data_6URM # _model_server_result.job_id BmSCVOCGqs6UEhpTyVwnyA _model_server_result.datetime_utc '2024-10-19 21:36:23' _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 6urm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":601}' # _entry.id 6URM # _exptl.entry_id 6URM _exptl.method 'X-RAY DIFFRACTION' # _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 96.93 _cell.angle_gamma 90 _cell.entry_id 6URM _cell.length_a 42.408 _cell.length_b 260.836 _cell.length_c 66.453 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6URM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 5 3 2 MAN 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 G NAG 1 A 1 NAG H 501 NAG 4 n G NAG 2 A 2 NAG H 502 NAG 5 n H NAG 1 B 1 NAG D 501 NAG 5 n H NAG 2 B 2 NAG D 502 NAG 5 n H MAN 3 B 3 MAN D 503 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 55 F CYS 64 1_555 A SG CYS 67 F CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 90 F CYS 97 1_555 A SG CYS 136 F CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 97 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 149 H CYS 140 1_555 B SG CYS 205 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 22 L CYS 23 1_555 C SG CYS 87 L CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 134 L CYS 134 1_555 C SG CYS 193 L CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 D SG CYS 55 C CYS 64 1_555 D SG CYS 67 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 D SG CYS 90 C CYS 97 1_555 D SG CYS 136 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 E SG CYS 22 D CYS 22 1_555 E SG CYS 97 D CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 E SG CYS 149 D CYS 140 1_555 E SG CYS 205 D CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf11 F SG CYS 22 E CYS 23 1_555 F SG CYS 87 E CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 F SG CYS 134 E CYS 134 1_555 F SG CYS 193 E CYS 193 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 87 F ASN 94 1_555 I C1 NAG . F NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale2 B ND2 ASN 62 H ASN 60 1_555 G C1 NAG . A NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 E ND2 ASN 62 D ASN 60 1_555 H C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 G O4 NAG . A NAG 1 1_555 G C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 H O4 NAG . B NAG 1 1_555 H C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.417 ? covale ? covale6 H O4 NAG . B NAG 2 1_555 H C1 MAN . B MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? # _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 274 n n C1 O1 NAG sing 275 n n C1 O5 NAG sing 276 n n C1 H1 NAG sing 277 n n C2 C3 NAG sing 278 n n C2 N2 NAG sing 279 n n C2 H2 NAG sing 280 n n C3 C4 NAG sing 281 n n C3 O3 NAG sing 282 n n C3 H3 NAG sing 283 n n C4 C5 NAG sing 284 n n C4 O4 NAG sing 285 n n C4 H4 NAG sing 286 n n C5 C6 NAG sing 287 n n C5 O5 NAG sing 288 n n C5 H5 NAG sing 289 n n C6 O6 NAG sing 290 n n C6 H61 NAG sing 291 n n C6 H62 NAG sing 292 n n C7 C8 NAG sing 293 n n C7 N2 NAG sing 294 n n C7 O7 NAG doub 295 n n C8 H81 NAG sing 296 n n C8 H82 NAG sing 297 n n C8 H83 NAG sing 298 n n N2 HN2 NAG sing 299 n n O1 HO1 NAG sing 300 n n O3 HO3 NAG sing 301 n n O4 HO4 NAG sing 302 n n O6 HO6 NAG sing 303 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 6URM _atom_sites.fract_transf_matrix[1][1] 0.02358 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002866 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003834 _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] 0.015159 _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 I 6 NAG F 1 601 694 NAG NAG . J 7 SO4 F 1 602 3 SO4 SO4 . K 8 GOL H 1 503 3 GOL GOL . L 7 SO4 L 1 301 2 SO4 SO4 . M 8 GOL D 1 504 1 GOL GOL . N 7 SO4 D 1 505 4 SO4 SO4 . O 7 SO4 E 1 301 1 SO4 SO4 . P 9 HOH F 1 701 39 HOH HOH . P 9 HOH F 2 702 67 HOH HOH . P 9 HOH F 3 703 46 HOH HOH . P 9 HOH F 4 704 70 HOH HOH . P 9 HOH F 5 705 98 HOH HOH . P 9 HOH F 6 706 99 HOH HOH . P 9 HOH F 7 707 23 HOH HOH . P 9 HOH F 8 708 51 HOH HOH . P 9 HOH F 9 709 97 HOH HOH . P 9 HOH F 10 710 52 HOH HOH . P 9 HOH F 11 711 56 HOH HOH . P 9 HOH F 12 712 35 HOH HOH . P 9 HOH F 13 713 89 HOH HOH . P 9 HOH F 14 714 45 HOH HOH . Q 9 HOH H 1 601 101 HOH HOH . Q 9 HOH H 2 602 18 HOH HOH . Q 9 HOH H 3 603 17 HOH HOH . Q 9 HOH H 4 604 7 HOH HOH . Q 9 HOH H 5 605 48 HOH HOH . Q 9 HOH H 6 606 93 HOH HOH . Q 9 HOH H 7 607 11 HOH HOH . Q 9 HOH H 8 608 59 HOH HOH . Q 9 HOH H 9 609 74 HOH HOH . Q 9 HOH H 10 610 71 HOH HOH . Q 9 HOH H 11 611 66 HOH HOH . Q 9 HOH H 12 612 100 HOH HOH . Q 9 HOH H 13 613 75 HOH HOH . Q 9 HOH H 14 614 73 HOH HOH . Q 9 HOH H 15 615 76 HOH HOH . R 9 HOH L 1 401 40 HOH HOH . R 9 HOH L 2 402 8 HOH HOH . R 9 HOH L 3 403 24 HOH HOH . R 9 HOH L 4 404 68 HOH HOH . R 9 HOH L 5 405 43 HOH HOH . R 9 HOH L 6 406 1 HOH HOH . R 9 HOH L 7 407 63 HOH HOH . R 9 HOH L 8 408 87 HOH HOH . R 9 HOH L 9 409 2 HOH HOH . R 9 HOH L 10 410 61 HOH HOH . R 9 HOH L 11 411 33 HOH HOH . R 9 HOH L 12 412 22 HOH HOH . R 9 HOH L 13 413 12 HOH HOH . R 9 HOH L 14 414 41 HOH HOH . R 9 HOH L 15 415 13 HOH HOH . R 9 HOH L 16 416 94 HOH HOH . R 9 HOH L 17 417 49 HOH HOH . R 9 HOH L 18 418 30 HOH HOH . S 9 HOH C 1 601 21 HOH HOH . S 9 HOH C 2 602 37 HOH HOH . S 9 HOH C 3 603 10 HOH HOH . S 9 HOH C 4 604 5 HOH HOH . S 9 HOH C 5 605 65 HOH HOH . S 9 HOH C 6 606 31 HOH HOH . S 9 HOH C 7 607 54 HOH HOH . S 9 HOH C 8 608 102 HOH HOH . T 9 HOH D 1 601 104 HOH HOH . T 9 HOH D 2 602 42 HOH HOH . T 9 HOH D 3 603 38 HOH HOH . T 9 HOH D 4 604 47 HOH HOH . T 9 HOH D 5 605 90 HOH HOH . T 9 HOH D 6 606 25 HOH HOH . T 9 HOH D 7 607 53 HOH HOH . T 9 HOH D 8 608 69 HOH HOH . T 9 HOH D 9 609 36 HOH HOH . T 9 HOH D 10 610 85 HOH HOH . T 9 HOH D 11 611 79 HOH HOH . T 9 HOH D 12 612 91 HOH HOH . T 9 HOH D 13 613 15 HOH HOH . T 9 HOH D 14 614 78 HOH HOH . T 9 HOH D 15 615 3 HOH HOH . T 9 HOH D 16 616 16 HOH HOH . T 9 HOH D 17 617 62 HOH HOH . T 9 HOH D 18 618 28 HOH HOH . T 9 HOH D 19 619 82 HOH HOH . T 9 HOH D 20 620 86 HOH HOH . T 9 HOH D 21 621 103 HOH HOH . T 9 HOH D 22 622 77 HOH HOH . T 9 HOH D 23 623 92 HOH HOH . T 9 HOH D 24 624 83 HOH HOH . T 9 HOH D 25 625 80 HOH HOH . T 9 HOH D 26 626 84 HOH HOH . T 9 HOH D 27 627 60 HOH HOH . U 9 HOH E 1 401 57 HOH HOH . U 9 HOH E 2 402 27 HOH HOH . U 9 HOH E 3 403 72 HOH HOH . U 9 HOH E 4 404 95 HOH HOH . U 9 HOH E 5 405 50 HOH HOH . U 9 HOH E 6 406 64 HOH HOH . U 9 HOH E 7 407 32 HOH HOH . U 9 HOH E 8 408 20 HOH HOH . U 9 HOH E 9 409 26 HOH HOH . U 9 HOH E 10 410 19 HOH HOH . U 9 HOH E 11 411 4 HOH HOH . U 9 HOH E 12 412 14 HOH HOH . U 9 HOH E 13 413 55 HOH HOH . U 9 HOH E 14 414 6 HOH HOH . U 9 HOH E 15 415 88 HOH HOH . U 9 HOH E 16 416 96 HOH HOH . U 9 HOH E 17 417 81 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 . . . I 6 -12.381 40.452 -0.482 1 57.78 ? C1 NAG 601 F 1 HETATM 2 C C2 NAG . . . I 6 -11.366 39.621 0.318 1 65.91 ? C2 NAG 601 F 1 HETATM 3 C C3 NAG . . . I 6 -11.972 38.284 0.745 1 70.14 ? C3 NAG 601 F 1 HETATM 4 C C4 NAG . . . I 6 -13.311 38.488 1.438 1 68.43 ? C4 NAG 601 F 1 HETATM 5 C C5 NAG . . . I 6 -14.231 39.307 0.543 1 65.79 ? C5 NAG 601 F 1 HETATM 6 C C6 NAG . . . I 6 -15.564 39.613 1.184 1 67.46 ? C6 NAG 601 F 1 HETATM 7 C C7 NAG . . . I 6 -9.162 40.288 -0.542 1 75.04 ? C7 NAG 601 F 1 HETATM 8 C C8 NAG . . . I 6 -7.993 39.883 -1.388 1 75.16 ? C8 NAG 601 F 1 HETATM 9 N N2 NAG . . . I 6 -10.156 39.399 -0.456 1 70.11 ? N2 NAG 601 F 1 HETATM 10 O O3 NAG . . . I 6 -11.068 37.63 1.629 1 76.11 ? O3 NAG 601 F 1 HETATM 11 O O4 NAG . . . I 6 -13.916 37.23 1.713 1 71.75 ? O4 NAG 601 F 1 HETATM 12 O O5 NAG . . . I 6 -13.607 40.565 0.256 1 62.96 ? O5 NAG 601 F 1 HETATM 13 O O6 NAG . . . I 6 -16.289 40.582 0.439 1 67.64 ? O6 NAG 601 F 1 HETATM 14 O O7 NAG . . . I 6 -9.206 41.37 0.034 1 78.35 ? O7 NAG 601 F 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 14 #