data_6NMY # _model_server_result.job_id jJmeulFcfIM_IiknCnOwDg _model_server_result.datetime_utc '2024-11-05 04:00:22' _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 6nmy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":301}' # _entry.id 6NMY # _exptl.entry_id 6NMY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 8 _entity.src_method nat _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 90 _cell.entry_id 6NMY _cell.length_a 111.647 _cell.length_b 157.251 _cell.length_c 168.306 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NMY _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 ? tetrameric 4 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,F,G,I,J,K,N,Q,S,V,W 1 1 B,D,E,H,L,M,O,P,R,T,U,X 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 # _struct_asym.details ? _struct_asym.entity_id 8 _struct_asym.id P _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 5 oligosaccharide 6 oligosaccharide 7 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 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 5 4 1 FUC NAG C1 O1 . O6 HO6 . sing 4 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 5 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 6 ? 7 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 5 n I NAG 1 E 1 NAG F 402 NAG 5 n I NAG 2 E 2 NAG F 403 NAG 5 n I BMA 3 E 3 BMA F 404 BMA 5 n I FUC 4 E 4 FUC F 401 FUC 5 n J NAG 1 G 1 NAG F 406 NAG 5 n J NAG 2 G 2 NAG F 407 NAG 5 n J BMA 3 G 3 BMA F 408 BMA 5 n J FUC 4 G 4 FUC F 405 FUC 6 n K NAG 1 H 1 NAG F 409 NAG 6 n K NAG 2 H 2 NAG F 410 NAG 6 n K BMA 3 H 3 BMA F 411 BMA 6 n L NAG 1 K 1 NAG M 401 NAG 6 n L NAG 2 K 2 NAG M 402 NAG 6 n L BMA 3 K 3 BMA M 403 BMA 7 n M NAG 1 L 1 NAG M 404 NAG 7 n M NAG 2 L 2 NAG M 405 NAG 6 n N NAG 1 N 1 NAG A 500 NAG 6 n N NAG 2 N 2 NAG A 501 NAG 6 n N BMA 3 N 3 BMA A 502 BMA 7 n O NAG 1 O 1 NAG C 301 NAG 7 n O NAG 2 O 2 NAG C 401 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 33 F CYS 52 1_555 A SG CYS 49 F CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 57 F CYS 76 1_555 A SG CYS 176 F CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 93 F CYS 112 1_555 A SG CYS 103 F CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 132 F CYS 151 1_555 A SG CYS 146 F CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 198 F CYS 217 1_555 A SG CYS 274 F CYS 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 B SG CYS 33 M CYS 52 1_555 B SG CYS 49 M CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 57 M CYS 76 1_555 B SG CYS 176 M CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 B SG CYS 93 M CYS 112 1_555 B SG CYS 103 M CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf9 B SG CYS 132 M CYS 151 1_555 B SG CYS 146 M CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 B SG CYS 198 M CYS 217 1_555 B SG CYS 274 M CYS 293 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf11 C SG CYS 11 A CYS 35 1_555 C SG CYS 21 A CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 C SG CYS 51 A CYS 75 1_555 C SG CYS 72 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf13 C SG CYS 62 A CYS 86 1_555 C SG CYS 67 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf14 D SG CYS 11 C CYS 35 1_555 D SG CYS 21 C CYS 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 D SG CYS 51 C CYS 75 1_555 D SG CYS 72 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf16 D SG CYS 62 C CYS 86 1_555 D SG CYS 67 C CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf17 E SG CYS 9 I CYS 16 1_555 E SG CYS 77 I CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf18 F SG CYS 9 J CYS 16 1_555 F SG CYS 77 J CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf19 G SG CYS 10 B CYS 250 1_555 G SG CYS 20 B CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf20 G SG CYS 49 B CYS 289 1_555 G SG CYS 66 B CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf21 H SG CYS 10 D CYS 250 1_555 H SG CYS 20 D CYS 260 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf22 H SG CYS 49 D CYS 289 1_555 H SG CYS 66 D CYS 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 45 F ASN 64 1_555 K C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale2 A ND2 ASN 61 F ASN 80 1_555 I C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 199 F ASN 218 1_555 J C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale4 B ND2 ASN 61 M ASN 80 1_555 M C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale5 B ND2 ASN 199 M ASN 218 1_555 L C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 C ND2 ASN 34 A ASN 58 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale7 D ND2 ASN 34 C ASN 58 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale8 D ND2 ASN 167 C ASN 191 1_555 P C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale9 I O4 NAG . E NAG 1 1_555 I C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale10 I O6 NAG . E NAG 1 1_555 I C1 FUC . E FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale11 I O4 NAG . E NAG 2 1_555 I C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale12 J O4 NAG . G NAG 1 1_555 J C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale13 J O6 NAG . G NAG 1 1_555 J C1 FUC . G FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale14 J O4 NAG . G NAG 2 1_555 J C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale15 K O4 NAG . H NAG 1 1_555 K C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale16 K O4 NAG . H NAG 2 1_555 K C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale17 L O4 NAG . K NAG 1 1_555 L C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale18 L O4 NAG . K NAG 2 1_555 L C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 M O4 NAG . L NAG 1 1_555 M C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale20 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale21 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale22 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 284 n n C1 O1 NAG sing 285 n n C1 O5 NAG sing 286 n n C1 H1 NAG sing 287 n n C2 C3 NAG sing 288 n n C2 N2 NAG sing 289 n n C2 H2 NAG sing 290 n n C3 C4 NAG sing 291 n n C3 O3 NAG sing 292 n n C3 H3 NAG sing 293 n n C4 C5 NAG sing 294 n n C4 O4 NAG sing 295 n n C4 H4 NAG sing 296 n n C5 C6 NAG sing 297 n n C5 O5 NAG sing 298 n n C5 H5 NAG sing 299 n n C6 O6 NAG sing 300 n n C6 H61 NAG sing 301 n n C6 H62 NAG sing 302 n n C7 C8 NAG sing 303 n n C7 N2 NAG sing 304 n n C7 O7 NAG doub 305 n n C8 H81 NAG sing 306 n n C8 H82 NAG sing 307 n n C8 H83 NAG sing 308 n n N2 HN2 NAG sing 309 n n O1 HO1 NAG sing 310 n n O3 HO3 NAG sing 311 n n O4 HO4 NAG sing 312 n n O6 HO6 NAG sing 313 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 6NMY _atom_sites.fract_transf_matrix[1][1] 0.008957 _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] 0.006359 _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] 0.005942 _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 P 8 NAG C 1 301 290 NAG NAG . Q 9 HOH F 1 501 10 HOH HOH . Q 9 HOH F 2 502 3 HOH HOH . R 9 HOH M 1 501 11 HOH HOH . R 9 HOH M 2 502 13 HOH HOH . S 9 HOH A 1 601 1 HOH HOH . T 9 HOH C 1 401 4 HOH HOH . U 9 HOH I 1 201 5 HOH HOH . V 9 HOH J 1 201 2 HOH HOH . V 9 HOH J 2 202 6 HOH HOH . W 9 HOH B 1 501 9 HOH HOH . W 9 HOH B 2 502 7 HOH HOH . X 9 HOH D 1 501 8 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 . . . P 8 57.365 86.445 17.07 1 131.46 ? C1 NAG 301 C 1 HETATM 2 C C2 NAG . . . P 8 58.723 86.131 16.428 1 134.41 ? C2 NAG 301 C 1 HETATM 3 C C3 NAG . . . P 8 59.743 87.214 16.776 1 132.8 ? C3 NAG 301 C 1 HETATM 4 C C4 NAG . . . P 8 59.215 88.585 16.38 1 130.48 ? C4 NAG 301 C 1 HETATM 5 C C5 NAG . . . P 8 57.861 88.835 17.035 1 127.28 ? C5 NAG 301 C 1 HETATM 6 C C6 NAG . . . P 8 57.227 90.131 16.584 1 121.71 ? C6 NAG 301 C 1 HETATM 7 C C7 NAG . . . P 8 59.72 83.935 15.971 1 126.31 ? C7 NAG 301 C 1 HETATM 8 C C8 NAG . . . P 8 60.176 82.634 16.56 1 119.12 ? C8 NAG 301 C 1 HETATM 9 N N2 NAG . . . P 8 59.209 84.821 16.832 1 132.46 ? N2 NAG 301 C 1 HETATM 10 O O3 NAG . . . P 8 60.967 86.957 16.098 1 126.93 ? O3 NAG 301 C 1 HETATM 11 O O4 NAG . . . P 8 60.13 89.597 16.785 1 126.03 ? O4 NAG 301 C 1 HETATM 12 O O5 NAG . . . P 8 56.944 87.782 16.692 1 131.7 ? O5 NAG 301 C 1 HETATM 13 O O6 NAG . . . P 8 56.013 90.394 17.275 1 116.91 ? O6 NAG 301 C 1 HETATM 14 O O7 NAG . . . P 8 59.809 84.172 14.769 1 134.58 ? O7 NAG 301 C 1 # _model_server_stats.io_time_ms 117 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #