data_2RIP # _model_server_result.job_id oE0C92xW22f7SLr5BgXiTw _model_server_result.datetime_utc '2024-11-21 17:36:53' _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 2rip # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1219}' # _entry.id 2RIP # _exptl.entry_id 2RIP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _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 4 _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 2RIP _cell.length_a 69.22 _cell.length_b 69.22 _cell.length_c 409.22 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RIP _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 8_775 -y+2,-x+2,-z+1/2 0 -1 0 -1 0 0 0 0 -1 138.44 138.44 204.61 # 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 ? 4 G N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN MAN C1 O1 . O6 HO6 . sing 4 ? 3 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 2 n B NAG 1 B 1 NAG C 1085 NAG 2 n B NAG 2 B 2 NAG C 2085 NAG 2 n B MAN 3 B 3 MAN C 3085 MAN 2 n B MAN 4 B 4 MAN C 4085 MAN 3 n C NAG 1 C 1 NAG D 150 NAG 3 n C NAG 2 C 2 NAG D 2150 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 291 A CYS 328 1_555 A SG CYS 302 A CYS 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 A SG CYS 348 A CYS 385 1_555 A SG CYS 357 A CYS 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf3 A SG CYS 407 A CYS 444 1_555 A SG CYS 410 A CYS 447 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? covale ? covale1 A ND2 ASN 48 A ASN 85 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale2 A ND2 ASN 113 A ASN 150 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale3 A ND2 ASN 182 A ASN 219 1_555 D C1 NAG . A NAG 1219 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale4 A ND2 ASN 192 A ASN 229 1_555 E C1 NAG . A NAG 1229 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 A ND2 ASN 244 A ASN 281 1_555 F C1 NAG . A NAG 1281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale6 A ND2 ASN 284 A ASN 321 1_555 G C1 NAG . A NAG 1321 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale7 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale8 B O4 NAG . B NAG 2 1_555 B C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale9 B O6 MAN . B MAN 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale10 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 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 310 n n C1 O1 NAG sing 311 n n C1 O5 NAG sing 312 n n C1 H1 NAG sing 313 n n C2 C3 NAG sing 314 n n C2 N2 NAG sing 315 n n C2 H2 NAG sing 316 n n C3 C4 NAG sing 317 n n C3 O3 NAG sing 318 n n C3 H3 NAG sing 319 n n C4 C5 NAG sing 320 n n C4 O4 NAG sing 321 n n C4 H4 NAG sing 322 n n C5 C6 NAG sing 323 n n C5 O5 NAG sing 324 n n C5 H5 NAG sing 325 n n C6 O6 NAG sing 326 n n C6 H61 NAG sing 327 n n C6 H62 NAG sing 328 n n C7 C8 NAG sing 329 n n C7 N2 NAG sing 330 n n C7 O7 NAG doub 331 n n C8 H81 NAG sing 332 n n C8 H82 NAG sing 333 n n C8 H83 NAG sing 334 n n N2 HN2 NAG sing 335 n n O1 HO1 NAG sing 336 n n O3 HO3 NAG sing 337 n n O4 HO4 NAG sing 338 n n O6 HO6 NAG sing 339 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 2RIP _atom_sites.fract_transf_matrix[1][1] 0.014447 _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] 0.014447 _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] 0.002444 _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 1219 1219 NAG NAG . E 4 NAG A 1 1229 1229 NAG NAG . F 4 NAG A 1 1281 1281 NAG NAG . G 4 NAG A 1 1321 1321 NAG NAG . H 5 34Q A 1 800 800 34Q 34Q . I 6 HOH A 1 1 1 HOH HOH . I 6 HOH A 2 2 2 HOH HOH . I 6 HOH A 3 3 3 HOH HOH . I 6 HOH A 4 4 4 HOH HOH . I 6 HOH A 5 5 5 HOH HOH . I 6 HOH A 6 6 6 HOH HOH . I 6 HOH A 7 7 7 HOH HOH . I 6 HOH A 8 8 8 HOH HOH . I 6 HOH A 9 9 9 HOH HOH . I 6 HOH A 10 10 10 HOH HOH . I 6 HOH A 11 11 11 HOH HOH . I 6 HOH A 12 12 12 HOH HOH . I 6 HOH A 13 13 13 HOH HOH . I 6 HOH A 14 14 14 HOH HOH . I 6 HOH A 15 15 15 HOH HOH . I 6 HOH A 16 16 16 HOH HOH . I 6 HOH A 17 17 17 HOH HOH . I 6 HOH A 18 18 18 HOH HOH . I 6 HOH A 19 19 19 HOH HOH . I 6 HOH A 20 20 20 HOH HOH . I 6 HOH A 21 21 21 HOH HOH . I 6 HOH A 22 22 22 HOH HOH . I 6 HOH A 23 23 23 HOH HOH . I 6 HOH A 24 24 24 HOH HOH . I 6 HOH A 25 25 25 HOH HOH . I 6 HOH A 26 26 26 HOH HOH . I 6 HOH A 27 27 27 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 44.429 69.587 57.028 1 64.43 ? C1 NAG 1219 A 1 HETATM 2 C C2 NAG . . . D 4 43.962 70.812 56.218 1 66.44 ? C2 NAG 1219 A 1 HETATM 3 C C3 NAG . . . D 4 42.782 71.519 56.9 1 66.95 ? C3 NAG 1219 A 1 HETATM 4 C C4 NAG . . . D 4 41.687 70.501 57.234 1 67.26 ? C4 NAG 1219 A 1 HETATM 5 C C5 NAG . . . D 4 42.303 69.389 58.107 1 66.26 ? C5 NAG 1219 A 1 HETATM 6 C C6 NAG . . . D 4 41.281 68.354 58.562 1 65.45 ? C6 NAG 1219 A 1 HETATM 7 C C7 NAG . . . D 4 45.91 71.604 54.963 1 66.74 ? C7 NAG 1219 A 1 HETATM 8 C C8 NAG . . . D 4 45.884 72.688 53.917 1 66.85 ? C8 NAG 1219 A 1 HETATM 9 N N2 NAG . . . D 4 45.066 71.736 55.992 1 66.54 ? N2 NAG 1219 A 1 HETATM 10 O O3 NAG . . . D 4 42.26 72.558 56.096 1 67.38 ? O3 NAG 1219 A 1 HETATM 11 O O4 NAG . . . D 4 40.583 71.148 57.851 1 67.87 ? O4 NAG 1219 A 1 HETATM 12 O O5 NAG . . . D 4 43.347 68.734 57.395 1 65.56 ? O5 NAG 1219 A 1 HETATM 13 O O6 NAG . . . D 4 40.682 68.834 59.74 1 64.13 ? O6 NAG 1219 A 1 HETATM 14 O O7 NAG . . . D 4 46.68 70.648 54.854 1 66.24 ? O7 NAG 1219 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #