data_8API # _model_server_result.job_id D8-mzsYum273irHRJ-bT4g _model_server_result.datetime_utc '2024-10-13 18:20:06' _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 8api # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":395}' # _entry.id 8API # _exptl.entry_id 8API _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 121.158 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description CYSTEINE _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 90 _cell.angle_gamma 120 _cell.entry_id 8API _cell.length_a 119.7 _cell.length_b 119.7 _cell.length_c 216.3 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8API _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 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 _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 5 _struct_asym.id F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 3 4 3 MAN MAN C1 O1 . O6 HO6 . sing 4 ? 3 5 4 NAG MAN C1 O1 . O2 HO2 . sing 5 ? 3 6 3 MAN MAN C1 O1 . O3 HO3 . sing 6 ? 4 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 3 n C NAG 1 C 1 NAG ? 501 NAG 3 n C NAG 2 C 2 NAG ? 502 NAG 3 n C MAN 3 C 3 MAN ? 503 MAN 3 n C MAN 4 C 4 MAN ? 504 MAN 3 n C NAG 5 C 5 NAG ? 505 NAG 3 n C MAN 6 C 6 MAN ? 506 MAN 4 n D NAG 1 D 1 NAG ? 510 NAG 4 n D NAG 2 D 2 NAG ? 511 NAG 4 n E NAG 1 E 1 NAG ? 520 NAG 4 n E NAG 2 E 2 NAG ? 521 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 221 A CYS 232 1_555 F SG CYS . A CYS 395 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? covale ? covale1 A ND2 ASN 35 A ASN 46 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? covale ? covale2 A ND2 ASN 72 A ASN 83 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? covale ? covale3 A ND2 ASN 236 A ASN 247 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? covale ? covale4 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale5 C O4 NAG . C NAG 2 1_555 C C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale6 C O6 MAN . C MAN 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale7 C O3 MAN . C MAN 3 1_555 C C1 MAN . C MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale8 C O2 MAN . C MAN 4 1_555 C C1 NAG . C NAG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale10 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? # _chem_comp.formula 'C3 H7 N O2 S' _chem_comp.formula_weight 121.158 _chem_comp.id CYS _chem_comp.mon_nstd_flag y _chem_comp.name CYSTEINE _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # 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 N CA CYS sing 70 n n N H CYS sing 71 n n N H2 CYS sing 72 n n CA C CYS sing 73 n n CA CB CYS sing 74 n n CA HA CYS sing 75 n n C O CYS doub 76 n n C OXT CYS sing 77 n n CB SG CYS sing 78 n n CB HB2 CYS sing 79 n n CB HB3 CYS sing 80 n n SG HG CYS sing 81 n n OXT HXT CYS sing 82 n n # _atom_sites.entry_id 8API _atom_sites.fract_transf_matrix[1][1] 0.008354 _atom_sites.fract_transf_matrix[1][2] 0.004823 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009647 _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] 0.004623 _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 F 5 CYS A 1 395 395 CYS CYS . G 6 HOH A 1 600 600 HOH HOH . G 6 HOH A 2 603 603 HOH HOH . G 6 HOH A 3 604 604 HOH HOH . G 6 HOH A 4 607 607 HOH HOH . G 6 HOH A 5 609 609 HOH HOH . G 6 HOH A 6 611 611 HOH HOH . G 6 HOH A 7 612 612 HOH HOH . G 6 HOH A 8 613 613 HOH HOH . G 6 HOH A 9 614 614 HOH HOH . G 6 HOH A 10 615 615 HOH HOH . G 6 HOH A 11 616 616 HOH HOH . G 6 HOH A 12 617 617 HOH HOH . G 6 HOH A 13 618 618 HOH HOH . G 6 HOH A 14 619 619 HOH HOH . G 6 HOH A 15 621 621 HOH HOH . G 6 HOH A 16 622 622 HOH HOH . G 6 HOH A 17 632 632 HOH HOH . G 6 HOH A 18 635 635 HOH HOH . G 6 HOH A 19 636 636 HOH HOH . G 6 HOH A 20 637 637 HOH HOH . G 6 HOH A 21 639 639 HOH HOH . G 6 HOH A 22 640 640 HOH HOH . G 6 HOH A 23 646 646 HOH HOH . G 6 HOH A 24 647 647 HOH HOH . G 6 HOH A 25 648 648 HOH HOH . G 6 HOH A 26 649 649 HOH HOH . G 6 HOH A 27 650 650 HOH HOH . G 6 HOH A 28 651 651 HOH HOH . G 6 HOH A 29 652 652 HOH HOH . G 6 HOH A 30 653 653 HOH HOH . G 6 HOH A 31 654 654 HOH HOH . G 6 HOH A 32 657 657 HOH HOH . G 6 HOH A 33 658 658 HOH HOH . G 6 HOH A 34 659 659 HOH HOH . G 6 HOH A 35 660 660 HOH HOH . G 6 HOH A 36 661 661 HOH HOH . G 6 HOH A 37 662 662 HOH HOH . G 6 HOH A 38 664 664 HOH HOH . G 6 HOH A 39 665 665 HOH HOH . G 6 HOH A 40 666 666 HOH HOH . G 6 HOH A 41 667 667 HOH HOH . G 6 HOH A 42 668 668 HOH HOH . G 6 HOH A 43 669 669 HOH HOH . G 6 HOH A 44 672 672 HOH HOH . G 6 HOH A 45 673 673 HOH HOH . G 6 HOH A 46 675 675 HOH HOH . G 6 HOH A 47 676 676 HOH HOH . G 6 HOH A 48 679 679 HOH HOH . G 6 HOH A 49 680 680 HOH HOH . G 6 HOH A 50 682 682 HOH HOH . G 6 HOH A 51 683 683 HOH HOH . G 6 HOH A 52 684 684 HOH HOH . G 6 HOH A 53 685 685 HOH HOH . G 6 HOH A 54 686 686 HOH HOH . G 6 HOH A 55 687 687 HOH HOH . G 6 HOH A 56 689 689 HOH HOH . G 6 HOH A 57 690 690 HOH HOH . G 6 HOH A 58 696 696 HOH HOH . G 6 HOH A 59 700 700 HOH HOH . G 6 HOH A 60 701 701 HOH HOH . G 6 HOH A 61 706 706 HOH HOH . G 6 HOH A 62 707 707 HOH HOH . G 6 HOH A 63 709 709 HOH HOH . G 6 HOH A 64 710 710 HOH HOH . G 6 HOH A 65 711 711 HOH HOH . G 6 HOH A 66 712 712 HOH HOH . G 6 HOH A 67 713 713 HOH HOH . G 6 HOH A 68 714 714 HOH HOH . G 6 HOH A 69 715 715 HOH HOH . G 6 HOH A 70 716 716 HOH HOH . G 6 HOH A 71 717 717 HOH HOH . G 6 HOH A 72 718 718 HOH HOH . G 6 HOH A 73 722 722 HOH HOH . G 6 HOH A 74 724 724 HOH HOH . G 6 HOH A 75 725 725 HOH HOH . G 6 HOH A 76 726 726 HOH HOH . G 6 HOH A 77 727 727 HOH HOH . G 6 HOH A 78 728 728 HOH HOH . G 6 HOH A 79 729 729 HOH HOH . G 6 HOH A 80 730 730 HOH HOH . G 6 HOH A 81 732 732 HOH HOH . G 6 HOH A 82 733 733 HOH HOH . G 6 HOH A 83 735 735 HOH HOH . G 6 HOH A 84 739 739 HOH HOH . G 6 HOH A 85 740 740 HOH HOH . G 6 HOH A 86 741 741 HOH HOH . G 6 HOH A 87 742 742 HOH HOH . G 6 HOH A 88 743 743 HOH HOH . G 6 HOH A 89 744 744 HOH HOH . G 6 HOH A 90 745 745 HOH HOH . G 6 HOH A 91 746 746 HOH HOH . G 6 HOH A 92 747 747 HOH HOH . G 6 HOH A 93 748 748 HOH HOH . G 6 HOH A 94 749 749 HOH HOH . G 6 HOH A 95 750 750 HOH HOH . G 6 HOH A 96 751 751 HOH HOH . G 6 HOH A 97 752 752 HOH HOH . G 6 HOH A 98 753 753 HOH HOH . G 6 HOH A 99 754 754 HOH HOH . G 6 HOH A 100 755 755 HOH HOH . G 6 HOH A 101 756 756 HOH HOH . G 6 HOH A 102 759 759 HOH HOH . G 6 HOH A 103 760 760 HOH HOH . G 6 HOH A 104 761 761 HOH HOH . G 6 HOH A 105 762 762 HOH HOH . G 6 HOH A 106 763 763 HOH HOH . G 6 HOH A 107 764 764 HOH HOH . G 6 HOH A 108 765 765 HOH HOH . G 6 HOH A 109 766 766 HOH HOH . G 6 HOH A 110 767 767 HOH HOH . G 6 HOH A 111 768 768 HOH HOH . G 6 HOH A 112 769 769 HOH HOH . G 6 HOH A 113 770 770 HOH HOH . G 6 HOH A 114 771 771 HOH HOH . G 6 HOH A 115 772 772 HOH HOH . G 6 HOH A 116 773 773 HOH HOH . G 6 HOH A 117 774 774 HOH HOH . G 6 HOH A 118 775 775 HOH HOH . G 6 HOH A 119 776 776 HOH HOH . G 6 HOH A 120 777 777 HOH HOH . G 6 HOH A 121 778 778 HOH HOH . G 6 HOH A 122 779 779 HOH HOH . G 6 HOH A 123 780 780 HOH HOH . G 6 HOH A 124 781 781 HOH HOH . G 6 HOH A 125 782 782 HOH HOH . G 6 HOH A 126 783 783 HOH HOH . G 6 HOH A 127 785 785 HOH HOH . G 6 HOH A 128 786 786 HOH HOH . G 6 HOH A 129 787 787 HOH HOH . G 6 HOH A 130 788 788 HOH HOH . G 6 HOH A 131 789 789 HOH HOH . G 6 HOH A 132 790 790 HOH HOH . G 6 HOH A 133 791 791 HOH HOH . G 6 HOH A 134 794 794 HOH HOH . G 6 HOH A 135 795 795 HOH HOH . G 6 HOH A 136 796 796 HOH HOH . G 6 HOH A 137 797 797 HOH HOH . H 6 HOH B 1 631 631 HOH HOH . H 6 HOH B 2 655 655 HOH HOH . H 6 HOH B 3 674 674 HOH HOH . H 6 HOH B 4 688 688 HOH HOH . H 6 HOH B 5 695 695 HOH HOH . H 6 HOH B 6 704 704 HOH HOH . H 6 HOH B 7 705 705 HOH HOH . H 6 HOH B 8 708 708 HOH HOH . H 6 HOH B 9 719 719 HOH HOH . H 6 HOH B 10 720 720 HOH HOH . H 6 HOH B 11 721 721 HOH HOH . H 6 HOH B 12 731 731 HOH HOH . H 6 HOH B 13 734 734 HOH HOH . H 6 HOH B 14 736 736 HOH HOH . H 6 HOH B 15 737 737 HOH HOH . H 6 HOH B 16 738 738 HOH HOH . H 6 HOH B 17 757 757 HOH HOH . H 6 HOH B 18 758 758 HOH HOH . H 6 HOH B 19 784 784 HOH HOH . H 6 HOH B 20 792 792 HOH HOH . H 6 HOH B 21 793 793 HOH HOH . H 6 HOH B 22 798 798 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 N N CYS . . . F 5 -21.237 47.79 -1.413 1 47.8 ? N CYS 395 A 1 HETATM 2 C CA CYS . . . F 5 -21.366 47.293 -0.037 1 47.4 ? CA CYS 395 A 1 HETATM 3 C C CYS . . . F 5 -22.378 46.13 0.041 1 56.99 ? C CYS 395 A 1 HETATM 4 O O CYS . . . F 5 -23.375 46.165 -0.691 1 51.07 ? O CYS 395 A 1 HETATM 5 C CB CYS . . . F 5 -21.712 48.48 0.915 1 41.62 ? CB CYS 395 A 1 HETATM 6 S SG CYS . . . F 5 -21.048 48.321 2.586 1 23.47 ? SG CYS 395 A 1 HETATM 7 O OXT CYS . . . F 5 -22.019 45.002 0.498 1 38.84 ? OXT CYS 395 A 1 # _model_server_stats.io_time_ms 79 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 7 #