data_6DZM # _model_server_result.job_id Rl-ZJIDPTCvEFAlUjG7ZLA _model_server_result.datetime_utc '2025-01-19 20:50:42' _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 6dzm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":701}' # _entry.id 6DZM # _exptl.entry_id 6DZM _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 6 _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 6DZM _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DZM _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_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,S,T,U,V,W,X _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 ? 7 S N N ? 7 T N N ? 7 U N N ? 7 V N N ? 7 W N N ? 7 X N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 6 4 3 MAN BMA C1 O1 . O3 HO3 . sing 5 ? 6 5 3 MAN BMA C1 O1 . O6 HO6 . 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 5 n M NAG 1 M 1 NAG A 1257 NAG 5 n M NAG 2 M 2 NAG A 1258 NAG 6 n N NAG 1 N 1 NAG D 1563 NAG 6 n N NAG 2 N 2 NAG D 1564 NAG 6 n N BMA 3 N 3 BMA D 1565 BMA 6 n N MAN 4 N 4 MAN D 1566 MAN 6 n N MAN 5 N 5 MAN D 1567 MAN 5 n O NAG 1 O 1 NAG B 1257 NAG 5 n O NAG 2 O 2 NAG B 1258 NAG 6 n P NAG 1 P 1 NAG E 1563 NAG 6 n P NAG 2 P 2 NAG E 1564 NAG 6 n P BMA 3 P 3 BMA E 1565 BMA 6 n P MAN 4 P 4 MAN E 1566 MAN 6 n P MAN 5 P 5 MAN E 1567 MAN 5 n Q NAG 1 Q 1 NAG C 1257 NAG 5 n Q NAG 2 Q 2 NAG C 1258 NAG 6 n R NAG 1 R 1 NAG F 1563 NAG 6 n R NAG 2 R 2 NAG F 1564 NAG 6 n R BMA 3 R 3 BMA F 1565 BMA 6 n R MAN 4 R 4 MAN F 1566 MAN 6 n R MAN 5 R 5 MAN F 1567 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 53 1_555 B SG CYS 108 D CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf2 A SG CYS 76 A CYS 108 1_555 A SG CYS 103 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 89 A CYS 121 1_555 A SG CYS 115 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 B SG CYS 10 D CYS 511 1_555 B SG CYS 55 D CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf5 B SG CYS 100 D CYS 601 1_555 B SG CYS 107 D CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf6 C SG CYS 23 H CYS 24 1_555 C SG CYS 88 H CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf7 D SG CYS 21 G CYS 22 1_555 D SG CYS 95 G CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 E SG CYS 21 B CYS 53 1_555 F SG CYS 108 E CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf9 E SG CYS 76 B CYS 108 1_555 E SG CYS 103 B CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf10 E SG CYS 89 B CYS 121 1_555 E SG CYS 115 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf11 F SG CYS 10 E CYS 511 1_555 F SG CYS 55 E CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf12 F SG CYS 100 E CYS 601 1_555 F SG CYS 107 E CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf13 G SG CYS 23 K CYS 24 1_555 G SG CYS 88 K CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 H SG CYS 21 I CYS 22 1_555 H SG CYS 95 I CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf15 I SG CYS 21 C CYS 53 1_555 J SG CYS 108 F CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? disulf ? disulf16 I SG CYS 76 C CYS 108 1_555 I SG CYS 103 C CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf17 I SG CYS 89 C CYS 121 1_555 I SG CYS 115 C CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf18 J SG CYS 10 F CYS 511 1_555 J SG CYS 55 F CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf19 J SG CYS 100 F CYS 601 1_555 J SG CYS 107 F CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf20 K SG CYS 23 L CYS 24 1_555 K SG CYS 88 L CYS 89 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf21 L SG CYS 21 J CYS 22 1_555 L SG CYS 95 J CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 A ND2 ASN 196 A ASN 228 1_555 S C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale2 A ND2 ASN 225 A ASN 257 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 B ND2 ASN 62 D ASN 563 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale4 B ND2 ASN 117 D ASN 618 1_555 T C1 NAG . D NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale5 E ND2 ASN 196 B ASN 228 1_555 U C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale6 E ND2 ASN 225 B ASN 257 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale7 F ND2 ASN 62 E ASN 563 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 F ND2 ASN 117 E ASN 618 1_555 V C1 NAG . E NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale9 I ND2 ASN 196 C ASN 228 1_555 W C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale10 I ND2 ASN 225 C ASN 257 1_555 Q C1 NAG . Q NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale11 J ND2 ASN 62 F ASN 563 1_555 R C1 NAG . R NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale12 J ND2 ASN 117 F ASN 618 1_555 X C1 NAG . F NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale13 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale14 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale15 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 N O3 BMA . N BMA 3 1_555 N C1 MAN . N MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale17 N O6 BMA . N BMA 3 1_555 N C1 MAN . N MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale18 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale19 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale20 P O4 NAG . P NAG 2 1_555 P C1 BMA . P BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale21 P O3 BMA . P BMA 3 1_555 P C1 MAN . P MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale22 P O6 BMA . P BMA 3 1_555 P C1 MAN . P MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale23 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale24 R O4 NAG . R NAG 1 1_555 R C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale25 R O4 NAG . R NAG 2 1_555 R C1 BMA . R BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale26 R O3 BMA . R BMA 3 1_555 R C1 MAN . R MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale27 R O6 BMA . R BMA 3 1_555 R C1 MAN . R MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 283 n n C1 O1 NAG sing 284 n n C1 O5 NAG sing 285 n n C1 H1 NAG sing 286 n n C2 C3 NAG sing 287 n n C2 N2 NAG sing 288 n n C2 H2 NAG sing 289 n n C3 C4 NAG sing 290 n n C3 O3 NAG sing 291 n n C3 H3 NAG sing 292 n n C4 C5 NAG sing 293 n n C4 O4 NAG sing 294 n n C4 H4 NAG sing 295 n n C5 C6 NAG sing 296 n n C5 O5 NAG sing 297 n n C5 H5 NAG sing 298 n n C6 O6 NAG sing 299 n n C6 H61 NAG sing 300 n n C6 H62 NAG sing 301 n n C7 C8 NAG sing 302 n n C7 N2 NAG sing 303 n n C7 O7 NAG doub 304 n n C8 H81 NAG sing 305 n n C8 H82 NAG sing 306 n n C8 H83 NAG sing 307 n n N2 HN2 NAG sing 308 n n O1 HO1 NAG sing 309 n n O3 HO3 NAG sing 310 n n O4 HO4 NAG sing 311 n n O6 HO6 NAG sing 312 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 6DZM _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 S 7 NAG A 1 403 1228 NAG NAG . T 7 NAG D 1 701 1618 NAG NAG . U 7 NAG B 1 403 1228 NAG NAG . V 7 NAG E 1 701 1618 NAG NAG . W 7 NAG C 1 403 1228 NAG NAG . X 7 NAG F 1 701 1618 NAG NAG . # 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 . . . V 7 217.457 203.931 161.748 1 266.68 ? C1 NAG 701 E 1 HETATM 2 C C2 NAG . . . V 7 216.293 203.504 162.698 1 266.68 ? C2 NAG 701 E 1 HETATM 3 C C3 NAG . . . V 7 216.328 202.004 162.935 1 266.68 ? C3 NAG 701 E 1 HETATM 4 C C4 NAG . . . V 7 216.332 201.246 161.618 1 266.68 ? C4 NAG 701 E 1 HETATM 5 C C5 NAG . . . V 7 217.54 201.685 160.802 1 266.68 ? C5 NAG 701 E 1 HETATM 6 C C6 NAG . . . V 7 217.614 201.014 159.447 1 266.68 ? C6 NAG 701 E 1 HETATM 7 C C7 NAG . . . V 7 215.284 204.337 164.778 1 266.68 ? C7 NAG 701 E 1 HETATM 8 C C8 NAG . . . V 7 215.504 205.076 166.061 1 266.68 ? C8 NAG 701 E 1 HETATM 9 N N2 NAG . . . V 7 216.349 204.211 163.969 1 266.68 ? N2 NAG 701 E 1 HETATM 10 O O3 NAG . . . V 7 215.192 201.638 163.701 1 266.68 ? O3 NAG 701 E 1 HETATM 11 O O4 NAG . . . V 7 216.385 199.847 161.877 1 266.68 ? O4 NAG 701 E 1 HETATM 12 O O5 NAG . . . V 7 217.445 203.094 160.562 1 266.68 ? O5 NAG 701 E 1 HETATM 13 O O6 NAG . . . V 7 218.408 201.782 158.556 1 266.68 ? O6 NAG 701 E 1 HETATM 14 O O7 NAG . . . V 7 214.188 203.859 164.492 1 266.68 ? O7 NAG 701 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #