data_2YGM # _model_server_result.job_id sLRfj_Q1Ccv-mzNn1hQ0WQ _model_server_result.datetime_utc '2024-11-09 02:21:08' _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 2ygm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":506}' # _entry.id 2YGM # _exptl.entry_id 2YGM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 2 _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 2YGM _cell.length_a 75.7 _cell.length_b 78.5 _cell.length_c 131.58 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YGM _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,I 1 1 B,D,G,H,J 2 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 ? 3 E N N ? 3 H N N # _pdbx_entity_branch.entity_id 2 _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 ? 2 2 1 GAL NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 FUC GAL C1 O1 . O2 HO2 . sing 3 ? 2 4 2 GLA GAL C1 O1 . 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 2 n C NAG 1 C 1 NAG A 1413 NAG 2 n C GAL 2 C 2 GAL A 1415 GAL 2 n C FUC 3 C 3 FUC A 1416 FUC 2 n C GLA 4 C 4 GLA A 1414 GLA 2 n D NAG 1 D 1 NAG B 1413 NAG 2 n D GAL 2 D 2 GAL B 1415 GAL 2 n D FUC 3 D 3 FUC B 1416 FUC 2 n D GLA 4 D 4 GLA B 1414 GLA # 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 covale ? covale1 C O4 NAG . C NAG 1 1_555 C C1 GAL . C GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 C O2 GAL . C GAL 2 1_555 C C1 FUC . C FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale3 C O3 GAL . C GAL 2 1_555 C C1 GLA . C GLA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale4 D O4 NAG . D NAG 1 1_555 D C1 GAL . D GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 D O2 GAL . D GAL 2 1_555 D C1 FUC . D FUC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale6 D O3 GAL . D GAL 2 1_555 D C1 GLA . D GLA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A O VAL 102 A VAL 161 1_555 E CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc2 A O ALA 152 A ALA 211 1_555 E CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc3 A O HIS 155 A HIS 214 1_555 E CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc4 A OD1 ASP 159 A ASP 218 1_555 E CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc5 A OD2 ASP 159 A ASP 218 1_555 E CA CA . A CA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc6 A O ASP 284 A ASP 343 1_555 F NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.846 ? metalc ? metalc7 A O THR 338 A THR 397 1_555 F NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.097 ? metalc ? metalc8 A OG1 THR 338 A THR 397 1_555 F NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.066 ? metalc ? metalc9 A O ALA 340 A ALA 399 1_555 F NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.107 ? metalc ? metalc10 A OD1 ASP 341 A ASP 400 1_555 F NA NA . A NA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.604 ? metalc ? metalc11 E CA CA . A CA 505 1_555 I O HOH . A HOH 632 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc12 B O VAL 102 B VAL 161 1_555 H CA CA . B CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? metalc ? metalc13 B O ALA 152 B ALA 211 1_555 H CA CA . B CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc14 B O HIS 155 B HIS 214 1_555 H CA CA . B CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc15 B OD1 ASP 159 B ASP 218 1_555 H CA CA . B CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3 ? metalc ? metalc16 B OD2 ASP 159 B ASP 218 1_555 H CA CA . B CA 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc17 B O ASP 284 B ASP 343 1_555 G NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc18 B O GLY 335 B GLY 394 1_555 G NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? metalc ? metalc19 B O THR 338 B THR 397 1_555 G NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc20 B OG1 THR 338 B THR 397 1_555 G NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.017 ? metalc ? metalc21 B O ALA 340 B ALA 399 1_555 G NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.947 ? metalc ? metalc22 B OD1 ASP 341 B ASP 400 1_555 G NA NA . B NA 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? # _chem_comp.formula 'Ca 2' _chem_comp.formula_weight 40.078 _chem_comp.id CA _chem_comp.mon_nstd_flag . _chem_comp.name 'CALCIUM ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2YGM _atom_sites.fract_transf_matrix[1][1] 0.01321 _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] 0.012739 _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] 0.0076 _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 E 3 CA A 1 505 1417 CA CA . F 4 NA A 1 506 1418 NA NA . G 4 NA B 1 505 1417 NA NA . H 3 CA B 1 506 1418 CA CA . I 5 HOH A 1 601 2030 HOH HOH . I 5 HOH A 2 602 2041 HOH HOH . I 5 HOH A 3 603 2066 HOH HOH . I 5 HOH A 4 604 2081 HOH HOH . I 5 HOH A 5 605 2051 HOH HOH . I 5 HOH A 6 606 2033 HOH HOH . I 5 HOH A 7 607 2096 HOH HOH . I 5 HOH A 8 608 2068 HOH HOH . I 5 HOH A 9 609 2023 HOH HOH . I 5 HOH A 10 610 2038 HOH HOH . I 5 HOH A 11 611 2079 HOH HOH . I 5 HOH A 12 612 2018 HOH HOH . I 5 HOH A 13 613 2049 HOH HOH . I 5 HOH A 14 614 2090 HOH HOH . I 5 HOH A 15 615 2047 HOH HOH . I 5 HOH A 16 616 2037 HOH HOH . I 5 HOH A 17 617 2060 HOH HOH . I 5 HOH A 18 618 2077 HOH HOH . I 5 HOH A 19 619 2097 HOH HOH . I 5 HOH A 20 620 2088 HOH HOH . I 5 HOH A 21 621 2011 HOH HOH . I 5 HOH A 22 622 2053 HOH HOH . I 5 HOH A 23 623 2002 HOH HOH . I 5 HOH A 24 624 2084 HOH HOH . I 5 HOH A 25 625 2025 HOH HOH . I 5 HOH A 26 626 2085 HOH HOH . I 5 HOH A 27 627 2058 HOH HOH . I 5 HOH A 28 628 2094 HOH HOH . I 5 HOH A 29 629 2040 HOH HOH . I 5 HOH A 30 630 2100 HOH HOH . I 5 HOH A 31 631 2087 HOH HOH . I 5 HOH A 32 632 2022 HOH HOH . I 5 HOH A 33 633 2048 HOH HOH . I 5 HOH A 34 634 2059 HOH HOH . I 5 HOH A 35 635 2089 HOH HOH . I 5 HOH A 36 636 2091 HOH HOH . I 5 HOH A 37 637 2046 HOH HOH . I 5 HOH A 38 638 2007 HOH HOH . I 5 HOH A 39 639 2092 HOH HOH . I 5 HOH A 40 640 2042 HOH HOH . I 5 HOH A 41 641 2035 HOH HOH . I 5 HOH A 42 642 2013 HOH HOH . I 5 HOH A 43 643 2045 HOH HOH . I 5 HOH A 44 644 2073 HOH HOH . I 5 HOH A 45 645 2043 HOH HOH . I 5 HOH A 46 646 2095 HOH HOH . I 5 HOH A 47 647 2071 HOH HOH . I 5 HOH A 48 648 2075 HOH HOH . I 5 HOH A 49 649 2078 HOH HOH . I 5 HOH A 50 650 2032 HOH HOH . I 5 HOH A 51 651 2015 HOH HOH . I 5 HOH A 52 652 2086 HOH HOH . I 5 HOH A 53 653 2065 HOH HOH . I 5 HOH A 54 654 2014 HOH HOH . I 5 HOH A 55 655 2031 HOH HOH . I 5 HOH A 56 656 2099 HOH HOH . I 5 HOH A 57 657 2098 HOH HOH . I 5 HOH A 58 658 2101 HOH HOH . I 5 HOH A 59 659 2004 HOH HOH . I 5 HOH A 60 660 2072 HOH HOH . I 5 HOH A 61 661 2003 HOH HOH . I 5 HOH A 62 662 2082 HOH HOH . I 5 HOH A 63 663 2061 HOH HOH . I 5 HOH A 64 664 2076 HOH HOH . I 5 HOH A 65 665 2044 HOH HOH . I 5 HOH A 66 666 2057 HOH HOH . I 5 HOH A 67 667 2069 HOH HOH . I 5 HOH A 68 668 2070 HOH HOH . I 5 HOH A 69 669 2026 HOH HOH . I 5 HOH A 70 670 2056 HOH HOH . I 5 HOH A 71 671 2064 HOH HOH . I 5 HOH A 72 672 2067 HOH HOH . I 5 HOH A 73 673 2054 HOH HOH . I 5 HOH A 74 674 2080 HOH HOH . I 5 HOH A 75 675 2052 HOH HOH . I 5 HOH A 76 676 2055 HOH HOH . I 5 HOH A 77 677 2063 HOH HOH . I 5 HOH A 78 678 2005 HOH HOH . I 5 HOH A 79 679 2050 HOH HOH . I 5 HOH A 80 680 2008 HOH HOH . I 5 HOH A 81 681 2083 HOH HOH . I 5 HOH A 82 682 2001 HOH HOH . I 5 HOH A 83 683 2020 HOH HOH . I 5 HOH A 84 684 2027 HOH HOH . I 5 HOH A 85 685 2093 HOH HOH . I 5 HOH A 86 686 2017 HOH HOH . I 5 HOH A 87 687 2074 HOH HOH . I 5 HOH A 88 688 2012 HOH HOH . I 5 HOH A 89 689 2062 HOH HOH . I 5 HOH A 90 690 2006 HOH HOH . I 5 HOH A 91 691 2016 HOH HOH . I 5 HOH A 92 692 2034 HOH HOH . I 5 HOH A 93 693 2028 HOH HOH . I 5 HOH A 94 694 2009 HOH HOH . I 5 HOH A 95 695 2021 HOH HOH . I 5 HOH A 96 696 2039 HOH HOH . I 5 HOH A 97 697 2024 HOH HOH . I 5 HOH A 98 698 2010 HOH HOH . J 5 HOH B 1 601 2018 HOH HOH . J 5 HOH B 2 602 2031 HOH HOH . J 5 HOH B 3 603 2042 HOH HOH . J 5 HOH B 4 604 2034 HOH HOH . J 5 HOH B 5 605 2026 HOH HOH . J 5 HOH B 6 606 2028 HOH HOH . J 5 HOH B 7 607 2037 HOH HOH . J 5 HOH B 8 608 2065 HOH HOH . J 5 HOH B 9 609 2007 HOH HOH . J 5 HOH B 10 610 2032 HOH HOH . J 5 HOH B 11 611 2069 HOH HOH . J 5 HOH B 12 612 2041 HOH HOH . J 5 HOH B 13 613 2010 HOH HOH . J 5 HOH B 14 614 2003 HOH HOH . J 5 HOH B 15 615 2006 HOH HOH . J 5 HOH B 16 616 2054 HOH HOH . J 5 HOH B 17 617 2005 HOH HOH . J 5 HOH B 18 618 2044 HOH HOH . J 5 HOH B 19 619 2017 HOH HOH . J 5 HOH B 20 620 2070 HOH HOH . J 5 HOH B 21 621 2020 HOH HOH . J 5 HOH B 22 622 2038 HOH HOH . J 5 HOH B 23 623 2073 HOH HOH . J 5 HOH B 24 624 2027 HOH HOH . J 5 HOH B 25 625 2011 HOH HOH . J 5 HOH B 26 626 2036 HOH HOH . J 5 HOH B 27 627 2045 HOH HOH . J 5 HOH B 28 628 2023 HOH HOH . J 5 HOH B 29 629 2040 HOH HOH . J 5 HOH B 30 630 2052 HOH HOH . J 5 HOH B 31 631 2025 HOH HOH . J 5 HOH B 32 632 2060 HOH HOH . J 5 HOH B 33 633 2062 HOH HOH . J 5 HOH B 34 634 2068 HOH HOH . J 5 HOH B 35 635 2036 HOH HOH . J 5 HOH B 36 636 2072 HOH HOH . J 5 HOH B 37 637 2029 HOH HOH . J 5 HOH B 38 638 2046 HOH HOH . J 5 HOH B 39 639 2047 HOH HOH . J 5 HOH B 40 640 2064 HOH HOH . J 5 HOH B 41 641 2056 HOH HOH . J 5 HOH B 42 642 2030 HOH HOH . J 5 HOH B 43 643 2022 HOH HOH . J 5 HOH B 44 644 2058 HOH HOH . J 5 HOH B 45 645 2055 HOH HOH . J 5 HOH B 46 646 2057 HOH HOH . J 5 HOH B 47 647 2061 HOH HOH . J 5 HOH B 48 648 2053 HOH HOH . J 5 HOH B 49 649 2016 HOH HOH . J 5 HOH B 50 650 2051 HOH HOH . J 5 HOH B 51 651 2043 HOH HOH . J 5 HOH B 52 652 2059 HOH HOH . J 5 HOH B 53 653 2050 HOH HOH . J 5 HOH B 54 654 2008 HOH HOH . J 5 HOH B 55 655 2066 HOH HOH . J 5 HOH B 56 656 2013 HOH HOH . J 5 HOH B 57 657 2024 HOH HOH . J 5 HOH B 58 658 2049 HOH HOH . J 5 HOH B 59 659 2071 HOH HOH . J 5 HOH B 60 660 2015 HOH HOH . J 5 HOH B 61 661 2014 HOH HOH . J 5 HOH B 62 662 2019 HOH HOH . J 5 HOH B 63 663 2063 HOH HOH . J 5 HOH B 64 664 2067 HOH HOH . J 5 HOH B 65 665 2019 HOH HOH . J 5 HOH B 66 666 2039 HOH HOH . J 5 HOH B 67 667 2048 HOH HOH . J 5 HOH B 68 668 2001 HOH HOH . J 5 HOH B 69 669 2033 HOH HOH . J 5 HOH B 70 670 2012 HOH HOH . J 5 HOH B 71 671 2009 HOH HOH . J 5 HOH B 72 672 2035 HOH HOH . J 5 HOH B 73 673 2074 HOH HOH . J 5 HOH B 74 674 2029 HOH HOH . J 5 HOH B 75 675 2002 HOH HOH . J 5 HOH B 76 676 2004 HOH HOH . J 5 HOH B 77 677 2021 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol CA _atom_site.label_atom_id CA _atom_site.label_comp_id CA _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id H _atom_site.label_entity_id 3 _atom_site.Cartn_x 20.645 _atom_site.Cartn_y 13.117 _atom_site.Cartn_z 38.377 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 53.64 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 506 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 301 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #