data_5M7M # _model_server_result.job_id 8ws7yFOxUHZAwB18XS4Nmw _model_server_result.datetime_utc '2024-10-19 03:53:58' _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 5m7m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":919}' # _entry.id 5M7M # _exptl.entry_id 5M7M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 7 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.87 _cell.angle_gamma 90 _cell.entry_id 5M7M _cell.length_a 77.45 _cell.length_b 78.89 _cell.length_c 78.57 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M7M _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 _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 ? 7 G N N ? 7 O N N ? 7 P N N ? 7 Q N N ? 7 R N N ? 7 S N N ? 7 T 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 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 2 5 4 MAN MAN C1 O1 . O3 HO3 . sing 5 ? 2 6 5 MAN MAN C1 O1 . O2 HO2 . 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 901 NAG 2 n B NAG 2 B 2 NAG A 902 NAG 2 n B BMA 3 B 3 BMA A 903 MAN 2 n B MAN 4 B 4 MAN A 904 MAN 2 n B MAN 5 B 5 MAN A 905 MAN 2 n B MAN 6 B 6 MAN A 906 MAN # 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 59 A CYS 59 1_555 A SG CYS 76 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf2 A SG CYS 63 A CYS 63 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf3 A SG CYS 74 A CYS 74 1_555 A SG CYS 87 A CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf4 A SG CYS 80 A CYS 80 1_555 A SG CYS 86 A CYS 86 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 A SG CYS 103 A CYS 103 1_555 A SG CYS 120 A CYS 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 A SG CYS 108 A CYS 108 1_555 A SG CYS 138 A CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf7 A SG CYS 118 A CYS 118 1_555 A SG CYS 131 A CYS 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf8 A SG CYS 124 A CYS 124 1_555 A SG CYS 130 A CYS 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf9 A SG CYS 149 A CYS 149 1_555 A SG CYS 195 A CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? disulf ? disulf10 A SG CYS 157 A CYS 157 1_555 A SG CYS 351 A CYS 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf11 A SG CYS 367 A CYS 367 1_555 A SG CYS 469 A CYS 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf12 A SG CYS 414 A CYS 414 1_555 A SG CYS 802 A CYS 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf13 A SG CYS 567 A CYS 567 1_555 A SG CYS 663 A CYS 667 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? disulf ? disulf14 A SG CYS 569 A CYS 569 1_555 A SG CYS 648 A CYS 652 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf15 A SG CYS 771 A CYS 775 1_555 A SG CYS 781 A CYS 785 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? covale ? covale1 A ND2 ASN 525 A ASN 525 1_555 B C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B O4 NAG . B NAG 1 1_555 B C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale3 B O4 NAG . B NAG 2 1_555 B C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale4 B O6 BMA . B BMA 3 1_555 B C1 MAN . B MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale5 B O3 MAN . B MAN 4 1_555 B C1 MAN . B MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale6 B O2 MAN . B MAN 5 1_555 B C1 MAN . B MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? metalc ? metalc1 A OD1 ASP 172 A ASP 172 1_555 L ZN ZN . A ZN 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc2 A OD2 ASP 172 A ASP 172 1_555 L ZN ZN . A ZN 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc3 A OG1 THR 210 A THR 210 1_555 L ZN ZN . A ZN 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc4 A OD1 ASP 312 A ASP 312 1_555 K ZN ZN . A ZN 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc5 A OD2 ASP 312 A ASP 312 1_555 K ZN ZN . A ZN 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc6 A NE2 HIS 316 A HIS 316 1_555 K ZN ZN . A ZN 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc7 A OD2 ASP 359 A ASP 359 1_555 L ZN ZN . A ZN 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc8 A NE2 HIS 360 A HIS 360 1_555 L ZN ZN . A ZN 916 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc9 A NE2 HIS 475 A HIS 475 1_555 K ZN ZN . A ZN 915 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc10 A OD1 ASP 736 A ASP 740 1_555 N ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc11 A OD1 ASP 738 A ASP 742 1_555 N ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc12 A OD1 ASP 740 A ASP 744 1_555 N ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc13 A O LEU 742 A LEU 746 1_555 N ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? metalc ? metalc14 A OD1 ASP 744 A ASP 748 1_555 N ZN ZN . A ZN 918 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc15 K ZN ZN . A ZN 915 1_555 U O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.502 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5M7M _atom_sites.fract_transf_matrix[1][1] 0.012912 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000422 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012676 _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] 0.012734 _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 7HR A 1 907 1 7HR LIG . D 4 IOD A 1 908 1 IOD IOD . E 5 CL A 1 909 2 CL CL . F 6 SCN A 1 910 3 SCN SCN . G 7 NI A 1 911 4 NI NI . H 8 PO4 A 1 912 5 PO4 PO4 . I 5 CL A 1 913 6 CL CL . J 9 K A 1 914 7 K K . K 10 ZN A 1 915 8 ZN ZN . L 10 ZN A 1 916 9 ZN ZN . M 10 ZN A 1 917 10 ZN ZN . N 10 ZN A 1 918 11 ZN ZN . O 7 NI A 1 919 12 NI NI . P 7 NI A 1 920 13 NI NI . Q 7 NI A 1 921 14 NI NI . R 7 NI A 1 922 15 NI NI . S 7 NI A 1 923 16 NI NI . T 7 NI A 1 924 17 NI NI . U 11 HOH A 1 1001 45 HOH HOH . U 11 HOH A 2 1002 3 HOH HOH . U 11 HOH A 3 1003 32 HOH HOH . U 11 HOH A 4 1004 21 HOH HOH . U 11 HOH A 5 1005 34 HOH HOH . U 11 HOH A 6 1006 7 HOH HOH . U 11 HOH A 7 1007 19 HOH HOH . U 11 HOH A 8 1008 25 HOH HOH . U 11 HOH A 9 1009 27 HOH HOH . U 11 HOH A 10 1010 1 HOH HOH . U 11 HOH A 11 1011 37 HOH HOH . U 11 HOH A 12 1012 4 HOH HOH . U 11 HOH A 13 1013 39 HOH HOH . U 11 HOH A 14 1014 13 HOH HOH . U 11 HOH A 15 1015 50 HOH HOH . U 11 HOH A 16 1016 6 HOH HOH . U 11 HOH A 17 1017 47 HOH HOH . U 11 HOH A 18 1018 5 HOH HOH . U 11 HOH A 19 1019 43 HOH HOH . U 11 HOH A 20 1020 33 HOH HOH . U 11 HOH A 21 1021 20 HOH HOH . U 11 HOH A 22 1022 24 HOH HOH . U 11 HOH A 23 1023 49 HOH HOH . U 11 HOH A 24 1024 17 HOH HOH . U 11 HOH A 25 1025 14 HOH HOH . U 11 HOH A 26 1026 35 HOH HOH . U 11 HOH A 27 1027 28 HOH HOH . U 11 HOH A 28 1028 41 HOH HOH . U 11 HOH A 29 1029 23 HOH HOH . U 11 HOH A 30 1030 8 HOH HOH . U 11 HOH A 31 1031 40 HOH HOH . U 11 HOH A 32 1032 38 HOH HOH . U 11 HOH A 33 1033 42 HOH HOH . U 11 HOH A 34 1034 16 HOH HOH . U 11 HOH A 35 1035 11 HOH HOH . U 11 HOH A 36 1036 36 HOH HOH . U 11 HOH A 37 1037 29 HOH HOH . U 11 HOH A 38 1038 2 HOH HOH . U 11 HOH A 39 1039 10 HOH HOH . U 11 HOH A 40 1040 12 HOH HOH . U 11 HOH A 41 1041 31 HOH HOH . U 11 HOH A 42 1042 51 HOH HOH . U 11 HOH A 43 1043 9 HOH HOH . U 11 HOH A 44 1044 18 HOH HOH . U 11 HOH A 45 1045 52 HOH HOH . U 11 HOH A 46 1046 46 HOH HOH . U 11 HOH A 47 1047 22 HOH HOH . U 11 HOH A 48 1048 30 HOH HOH . U 11 HOH A 49 1049 26 HOH HOH . U 11 HOH A 50 1050 53 HOH HOH . U 11 HOH A 51 1051 15 HOH HOH . U 11 HOH A 52 1052 44 HOH HOH . U 11 HOH A 53 1053 48 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id O _atom_site.label_entity_id 7 _atom_site.Cartn_x 56.689 _atom_site.Cartn_y -10.477 _atom_site.Cartn_z 0.84 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 53.91 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 919 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #