data_5MKF # _model_server_result.job_id wLOkC5nYZBiStOFmDySKrQ _model_server_result.datetime_utc '2025-03-06 09:38:21' _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 5mkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":1012}' # _entry.id 5MKF # _exptl.entry_id 5MKF _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 40.078 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM 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 5MKF _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA _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 ? _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 R N N ? 7 S N N ? 7 T N N ? 7 U N N ? 7 EA 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 E NAG 1 E 1 NAG A 803 NAG 2 n E NAG 2 E 2 NAG A 804 NAG 2 n F NAG 1 F 1 NAG B 803 NAG 2 n F NAG 2 F 2 NAG B 804 NAG 2 n G NAG 1 G 1 NAG C 803 NAG 2 n G NAG 2 G 2 NAG C 804 NAG 2 n H NAG 1 H 1 NAG D 803 NAG 2 n H NAG 2 H 2 NAG D 804 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 331 A CYS 331 1_555 A SG CYS 344 A CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 B SG CYS 331 B CYS 331 1_555 B SG CYS 344 B CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf3 C SG CYS 331 C CYS 331 1_555 C SG CYS 344 C CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 D SG CYS 331 D CYS 331 1_555 D SG CYS 344 D CYS 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? covale ? covale1 A ND2 ASN 328 A ASN 328 1_555 I C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale2 A ND2 ASN 362 A ASN 362 1_555 J C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.548 ? covale ? covale3 B ND2 ASN 328 B ASN 328 1_555 V C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale4 B ND2 ASN 362 B ASN 362 1_555 W C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.548 ? covale ? covale5 C ND2 ASN 328 C ASN 328 1_555 FA C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale6 C ND2 ASN 362 C ASN 362 1_555 GA C1 NAG . C NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.549 ? covale ? covale7 D ND2 ASN 328 D ASN 328 1_555 OA C1 NAG . D NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.248 ? covale ? covale8 D ND2 ASN 362 D ASN 362 1_555 PA C1 NAG . D NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.563 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale11 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale12 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? metalc ? metalc1 A OD1 ASN 681 A ASN 681 1_555 R CA CA . A CA 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc2 R CA CA . A CA 1012 1_555 B OD1 ASN 681 B ASN 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc3 R CA CA . A CA 1012 1_555 C OD1 ASN 681 C ASN 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc4 R CA CA . A CA 1012 1_555 D OD1 ASN 681 D ASN 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? # _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 5MKF _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 3 NAG A 1 1001 801 NAG NAG . J 3 NAG A 1 1002 802 NAG NAG . K 3 NAG A 1 1005 800 NAG NAG . L 4 PX6 A 1 1006 7 PX6 PX6 . M 5 PLM A 1 1007 4 PLM PLM . N 5 PLM A 1 1008 5 PLM PLM . O 5 PLM A 1 1009 6 PLM PLM . P 6 CHS A 1 1010 5 CHS CHS . Q 6 CHS A 1 1011 6 CHS CHS . R 7 CA A 1 1012 4 CA CA . S 7 CA A 1 1013 5 CA CA . T 7 CA A 1 1014 6 CA CA . U 7 CA A 1 1015 7 CA CA . V 3 NAG B 1 1001 801 NAG NAG . W 3 NAG B 1 1002 802 NAG NAG . X 3 NAG B 1 1005 800 NAG NAG . Y 4 PX6 B 1 1006 8 PX6 PX6 . Z 5 PLM B 1 1007 7 PLM PLM . AA 5 PLM B 1 1008 8 PLM PLM . BA 5 PLM B 1 1009 9 PLM PLM . CA 6 CHS B 1 1010 7 CHS CHS . DA 6 CHS B 1 1011 8 CHS CHS . EA 7 CA B 1 1012 2 CA CA . FA 3 NAG C 1 1001 801 NAG NAG . GA 3 NAG C 1 1002 802 NAG NAG . HA 3 NAG C 1 1005 800 NAG NAG . IA 4 PX6 C 1 1006 9 PX6 PX6 . JA 5 PLM C 1 1007 10 PLM PLM . KA 5 PLM C 1 1008 11 PLM PLM . LA 5 PLM C 1 1009 12 PLM PLM . MA 6 CHS C 1 1010 9 CHS CHS . NA 6 CHS C 1 1011 10 CHS CHS . OA 3 NAG D 1 1001 801 NAG NAG . PA 3 NAG D 1 1002 802 NAG NAG . QA 3 NAG D 1 1005 800 NAG NAG . RA 4 PX6 D 1 1006 10 PX6 PX6 . SA 5 PLM D 1 1007 13 PLM PLM . TA 5 PLM D 1 1008 14 PLM PLM . UA 5 PLM D 1 1009 15 PLM PLM . VA 6 CHS D 1 1010 3 CHS CHS . WA 6 CHS D 1 1011 4 CHS CHS . # _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 R _atom_site.label_entity_id 7 _atom_site.Cartn_x 95.802 _atom_site.Cartn_y 95.751 _atom_site.Cartn_z 66.123 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 30 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 1012 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #