data_8TP6 # _model_server_result.job_id GHwdzkgmvRtw7r85QXckdQ _model_server_result.datetime_utc '2024-10-25 20:37:09' _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 8tp6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":501}' # _entry.id 8TP6 # _exptl.entry_id 8TP6 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 9 _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 8TP6 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8TP6 _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 nonameric _pdbx_struct_assembly.oligomeric_count 9 _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 ? _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 ? 6 P N N ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T N N ? 6 U N N ? 6 V N N ? 6 W N N ? 6 X N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 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 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 1 FUC NAG C1 O1 . O6 HO6 . sing 4 ? 5 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 4 n J NAG 1 K 1 NAG A 496 NAG 4 n J NAG 2 K 2 NAG A 497 NAG 4 n J BMA 3 K 3 BMA A 499 BMA 4 n J FUC 4 K 4 FUC A 498 FUC 5 n K NAG 1 P 1 NAG A 500 NAG 5 n K NAG 2 P 2 NAG A 501 NAG 4 n L NAG 1 U 1 NAG B 496 NAG 4 n L NAG 2 U 2 NAG B 497 NAG 4 n L BMA 3 U 3 BMA B 499 BMA 4 n L FUC 4 U 4 FUC B 498 FUC 5 n M NAG 1 Y 1 NAG B 500 NAG 5 n M NAG 2 Y 2 NAG B 501 NAG 4 n N NAG 1 d 1 NAG E 496 NAG 4 n N NAG 2 d 2 NAG E 497 NAG 4 n N BMA 3 d 3 BMA E 499 BMA 4 n N FUC 4 d 4 FUC E 498 FUC 5 n O NAG 1 h 1 NAG E 500 NAG 5 n O NAG 2 h 2 NAG E 501 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 19 A CYS 14 1_555 A SG CYS 477 A CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 57 A CYS 52 1_555 A SG CYS 288 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 A SG CYS 70 A CYS 64 1_555 A SG CYS 82 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf4 A SG CYS 105 A CYS 97 1_555 A SG CYS 149 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 A SG CYS 292 A CYS 281 1_555 A SG CYS 316 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 A SG CYS 484 A CYS 473 1_555 A SG CYS 488 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf7 B SG CYS 22 H CYS 22 1_555 B SG CYS 97 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 C SG CYS 23 L CYS 23 1_555 C SG CYS 88 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf9 D SG CYS 19 B CYS 14 1_555 D SG CYS 477 B CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 D SG CYS 57 B CYS 52 1_555 D SG CYS 288 B CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 D SG CYS 70 B CYS 64 1_555 D SG CYS 82 B CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf12 D SG CYS 105 B CYS 97 1_555 D SG CYS 149 B CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 D SG CYS 292 B CYS 281 1_555 D SG CYS 316 B CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf14 D SG CYS 484 B CYS 473 1_555 D SG CYS 488 B CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf15 E SG CYS 22 C CYS 22 1_555 E SG CYS 97 C CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf16 F SG CYS 23 D CYS 23 1_555 F SG CYS 88 D CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf17 G SG CYS 19 E CYS 14 1_555 G SG CYS 477 E CYS 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf18 G SG CYS 57 E CYS 52 1_555 G SG CYS 288 E CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf19 G SG CYS 70 E CYS 64 1_555 G SG CYS 82 E CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf20 G SG CYS 105 E CYS 97 1_555 G SG CYS 149 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 G SG CYS 292 E CYS 281 1_555 G SG CYS 316 E CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf22 G SG CYS 484 E CYS 473 1_555 G SG CYS 488 E CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf23 H SG CYS 22 F CYS 22 1_555 H SG CYS 97 F CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf24 I SG CYS 23 G CYS 23 1_555 I SG CYS 88 G CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? covale ? covale1 A ND2 ASN 26 A ASN 21 1_555 P C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale2 A ND2 ASN 38 A ASN 33 1_555 Q C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale3 A ND2 ASN 179 A ASN 169 1_555 J C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale4 A ND2 ASN 300 A ASN 289 1_555 K C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale5 A ND2 ASN 494 A ASN 483 1_555 R C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale6 D ND2 ASN 26 B ASN 21 1_555 S C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale7 D ND2 ASN 38 B ASN 33 1_555 T C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale8 D ND2 ASN 179 B ASN 169 1_555 L C1 NAG . U NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.515 ? covale ? covale9 D ND2 ASN 300 B ASN 289 1_555 M C1 NAG . Y NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale10 D ND2 ASN 494 B ASN 483 1_555 U C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.518 ? covale ? covale11 G ND2 ASN 26 E ASN 21 1_555 V C1 NAG . E NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.525 ? covale ? covale12 G ND2 ASN 38 E ASN 33 1_555 W C1 NAG . E NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.526 ? covale ? covale13 G ND2 ASN 179 E ASN 169 1_555 N C1 NAG . d NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale14 G ND2 ASN 300 E ASN 289 1_555 O C1 NAG . h NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale15 G ND2 ASN 494 E ASN 483 1_555 X C1 NAG . E NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.518 ? covale ? covale16 J O4 NAG . K NAG 1 1_555 J C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? covale ? covale17 J O6 NAG . K NAG 1 1_555 J C1 FUC . K FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.486 ? covale ? covale18 J O4 NAG . K NAG 2 1_555 J C1 BMA . K BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale19 K O4 NAG . P NAG 1 1_555 K C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.52 ? covale ? covale20 L O4 NAG . U NAG 1 1_555 L C1 NAG . U NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.507 ? covale ? covale21 L O6 NAG . U NAG 1 1_555 L C1 FUC . U FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.486 ? covale ? covale22 L O4 NAG . U NAG 2 1_555 L C1 BMA . U BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? covale ? covale23 M O4 NAG . Y NAG 1 1_555 M C1 NAG . Y NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.52 ? covale ? covale24 N O4 NAG . d NAG 1 1_555 N C1 NAG . d NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.508 ? covale ? covale25 N O6 NAG . d NAG 1 1_555 N C1 FUC . d FUC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.486 ? covale ? covale26 N O4 NAG . d NAG 2 1_555 N C1 BMA . d BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.51 ? covale ? covale27 O O4 NAG . h NAG 1 1_555 O C1 NAG . h NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.52 ? # _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 282 n n C1 O1 NAG sing 283 n n C1 O5 NAG sing 284 n n C1 H1 NAG sing 285 n n C2 C3 NAG sing 286 n n C2 N2 NAG sing 287 n n C2 H2 NAG sing 288 n n C3 C4 NAG sing 289 n n C3 O3 NAG sing 290 n n C3 H3 NAG sing 291 n n C4 C5 NAG sing 292 n n C4 O4 NAG sing 293 n n C4 H4 NAG sing 294 n n C5 C6 NAG sing 295 n n C5 O5 NAG sing 296 n n C5 H5 NAG sing 297 n n C6 O6 NAG sing 298 n n C6 H61 NAG sing 299 n n C6 H62 NAG sing 300 n n C7 C8 NAG sing 301 n n C7 N2 NAG sing 302 n n C7 O7 NAG doub 303 n n C8 H81 NAG sing 304 n n C8 H82 NAG sing 305 n n C8 H83 NAG sing 306 n n N2 HN2 NAG sing 307 n n O1 HO1 NAG sing 308 n n O3 HO3 NAG sing 309 n n O4 HO4 NAG sing 310 n n O6 HO6 NAG sing 311 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 8TP6 _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 P 6 NAG A 1 501 494 NAG NAG . Q 6 NAG A 1 502 495 NAG NAG . R 6 NAG A 1 503 502 NAG NAG . S 6 NAG B 1 501 494 NAG NAG . T 6 NAG B 1 502 495 NAG NAG . U 6 NAG B 1 503 502 NAG NAG . V 6 NAG E 1 501 494 NAG NAG . W 6 NAG E 1 502 495 NAG NAG . X 6 NAG E 1 503 502 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 6 170.363 154.449 156.327 1 73.67 ? C1 NAG 501 E 1 HETATM 2 C C2 NAG . . . V 6 171.814 153.861 155.981 1 74.86 ? C2 NAG 501 E 1 HETATM 3 C C3 NAG . . . V 6 171.675 152.835 154.801 1 76.88 ? C3 NAG 501 E 1 HETATM 4 C C4 NAG . . . V 6 170.664 151.701 155.177 1 80.53 ? C4 NAG 501 E 1 HETATM 5 C C5 NAG . . . V 6 169.272 152.354 155.495 1 81.37 ? C5 NAG 501 E 1 HETATM 6 C C6 NAG . . . V 6 168.207 151.336 155.922 1 86.23 ? C6 NAG 501 E 1 HETATM 7 C C7 NAG . . . V 6 173.583 155.62 156.259 1 65.57 ? C7 NAG 501 E 1 HETATM 8 C C8 NAG . . . V 6 174.396 156.719 155.641 1 61.38 ? C8 NAG 501 E 1 HETATM 9 N N2 NAG . . . V 6 172.69 154.969 155.501 1 72.58 ? N2 NAG 501 E 1 HETATM 10 O O3 NAG . . . V 6 172.964 152.243 154.537 1 75.22 ? O3 NAG 501 E 1 HETATM 11 O O4 NAG . . . V 6 170.541 150.786 154.085 1 80.61 ? O4 NAG 501 E 1 HETATM 12 O O5 NAG . . . V 6 169.44 153.33 156.609 1 76.43 ? O5 NAG 501 E 1 HETATM 13 O O6 NAG . . . V 6 166.899 151.904 155.904 1 85.04 ? O6 NAG 501 E 1 HETATM 14 O O7 NAG . . . V 6 173.752 155.336 157.454 1 63.95 ? O7 NAG 501 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 339 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #