.38 ? C7 NAG 505 A 1 HETATM 8 C C8 NAG . . . D 4 -20.671 -17.936 23.795 1 123.39 ? C8 NAG 505 A 1 HETATM 9 N N2 NAG . . . D 4 -22.404 -17.597 25.442 1 123.62 ? N2 NAG 505 A 1 HETATM 10 O O3 NAG . . . D 4 -24.532 -19.641 25.341 1 122.26 ? O3 NAG 505 A 1 HETATM 11 O O4 NAG . . . D 4 -26.962 -18.845 26.567 1 127.7 ? O4 NAG 505 A 1 HETATM 12 O O5 NAG . . . D 4 -24.514 -16.793 28.375 1 121.14 ? O5 NAG 505 A 1 HETATM 13 O O6 NAG . . . D 4 -28.097 -17.32 28.75 1 122.46 ? O6 NAG 505 A 1 HETATM 14 O O7 NAG . . . D 4 -21.833 -19.712 24.889 1 125.51 ? O7 NAG 505 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #