data_2PM8 # _model_server_result.job_id '_mZcditsvzeifarSoJfXAg' _model_server_result.datetime_utc '2024-11-04 22:50:25' _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 2pm8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":602}' # _entry.id 2PM8 # _exptl.entry_id 2PM8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 5 _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 2PM8 _cell.length_a 150.803 _cell.length_b 150.803 _cell.length_c 142.12 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2PM8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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,J,K,L,M,N,O,P,Q,R,S,T,U,V _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 0 -150.803 0 3 'crystal symmetry operation' 3_445 -y-1/2,x-1/2,z 0 -1 0 1 0 0 0 0 1 -75.4015 -75.4015 0 4 'crystal symmetry operation' 4_545 y+1/2,-x-1/2,z 0 1 0 -1 0 0 0 0 1 75.4015 -75.4015 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 E N N ? 3 F N N ? 3 O N N ? 3 P N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 C NAG 1 C 1 NAG A 781 NAG 2 n C NAG 2 C 2 NAG A 782 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 65 A CYS 65 1_555 A SG CYS 92 A CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf2 A SG CYS 252 A CYS 252 1_555 A SG CYS 263 A CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf3 A SG CYS 400 A CYS 400 1_555 A SG CYS 519 A CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? disulf ? disulf4 B SG CYS 65 B CYS 65 1_555 B SG CYS 92 B CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 B SG CYS 252 B CYS 252 1_555 B SG CYS 263 B CYS 263 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf6 B SG CYS 400 B CYS 400 1_555 B SG CYS 519 B CYS 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? covale ? covale1 A ND2 ASN 57 A ASN 57 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale2 A ND2 ASN 106 A ASN 106 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale3 A ND2 ASN 341 A ASN 341 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 A ND2 ASN 485 A ASN 485 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale5 B ND2 ASN 106 B ASN 106 1_555 P C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _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 250 n n C1 O1 NAG sing 251 n n C1 O5 NAG sing 252 n n C1 H1 NAG sing 253 n n C2 C3 NAG sing 254 n n C2 N2 NAG sing 255 n n C2 H2 NAG sing 256 n n C3 C4 NAG sing 257 n n C3 O3 NAG sing 258 n n C3 H3 NAG sing 259 n n C4 C5 NAG sing 260 n n C4 O4 NAG sing 261 n n C4 H4 NAG sing 262 n n C5 C6 NAG sing 263 n n C5 O5 NAG sing 264 n n C5 H5 NAG sing 265 n n C6 O6 NAG sing 266 n n C6 H61 NAG sing 267 n n C6 H62 NAG sing 268 n n C7 C8 NAG sing 269 n n C7 N2 NAG sing 270 n n C7 O7 NAG doub 271 n n C8 H81 NAG sing 272 n n C8 H82 NAG sing 273 n n C8 H83 NAG sing 274 n n N2 HN2 NAG sing 275 n n O1 HO1 NAG sing 276 n n O3 HO3 NAG sing 277 n n O4 HO4 NAG sing 278 n n O6 HO6 NAG sing 279 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 2PM8 _atom_sites.fract_transf_matrix[1][1] 0.006631 _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] 0.006631 _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] 0.007036 _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 3 NAG A 1 601 791 NAG NAG . E 3 NAG A 1 602 678 NAG NAG . F 3 NAG A 1 603 798 NAG NAG . G 4 SO4 A 1 604 601 SO4 SO4 . H 4 SO4 A 1 605 602 SO4 SO4 . I 4 SO4 A 1 606 603 SO4 SO4 . J 4 SO4 A 1 607 604 SO4 SO4 . K 4 SO4 A 1 608 606 SO4 SO4 . L 5 GOL A 1 609 999 GOL GOL . M 5 GOL A 1 610 774 GOL GOL . N 5 GOL A 1 611 777 GOL GOL . O 3 NAG B 1 601 781 NAG NAG . P 3 NAG B 1 602 791 NAG NAG . Q 4 SO4 B 1 603 601 SO4 SO4 . R 4 SO4 B 1 604 602 SO4 SO4 . S 5 GOL B 1 605 774 GOL GOL . T 5 GOL B 1 606 777 GOL GOL . U 6 HOH A 1 701 8 HOH HOH . U 6 HOH A 2 702 43 HOH HOH . U 6 HOH A 3 703 36 HOH HOH . U 6 HOH A 4 704 25 HOH HOH . U 6 HOH A 5 705 10 HOH HOH . U 6 HOH A 6 706 19 HOH HOH . U 6 HOH A 7 707 11 HOH HOH . U 6 HOH A 8 708 5 HOH HOH . U 6 HOH A 9 709 85 HOH HOH . U 6 HOH A 10 710 44 HOH HOH . U 6 HOH A 11 711 34 HOH HOH . U 6 HOH A 12 712 47 HOH HOH . U 6 HOH A 13 713 84 HOH HOH . U 6 HOH A 14 714 30 HOH HOH . U 6 HOH A 15 715 40 HOH HOH . U 6 HOH A 16 716 35 HOH HOH . U 6 HOH A 17 717 41 HOH HOH . U 6 HOH A 18 718 12 HOH HOH . U 6 HOH A 19 719 97 HOH HOH . U 6 HOH A 20 720 50 HOH HOH . U 6 HOH A 21 721 6 HOH HOH . U 6 HOH A 22 722 21 HOH HOH . U 6 HOH A 23 723 2 HOH HOH . U 6 HOH A 24 724 58 HOH HOH . U 6 HOH A 25 725 9 HOH HOH . U 6 HOH A 26 726 23 HOH HOH . U 6 HOH A 27 727 46 HOH HOH . U 6 HOH A 28 728 11 HOH HOH . U 6 HOH A 29 729 51 HOH HOH . U 6 HOH A 30 730 45 HOH HOH . U 6 HOH A 31 731 83 HOH HOH . U 6 HOH A 32 732 18 HOH HOH . U 6 HOH A 33 733 25 HOH HOH . U 6 HOH A 34 734 32 HOH HOH . U 6 HOH A 35 735 42 HOH HOH . U 6 HOH A 36 736 23 HOH HOH . U 6 HOH A 37 737 73 HOH HOH . U 6 HOH A 38 738 31 HOH HOH . U 6 HOH A 39 739 26 HOH HOH . U 6 HOH A 40 740 66 HOH HOH . U 6 HOH A 41 741 18 HOH HOH . U 6 HOH A 42 742 76 HOH HOH . U 6 HOH A 43 743 37 HOH HOH . U 6 HOH A 44 744 24 HOH HOH . U 6 HOH A 45 745 13 HOH HOH . U 6 HOH A 46 746 13 HOH HOH . U 6 HOH A 47 747 90 HOH HOH . U 6 HOH A 48 748 48 HOH HOH . U 6 HOH A 49 749 1 HOH HOH . U 6 HOH A 50 750 28 HOH HOH . U 6 HOH A 51 751 70 HOH HOH . U 6 HOH A 52 752 7 HOH HOH . V 6 HOH B 1 701 17 HOH HOH . V 6 HOH B 2 702 6 HOH HOH . V 6 HOH B 3 703 29 HOH HOH . V 6 HOH B 4 704 63 HOH HOH . V 6 HOH B 5 705 33 HOH HOH . V 6 HOH B 6 706 94 HOH HOH . V 6 HOH B 7 707 15 HOH HOH . V 6 HOH B 8 708 32 HOH HOH . V 6 HOH B 9 709 95 HOH HOH . V 6 HOH B 10 710 31 HOH HOH . V 6 HOH B 11 711 27 HOH HOH . V 6 HOH B 12 712 53 HOH HOH . V 6 HOH B 13 713 39 HOH HOH . V 6 HOH B 14 714 12 HOH HOH . V 6 HOH B 15 715 54 HOH HOH . V 6 HOH B 16 716 24 HOH HOH . V 6 HOH B 17 717 14 HOH HOH . V 6 HOH B 18 718 22 HOH HOH . V 6 HOH B 19 719 9 HOH HOH . V 6 HOH B 20 720 52 HOH HOH . V 6 HOH B 21 721 14 HOH HOH . V 6 HOH B 22 722 29 HOH HOH . V 6 HOH B 23 723 71 HOH HOH . V 6 HOH B 24 724 30 HOH HOH . V 6 HOH B 25 725 60 HOH HOH . V 6 HOH B 26 726 49 HOH HOH . V 6 HOH B 27 727 21 HOH HOH . V 6 HOH B 28 728 38 HOH HOH . V 6 HOH B 29 729 22 HOH HOH . V 6 HOH B 30 730 15 HOH HOH . V 6 HOH B 31 731 69 HOH HOH . V 6 HOH B 32 732 100 HOH HOH . V 6 HOH B 33 733 3 HOH HOH . V 6 HOH B 34 734 7 HOH HOH . V 6 HOH B 35 735 16 HOH HOH . V 6 HOH B 36 736 99 HOH HOH . V 6 HOH B 37 737 16 HOH HOH . V 6 HOH B 38 738 4 HOH HOH . V 6 HOH B 39 739 27 HOH HOH . V 6 HOH B 40 740 80 HOH HOH . V 6 HOH B 41 741 5 HOH HOH . V 6 HOH B 42 742 20 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 . . . P 3 2.944 -56.899 68.788 1 65.2 ? C1 NAG 602 B 1 HETATM 2 C C2 NAG . . . P 3 2.075 -57.593 69.845 1 65.99 ? C2 NAG 602 B 1 HETATM 3 C C3 NAG . . . P 3 2.176 -59.112 69.74 1 64.65 ? C3 NAG 602 B 1 HETATM 4 C C4 NAG . . . P 3 1.943 -59.551 68.284 1 64.68 ? C4 NAG 602 B 1 HETATM 5 C C5 NAG . . . P 3 2.799 -58.753 67.266 1 64.67 ? C5 NAG 602 B 1 HETATM 6 C C6 NAG . . . P 3 2.452 -59.096 65.806 1 64.63 ? C6 NAG 602 B 1 HETATM 7 C C7 NAG . . . P 3 1.543 -56.844 72.093 1 67.01 ? C7 NAG 602 B 1 HETATM 8 C C8 NAG . . . P 3 1.153 -55.401 72.286 1 64.94 ? C8 NAG 602 B 1 HETATM 9 N N2 NAG . . . P 3 2.453 -57.127 71.17 1 67.15 ? N2 NAG 602 B 1 HETATM 10 O O3 NAG . . . P 3 1.227 -59.677 70.621 1 62.77 ? O3 NAG 602 B 1 HETATM 11 O O4 NAG . . . P 3 2.159 -60.945 68.171 1 64.24 ? O4 NAG 602 B 1 HETATM 12 O O5 NAG . . . P 3 2.633 -57.351 67.466 1 64.92 ? O5 NAG 602 B 1 HETATM 13 O O6 NAG . . . P 3 3.489 -58.813 64.88 1 63.33 ? O6 NAG 602 B 1 HETATM 14 O O7 NAG . . . P 3 1.049 -57.749 72.764 1 68.27 ? O7 NAG 602 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 14 #