data_2GAZ # _model_server_result.job_id IAtvbU5H3EBp7z5aKCdsSA _model_server_result.datetime_utc '2024-11-02 05:25:04' _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 2gaz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 2GAZ # _exptl.entry_id 2GAZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details '2,6-(Di-O- -D-mannopyranosyl)-1-O-(1,2-di-O-palmitoyl-sn-glycero-3-phosphoryl)-D-myo-inositol' _entity.formula_weight 221.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 2GAZ _cell.length_a 41.835 _cell.length_b 110.757 _cell.length_c 107.396 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GAZ _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 _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 # _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 4 ? 3 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 3 n C NAG 1 C 1 NAG E 520 NAG 3 n C NAG 2 C 2 NAG E 521 NAG 3 n C BMA 3 C 3 BMA E 522 MAN 3 n C MAN 4 C 4 MAN E 523 MAN 3 n C MAN 5 C 5 MAN E 524 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 104 A CYS 104 1_555 A SG CYS 168 A CYS 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? disulf ? disulf2 A SG CYS 208 A CYS 208 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 B SG CYS 25 B CYS 25 1_555 B SG CYS 80 B CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? covale ? covale1 A ND2 ASN 20 A ASN 20 1_555 D C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 42 A ASN 42 1_555 E C1 NAG . A NAG 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 A ND2 ASN 165 A ASN 165 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale6 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale7 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? # _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 285 n n C1 O1 NAG sing 286 n n C1 O5 NAG sing 287 n n C1 H1 NAG sing 288 n n C2 C3 NAG sing 289 n n C2 N2 NAG sing 290 n n C2 H2 NAG sing 291 n n C3 C4 NAG sing 292 n n C3 O3 NAG sing 293 n n C3 H3 NAG sing 294 n n C4 C5 NAG sing 295 n n C4 O4 NAG sing 296 n n C4 H4 NAG sing 297 n n C5 C6 NAG sing 298 n n C5 O5 NAG sing 299 n n C5 H5 NAG sing 300 n n C6 O6 NAG sing 301 n n C6 H61 NAG sing 302 n n C6 H62 NAG sing 303 n n C7 C8 NAG sing 304 n n C7 N2 NAG sing 305 n n C7 O7 NAG doub 306 n n C8 H81 NAG sing 307 n n C8 H82 NAG sing 308 n n C8 H83 NAG sing 309 n n N2 HN2 NAG sing 310 n n O1 HO1 NAG sing 311 n n O3 HO3 NAG sing 312 n n O4 HO4 NAG sing 313 n n O6 HO6 NAG sing 314 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 2GAZ _atom_sites.fract_transf_matrix[1][1] 0.023903 _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] 0.009029 _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] 0.009311 _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 1 501 501 NAG NAG . E 4 NAG A 1 510 510 NAG NAG . F 5 XPX A 1 525 1 XPX XPX . G 6 HOH A 1 526 1 HOH HOH . G 6 HOH A 2 527 2 HOH HOH . G 6 HOH A 3 528 5 HOH HOH . G 6 HOH A 4 529 6 HOH HOH . G 6 HOH A 5 530 7 HOH HOH . G 6 HOH A 6 531 10 HOH HOH . G 6 HOH A 7 532 11 HOH HOH . G 6 HOH A 8 533 12 HOH HOH . G 6 HOH A 9 534 14 HOH HOH . G 6 HOH A 10 535 15 HOH HOH . G 6 HOH A 11 536 16 HOH HOH . G 6 HOH A 12 537 19 HOH HOH . G 6 HOH A 13 538 20 HOH HOH . G 6 HOH A 14 539 22 HOH HOH . G 6 HOH A 15 540 24 HOH HOH . G 6 HOH A 16 541 25 HOH HOH . G 6 HOH A 17 542 27 HOH HOH . G 6 HOH A 18 543 29 HOH HOH . G 6 HOH A 19 544 32 HOH HOH . G 6 HOH A 20 545 34 HOH HOH . G 6 HOH A 21 546 36 HOH HOH . G 6 HOH A 22 547 37 HOH HOH . G 6 HOH A 23 548 42 HOH HOH . G 6 HOH A 24 549 43 HOH HOH . G 6 HOH A 25 550 44 HOH HOH . G 6 HOH A 26 551 45 HOH HOH . G 6 HOH A 27 552 46 HOH HOH . G 6 HOH A 28 553 48 HOH HOH . G 6 HOH A 29 554 49 HOH HOH . G 6 HOH A 30 555 50 HOH HOH . G 6 HOH A 31 556 54 HOH HOH . G 6 HOH A 32 557 58 HOH HOH . H 6 HOH B 1 100 3 HOH HOH . H 6 HOH B 2 101 4 HOH HOH . H 6 HOH B 3 102 8 HOH HOH . H 6 HOH B 4 103 9 HOH HOH . H 6 HOH B 5 104 23 HOH HOH . H 6 HOH B 6 105 26 HOH HOH . H 6 HOH B 7 106 28 HOH HOH . H 6 HOH B 8 107 30 HOH HOH . H 6 HOH B 9 108 35 HOH HOH . H 6 HOH B 10 109 38 HOH HOH . H 6 HOH B 11 110 47 HOH HOH . H 6 HOH B 12 111 52 HOH HOH . H 6 HOH B 13 112 59 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 3.011 -21.631 6.724 1 53.47 ? C1 NAG 501 A 1 HETATM 2 C C2 NAG . . . D 4 3.131 -22.792 5.73 1 55.93 ? C2 NAG 501 A 1 HETATM 3 C C3 NAG . . . D 4 4.623 -23.084 5.481 1 56.94 ? C3 NAG 501 A 1 HETATM 4 C C4 NAG . . . D 4 5.284 -21.877 4.795 1 56.7 ? C4 NAG 501 A 1 HETATM 5 C C5 NAG . . . D 4 4.953 -20.574 5.553 1 56.61 ? C5 NAG 501 A 1 HETATM 6 C C6 NAG . . . D 4 5.135 -19.404 4.576 1 57.45 ? C6 NAG 501 A 1 HETATM 7 C C7 NAG . . . D 4 1.474 -24.578 5.298 1 55.51 ? C7 NAG 501 A 1 HETATM 8 C C8 NAG . . . D 4 1.825 -25.954 4.784 1 55.84 ? C8 NAG 501 A 1 HETATM 9 N N2 NAG . . . D 4 2.365 -23.985 6.113 1 55.82 ? N2 NAG 501 A 1 HETATM 10 O O3 NAG . . . D 4 4.773 -24.244 4.687 1 57.48 ? O3 NAG 501 A 1 HETATM 11 O O4 NAG . . . D 4 6.69 -22.065 4.6 1 55.05 ? O4 NAG 501 A 1 HETATM 12 O O5 NAG . . . D 4 3.627 -20.497 6.11 1 54.88 ? O5 NAG 501 A 1 HETATM 13 O O6 NAG . . . D 4 5.681 -18.262 5.214 1 57.37 ? O6 NAG 501 A 1 HETATM 14 O O7 NAG . . . D 4 0.407 -24.053 4.963 1 53.16 ? O7 NAG 501 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #