data_8DCB # _model_server_result.job_id Kjyvk03UxzlHE7w8PqVMdQ _model_server_result.datetime_utc '2024-11-16 01:50:13' _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 8dcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":504}' # _entry.id 8DCB # _exptl.entry_id 8DCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _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 8DCB _cell.length_a 81.241 _cell.length_b 137.492 _cell.length_c 149.559 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8DCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,G,H,I,J,K,L,M,N,Y 1 1 B,D,O,P,Q,R,S,T,U,V,W,X,Z 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 ? 5 G N N ? 5 H N N ? 5 P N N ? 5 Q N N ? 5 R 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 1 _pdbx_entity_branch_link.entity_branch_list_num_2 2 _pdbx_entity_branch_link.comp_id_1 GLC _pdbx_entity_branch_link.comp_id_2 FRU _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 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _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 GLC 1 C 1 GLC A 503 SUC 2 n C FRU 2 C 2 FRU A 503 SUC 2 n D GLC 1 D 1 GLC B 502 SUC 2 n D FRU 2 D 2 FRU B 502 SUC # 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 C1 GLC . C GLC 1 1_555 C O2 FRU . C FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale2 D C1 GLC . D GLC 1 1_555 D O2 FRU . D FRU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? metalc ? metalc1 A OD2 ASP 115 A ASP 95 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc2 A SG CYS 118 A CYS 98 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc3 A SG CYS 118 A CYS 98 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? metalc ? metalc4 A NE2 HIS 223 A HIS 203 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc5 A NE2 HIS 254 A HIS 234 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc6 A NE2 HIS 349 A HIS 329 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc7 E O1B GTP . A GTP 501 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc8 E O2A GTP . A GTP 501 1_555 G NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.639 ? metalc ? metalc9 E O2G GTP . A GTP 501 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc10 E O1B GTP . A GTP 501 1_555 H NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc11 G NI NI . A NI 503 1_555 Y O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc12 B OD2 ASP 115 B ASP 95 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? metalc ? metalc13 B SG CYS 118 B CYS 98 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc14 B SG CYS 118 B CYS 98 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc15 B NE2 HIS 223 B HIS 203 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc16 B NE2 HIS 254 B HIS 234 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc17 B OE2 GLU 325 B GLU 305 1_555 R NI NI . B NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? metalc ? metalc18 B NE2 HIS 349 B HIS 329 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc19 O O2G GTP . B GTP 501 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? metalc ? metalc20 O O1B GTP . B GTP 501 1_555 P NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc21 O O1B GTP . B GTP 501 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc22 O O2A GTP . B GTP 501 1_555 Q NI NI . B NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc23 Q NI NI . B NI 503 1_555 Z O HOH . B HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? # _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 8DCB _atom_sites.fract_transf_matrix[1][1] 0.012309 _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] 0.007273 _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] 0.006686 _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 GTP A 1 501 501 GTP GTP . F 4 GOL A 1 502 502 GOL GOL . G 5 NI A 1 503 3 NI NI . H 5 NI A 1 504 4 NI NI . I 6 SO4 A 1 505 3 SO4 SO4 . J 6 SO4 A 1 506 4 SO4 SO4 . K 6 SO4 A 1 507 6 SO4 SO4 . L 6 SO4 A 1 508 8 SO4 SO4 . M 6 SO4 A 1 509 12 SO4 SO4 . N 7 CL A 1 510 2 CL CL . O 3 GTP B 1 501 501 GTP GTP . P 5 NI B 1 502 1 NI NI . Q 5 NI B 1 503 2 NI NI . R 5 NI B 1 504 5 NI NI . S 6 SO4 B 1 505 1 SO4 SO4 . T 6 SO4 B 1 506 2 SO4 SO4 . U 6 SO4 B 1 507 7 SO4 SO4 . V 6 SO4 B 1 508 15 SO4 SO4 . W 6 SO4 B 1 509 16 SO4 SO4 . X 7 CL B 1 510 3 CL CL . Y 8 HOH A 1 601 18 HOH HOH . Y 8 HOH A 2 602 5 HOH HOH . Y 8 HOH A 3 603 3 HOH HOH . Y 8 HOH A 4 604 2 HOH HOH . Y 8 HOH A 5 605 20 HOH HOH . Y 8 HOH A 6 606 22 HOH HOH . Y 8 HOH A 7 607 19 HOH HOH . Y 8 HOH A 8 608 15 HOH HOH . Z 8 HOH B 1 601 12 HOH HOH . Z 8 HOH B 2 602 1 HOH HOH . Z 8 HOH B 3 603 13 HOH HOH . Z 8 HOH B 4 604 14 HOH HOH . Z 8 HOH B 5 605 6 HOH HOH . Z 8 HOH B 6 606 21 HOH HOH . Z 8 HOH B 7 607 16 HOH HOH . Z 8 HOH B 8 608 23 HOH HOH . Z 8 HOH B 9 609 7 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 H _atom_site.label_entity_id 5 _atom_site.Cartn_x 18.497 _atom_site.Cartn_y 10.856 _atom_site.Cartn_z 34.904 _atom_site.occupancy 0.6 _atom_site.B_iso_or_equiv 68.95 _atom_site.pdbx_formal_charge 2 _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 504 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 1 #