data_4KOM # _model_server_result.job_id A501UJ3g1y3Bvx84VuXWAg _model_server_result.datetime_utc '2024-11-29 19:25:11' _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 4kom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 4KOM # _exptl.entry_id 4KOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 4KOM _cell.length_a 117.06 _cell.length_b 117.06 _cell.length_c 296.429 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KOM _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 1,2,3 # 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' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 58.53 -101.376934 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 117.06 0 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 ? 4 F 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 GAL C1 O1 . O3 HO3 . sing 2 ? 3 3 2 GAL NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 SIA GAL C2 O2 . O3 HO3 . 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 GAL 1 C 1 GAL A 804 GAL 3 n C NAG 2 C 2 NAG A 803 NAG 3 n C GAL 3 C 3 GAL A 802 GAL 3 n C SIA 4 C 4 SIA A 801 SIA # 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 2 A CYS 4 1_555 B SG CYS 137 B CYS 458 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 40 A CYS 42 1_555 A SG CYS 266 A CYS 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 52 A CYS 54 1_555 A SG CYS 64 A CYS 66 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf4 A SG CYS 85 A CYS 87 1_555 A SG CYS 127 A CYS 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 270 A CYS 272 1_555 A SG CYS 294 A CYS 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf6 B SG CYS 144 B CYS 465 1_555 B SG CYS 148 B CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 26 A ASN 28 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 229 A ASN 231 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale3 B ND2 ASN 82 B ASN 403 1_555 F C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 C O3 GAL . C GAL 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 GAL . C GAL 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 C O3 GAL . C GAL 3 1_555 C C2 SIA . C SIA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? # _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 261 n n C1 O1 NAG sing 262 n n C1 O5 NAG sing 263 n n C1 H1 NAG sing 264 n n C2 C3 NAG sing 265 n n C2 N2 NAG sing 266 n n C2 H2 NAG sing 267 n n C3 C4 NAG sing 268 n n C3 O3 NAG sing 269 n n C3 H3 NAG sing 270 n n C4 C5 NAG sing 271 n n C4 O4 NAG sing 272 n n C4 H4 NAG sing 273 n n C5 C6 NAG sing 274 n n C5 O5 NAG sing 275 n n C5 H5 NAG sing 276 n n C6 O6 NAG sing 277 n n C6 H61 NAG sing 278 n n C6 H62 NAG sing 279 n n C7 C8 NAG sing 280 n n C7 N2 NAG sing 281 n n C7 O7 NAG doub 282 n n C8 H81 NAG sing 283 n n C8 H82 NAG sing 284 n n C8 H83 NAG sing 285 n n N2 HN2 NAG sing 286 n n O1 HO1 NAG sing 287 n n O3 HO3 NAG sing 288 n n O4 HO4 NAG sing 289 n n O6 HO6 NAG sing 290 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 4KOM _atom_sites.fract_transf_matrix[1][1] 0.008543 _atom_sites.fract_transf_matrix[1][2] 0.004932 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009864 _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] 0.003373 _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 1 601 601 NAG NAG . E 4 NAG A 1 602 602 NAG NAG . F 4 NAG B 1 501 603 NAG NAG . G 5 HOH A 1 701 3 HOH HOH . G 5 HOH A 2 702 4 HOH HOH . G 5 HOH A 3 703 5 HOH HOH . G 5 HOH A 4 704 8 HOH HOH . G 5 HOH A 5 705 9 HOH HOH . G 5 HOH A 6 706 10 HOH HOH . G 5 HOH A 7 707 11 HOH HOH . G 5 HOH A 8 708 12 HOH HOH . G 5 HOH A 9 709 13 HOH HOH . G 5 HOH A 10 710 15 HOH HOH . G 5 HOH A 11 711 17 HOH HOH . G 5 HOH A 12 712 18 HOH HOH . G 5 HOH A 13 713 19 HOH HOH . G 5 HOH A 14 714 20 HOH HOH . G 5 HOH A 15 715 21 HOH HOH . G 5 HOH A 16 716 22 HOH HOH . G 5 HOH A 17 717 25 HOH HOH . G 5 HOH A 18 718 26 HOH HOH . G 5 HOH A 19 719 27 HOH HOH . G 5 HOH A 20 720 29 HOH HOH . G 5 HOH A 21 721 30 HOH HOH . G 5 HOH A 22 722 31 HOH HOH . G 5 HOH A 23 723 32 HOH HOH . G 5 HOH A 24 724 33 HOH HOH . G 5 HOH A 25 725 34 HOH HOH . G 5 HOH A 26 726 36 HOH HOH . G 5 HOH A 27 727 37 HOH HOH . G 5 HOH A 28 728 38 HOH HOH . G 5 HOH A 29 729 39 HOH HOH . G 5 HOH A 30 730 40 HOH HOH . G 5 HOH A 31 731 42 HOH HOH . G 5 HOH A 32 732 44 HOH HOH . G 5 HOH A 33 733 46 HOH HOH . G 5 HOH A 34 734 49 HOH HOH . G 5 HOH A 35 735 50 HOH HOH . G 5 HOH A 36 736 51 HOH HOH . G 5 HOH A 37 737 52 HOH HOH . G 5 HOH A 38 738 53 HOH HOH . G 5 HOH A 39 739 56 HOH HOH . G 5 HOH A 40 740 57 HOH HOH . G 5 HOH A 41 741 58 HOH HOH . G 5 HOH A 42 742 59 HOH HOH . G 5 HOH A 43 743 60 HOH HOH . G 5 HOH A 44 744 62 HOH HOH . G 5 HOH A 45 745 63 HOH HOH . G 5 HOH A 46 746 65 HOH HOH . G 5 HOH A 47 747 66 HOH HOH . G 5 HOH A 48 748 68 HOH HOH . G 5 HOH A 49 749 69 HOH HOH . G 5 HOH A 50 750 74 HOH HOH . G 5 HOH A 51 751 75 HOH HOH . G 5 HOH A 52 752 77 HOH HOH . G 5 HOH A 53 753 81 HOH HOH . G 5 HOH A 54 754 82 HOH HOH . G 5 HOH A 55 755 83 HOH HOH . G 5 HOH A 56 756 84 HOH HOH . G 5 HOH A 57 757 85 HOH HOH . G 5 HOH A 58 758 86 HOH HOH . H 5 HOH B 1 601 1 HOH HOH . H 5 HOH B 2 602 2 HOH HOH . H 5 HOH B 3 603 6 HOH HOH . H 5 HOH B 4 604 7 HOH HOH . H 5 HOH B 5 605 14 HOH HOH . H 5 HOH B 6 606 16 HOH HOH . H 5 HOH B 7 607 23 HOH HOH . H 5 HOH B 8 608 24 HOH HOH . H 5 HOH B 9 609 35 HOH HOH . H 5 HOH B 10 610 41 HOH HOH . H 5 HOH B 11 611 43 HOH HOH . H 5 HOH B 12 612 45 HOH HOH . H 5 HOH B 13 613 47 HOH HOH . H 5 HOH B 14 614 48 HOH HOH . H 5 HOH B 15 615 55 HOH HOH . H 5 HOH B 16 616 61 HOH HOH . H 5 HOH B 17 617 64 HOH HOH . H 5 HOH B 18 618 67 HOH HOH . H 5 HOH B 19 619 70 HOH HOH . H 5 HOH B 20 620 71 HOH HOH . H 5 HOH B 21 621 72 HOH HOH . H 5 HOH B 22 622 73 HOH HOH . H 5 HOH B 23 623 76 HOH HOH . H 5 HOH B 24 624 78 HOH HOH . H 5 HOH B 25 625 79 HOH HOH . H 5 HOH B 26 626 80 HOH HOH . H 5 HOH B 27 627 87 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 35.648 -32.904 -32.708 1 117.08 ? C1 NAG 601 A 1 HETATM 2 C C2 NAG . . . D 4 34.877 -33.927 -33.537 1 126.6 ? C2 NAG 601 A 1 HETATM 3 C C3 NAG . . . D 4 34.201 -34.942 -32.63 1 127.79 ? C3 NAG 601 A 1 HETATM 4 C C4 NAG . . . D 4 35.254 -35.603 -31.756 1 125.27 ? C4 NAG 601 A 1 HETATM 5 C C5 NAG . . . D 4 36.098 -34.569 -31.012 1 118.02 ? C5 NAG 601 A 1 HETATM 6 C C6 NAG . . . D 4 37.299 -35.255 -30.371 1 112.64 ? C6 NAG 601 A 1 HETATM 7 C C7 NAG . . . D 4 33.857 -33.569 -35.699 1 126.5 ? C7 NAG 601 A 1 HETATM 8 C C8 NAG . . . D 4 33.396 -32.474 -36.614 1 124.23 ? C8 NAG 601 A 1 HETATM 9 N N2 NAG . . . D 4 33.901 -33.286 -34.399 1 125.89 ? N2 NAG 601 A 1 HETATM 10 O O3 NAG . . . D 4 33.547 -35.917 -33.411 1 127.71 ? O3 NAG 601 A 1 HETATM 11 O O4 NAG . . . D 4 34.62 -36.457 -30.828 1 118.09 ? O4 NAG 601 A 1 HETATM 12 O O5 NAG . . . D 4 36.586 -33.541 -31.858 1 114.29 ? O5 NAG 601 A 1 HETATM 13 O O6 NAG . . . D 4 36.92 -36.532 -29.908 1 118.31 ? O6 NAG 601 A 1 HETATM 14 O O7 NAG . . . D 4 34.175 -34.668 -36.15 1 128.88 ? O7 NAG 601 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 471 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #