data_3UBA # _model_server_result.job_id 99lwwNJcXByCWPfdkUWWbg _model_server_result.datetime_utc '2024-11-28 08:30:10' _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 3uba # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":604}' # _entry.id 3UBA # _exptl.entry_id 3UBA _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 103.33 _cell.angle_gamma 90 _cell.entry_id 3UBA _cell.length_a 54.05 _cell.length_b 80.23 _cell.length_c 76.1 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UBA _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,W,X _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 ? 4 F 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 B NAG 1 B 1 NAG A 601 NAG 2 n B NAG 2 B 2 NAG A 602 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 6 A CYS 6 1_555 A SG CYS 167 A CYS 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? disulf ? disulf2 A SG CYS 15 A CYS 15 1_555 A SG CYS 28 A CYS 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.563 ? disulf ? disulf3 A SG CYS 129 A CYS 129 1_555 A SG CYS 139 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 133 A CYS 133 1_555 A SG CYS 157 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 237 A CYS 237 1_555 A SG CYS 248 A CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf6 A SG CYS 456 A CYS 456 1_555 A SG CYS 513 A CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 A SG CYS 554 A CYS 554 1_555 A SG CYS 579 A CYS 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A ND2 ASN 95 A ASN 95 1_555 D C1 NAG . A NAG 596 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale2 A C PRO 197 A PRO 197 1_555 A N SEP 198 A SEP 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale3 A C SEP 198 A SEP 198 1_555 A N LEU 199 A LEU 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 A ND2 ASN 205 A ASN 205 1_555 E C1 NAG . A NAG 599 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 241 A ASN 241 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale6 A ND2 ASN 332 A ASN 332 1_555 F C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? covale ? covale7 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? metalc ? metalc1 A O ASP 110 A ASP 110 1_555 P CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc2 A OD1 ASP 110 A ASP 110 1_555 P CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc3 A O THR 184 A THR 184 1_555 P CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc4 A OG1 THR 184 A THR 184 1_555 P CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc5 A O PHE 186 A PHE 186 1_555 P CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? metalc ? metalc6 A OD1 ASP 188 A ASP 188 1_555 P CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc7 A OG SER 190 A SER 190 1_555 P CA CA . A CA 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc8 A NE2 HIS 351 A HIS 351 1_555 C FE HEM . A HEM 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? # _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 361 n n C1 O1 NAG sing 362 n n C1 O5 NAG sing 363 n n C1 H1 NAG sing 364 n n C2 C3 NAG sing 365 n n C2 N2 NAG sing 366 n n C2 H2 NAG sing 367 n n C3 C4 NAG sing 368 n n C3 O3 NAG sing 369 n n C3 H3 NAG sing 370 n n C4 C5 NAG sing 371 n n C4 O4 NAG sing 372 n n C4 H4 NAG sing 373 n n C5 C6 NAG sing 374 n n C5 O5 NAG sing 375 n n C5 H5 NAG sing 376 n n C6 O6 NAG sing 377 n n C6 H61 NAG sing 378 n n C6 H62 NAG sing 379 n n C7 C8 NAG sing 380 n n C7 N2 NAG sing 381 n n C7 O7 NAG doub 382 n n C8 H81 NAG sing 383 n n C8 H82 NAG sing 384 n n C8 H83 NAG sing 385 n n N2 HN2 NAG sing 386 n n O1 HO1 NAG sing 387 n n O3 HO3 NAG sing 388 n n O4 HO4 NAG sing 389 n n O6 HO6 NAG sing 390 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 3UBA _atom_sites.fract_transf_matrix[1][1] 0.018501 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004384 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012464 _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] 0.013504 _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 C 3 HEM A 1 605 605 HEM HEM . D 4 NAG A 1 596 596 NAG NAG . E 4 NAG A 1 599 599 NAG NAG . F 4 NAG A 1 604 604 NAG NAG . G 5 IOD A 1 607 607 IOD IOD . H 5 IOD A 1 608 608 IOD IOD . I 5 IOD A 1 609 609 IOD IOD . J 5 IOD A 1 610 610 IOD IOD . K 5 IOD A 1 611 611 IOD IOD . L 5 IOD A 1 612 612 IOD IOD . M 5 IOD A 1 615 615 IOD IOD . N 5 IOD A 1 616 616 IOD IOD . O 5 IOD A 1 617 617 IOD IOD . P 6 CA A 1 606 606 CA CA . Q 7 SCN A 1 620 620 SCN SCN . R 8 HC4 A 1 700 700 HC4 HC4 . S 9 PEG A 1 603 603 PEG PEG . T 9 PEG A 1 619 619 PEG PEG . U 10 GOL A 1 621 621 GOL GOL . V 11 EDO A 1 623 623 EDO EDO . W 11 EDO A 1 624 624 EDO EDO . X 12 HOH A 1 597 1 HOH HOH . X 12 HOH A 2 598 2 HOH HOH . X 12 HOH A 3 600 3 HOH HOH . X 12 HOH A 4 613 4 HOH HOH . X 12 HOH A 5 614 5 HOH HOH . X 12 HOH A 6 618 6 HOH HOH . X 12 HOH A 7 622 7 HOH HOH . X 12 HOH A 8 625 10 HOH HOH . X 12 HOH A 9 626 11 HOH HOH . X 12 HOH A 10 627 14 HOH HOH . X 12 HOH A 11 628 16 HOH HOH . X 12 HOH A 12 629 18 HOH HOH . X 12 HOH A 13 630 19 HOH HOH . X 12 HOH A 14 631 20 HOH HOH . X 12 HOH A 15 632 21 HOH HOH . X 12 HOH A 16 633 22 HOH HOH . X 12 HOH A 17 634 23 HOH HOH . X 12 HOH A 18 635 24 HOH HOH . X 12 HOH A 19 636 25 HOH HOH . X 12 HOH A 20 637 26 HOH HOH . X 12 HOH A 21 638 27 HOH HOH . X 12 HOH A 22 639 28 HOH HOH . X 12 HOH A 23 640 29 HOH HOH . X 12 HOH A 24 641 30 HOH HOH . X 12 HOH A 25 642 31 HOH HOH . X 12 HOH A 26 643 32 HOH HOH . X 12 HOH A 27 644 33 HOH HOH . X 12 HOH A 28 645 34 HOH HOH . X 12 HOH A 29 646 35 HOH HOH . X 12 HOH A 30 647 36 HOH HOH . X 12 HOH A 31 648 37 HOH HOH . X 12 HOH A 32 649 38 HOH HOH . X 12 HOH A 33 650 39 HOH HOH . X 12 HOH A 34 651 40 HOH HOH . X 12 HOH A 35 652 41 HOH HOH . X 12 HOH A 36 653 42 HOH HOH . X 12 HOH A 37 654 43 HOH HOH . X 12 HOH A 38 655 44 HOH HOH . X 12 HOH A 39 656 45 HOH HOH . X 12 HOH A 40 657 46 HOH HOH . X 12 HOH A 41 658 47 HOH HOH . X 12 HOH A 42 659 48 HOH HOH . X 12 HOH A 43 660 49 HOH HOH . X 12 HOH A 44 661 50 HOH HOH . X 12 HOH A 45 662 51 HOH HOH . X 12 HOH A 46 663 52 HOH HOH . X 12 HOH A 47 664 54 HOH HOH . X 12 HOH A 48 665 55 HOH HOH . X 12 HOH A 49 666 56 HOH HOH . X 12 HOH A 50 667 57 HOH HOH . X 12 HOH A 51 668 58 HOH HOH . X 12 HOH A 52 669 59 HOH HOH . X 12 HOH A 53 670 60 HOH HOH . X 12 HOH A 54 671 61 HOH HOH . X 12 HOH A 55 672 62 HOH HOH . X 12 HOH A 56 673 63 HOH HOH . X 12 HOH A 57 674 64 HOH HOH . X 12 HOH A 58 675 65 HOH HOH . X 12 HOH A 59 676 66 HOH HOH . X 12 HOH A 60 677 67 HOH HOH . X 12 HOH A 61 678 68 HOH HOH . X 12 HOH A 62 679 69 HOH HOH . X 12 HOH A 63 680 70 HOH HOH . X 12 HOH A 64 681 71 HOH HOH . X 12 HOH A 65 682 73 HOH HOH . X 12 HOH A 66 683 74 HOH HOH . X 12 HOH A 67 684 75 HOH HOH . X 12 HOH A 68 685 76 HOH HOH . X 12 HOH A 69 686 77 HOH HOH . X 12 HOH A 70 687 78 HOH HOH . X 12 HOH A 71 688 79 HOH HOH . X 12 HOH A 72 689 80 HOH HOH . X 12 HOH A 73 690 81 HOH HOH . X 12 HOH A 74 691 82 HOH HOH . X 12 HOH A 75 692 83 HOH HOH . X 12 HOH A 76 693 84 HOH HOH . X 12 HOH A 77 694 85 HOH HOH . X 12 HOH A 78 695 86 HOH HOH . X 12 HOH A 79 696 87 HOH HOH . X 12 HOH A 80 697 91 HOH HOH . X 12 HOH A 81 698 92 HOH HOH . X 12 HOH A 82 699 93 HOH HOH . X 12 HOH A 83 701 94 HOH HOH . X 12 HOH A 84 702 95 HOH HOH . X 12 HOH A 85 703 96 HOH HOH . X 12 HOH A 86 704 97 HOH HOH . X 12 HOH A 87 705 98 HOH HOH . X 12 HOH A 88 706 99 HOH HOH . X 12 HOH A 89 707 100 HOH HOH . X 12 HOH A 90 708 101 HOH HOH . X 12 HOH A 91 709 102 HOH HOH . X 12 HOH A 92 710 103 HOH HOH . X 12 HOH A 93 711 104 HOH HOH . X 12 HOH A 94 712 105 HOH HOH . X 12 HOH A 95 713 106 HOH HOH . X 12 HOH A 96 714 107 HOH HOH . X 12 HOH A 97 715 111 HOH HOH . X 12 HOH A 98 716 112 HOH HOH . X 12 HOH A 99 717 113 HOH HOH . X 12 HOH A 100 718 114 HOH HOH . X 12 HOH A 101 719 116 HOH HOH . X 12 HOH A 102 720 117 HOH HOH . X 12 HOH A 103 721 119 HOH HOH . X 12 HOH A 104 722 120 HOH HOH . X 12 HOH A 105 723 121 HOH HOH . X 12 HOH A 106 724 122 HOH HOH . X 12 HOH A 107 725 123 HOH HOH . X 12 HOH A 108 726 124 HOH HOH . X 12 HOH A 109 727 125 HOH HOH . X 12 HOH A 110 728 126 HOH HOH . X 12 HOH A 111 729 127 HOH HOH . X 12 HOH A 112 730 128 HOH HOH . X 12 HOH A 113 731 129 HOH HOH . X 12 HOH A 114 732 130 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 . . . F 4 8.134 -25.734 11.95 1 59.02 ? C1 NAG 604 A 1 HETATM 2 C C2 NAG . . . F 4 9.367 -25.978 11.111 1 60.07 ? C2 NAG 604 A 1 HETATM 3 C C3 NAG . . . F 4 10.159 -27.099 11.703 1 60.28 ? C3 NAG 604 A 1 HETATM 4 C C4 NAG . . . F 4 10.398 -26.818 13.178 1 58.92 ? C4 NAG 604 A 1 HETATM 5 C C5 NAG . . . F 4 9.091 -26.535 13.917 1 57.42 ? C5 NAG 604 A 1 HETATM 6 C C6 NAG . . . F 4 9.34 -26.085 15.329 1 53.96 ? C6 NAG 604 A 1 HETATM 7 C C7 NAG . . . F 4 9.721 -25.728 8.726 1 63.13 ? C7 NAG 604 A 1 HETATM 8 C C8 NAG . . . F 4 9.258 -25.985 7.309 1 64.4 ? C8 NAG 604 A 1 HETATM 9 N N2 NAG . . . F 4 8.98 -26.228 9.721 1 62.13 ? N2 NAG 604 A 1 HETATM 10 O O3 NAG . . . F 4 11.418 -27.176 11.078 1 59.42 ? O3 NAG 604 A 1 HETATM 11 O O4 NAG . . . F 4 11.037 -27.934 13.75 1 59.48 ? O4 NAG 604 A 1 HETATM 12 O O5 NAG . . . F 4 8.421 -25.507 13.294 1 58.05 ? O5 NAG 604 A 1 HETATM 13 O O6 NAG . . . F 4 9.827 -24.741 15.377 1 49.38 ? O6 NAG 604 A 1 HETATM 14 O O7 NAG . . . F 4 10.764 -25.09 8.935 1 62.1 ? O7 NAG 604 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #