data_8V8D # _model_server_result.job_id TI5giVE9ikT5lBjiIYBfmQ _model_server_result.datetime_utc '2024-12-27 12:32:05' _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 8v8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Z","auth_seq_id":602}' # _entry.id 8V8D # _exptl.entry_id 8V8D _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 40.078 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 3 _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 8V8D _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8V8D _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 ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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 _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 ? 6 P N N ? 6 U N N ? 6 Z 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 F NAG 1 F 1 NAG A 513 NAG 2 n F NAG 2 F 2 NAG A 514 NAG 2 n G NAG 1 G 1 NAG B 513 NAG 2 n G NAG 2 G 2 NAG B 514 NAG 2 n H NAG 1 H 1 NAG C 513 NAG 2 n H NAG 2 H 2 NAG C 514 NAG 2 n I NAG 1 I 1 NAG D 513 NAG 2 n I NAG 2 I 2 NAG D 514 NAG 2 n J NAG 1 J 1 NAG E 513 NAG 2 n J NAG 2 J 2 NAG E 514 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 127 A CYS 127 1_555 A SG CYS 141 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 189 A CYS 189 1_555 A SG CYS 190 A CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 B SG CYS 127 B CYS 127 1_555 B SG CYS 141 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 189 B CYS 189 1_555 B SG CYS 190 B CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 C SG CYS 127 C CYS 127 1_555 C SG CYS 141 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf6 C SG CYS 189 C CYS 189 1_555 C SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf7 D SG CYS 127 D CYS 127 1_555 D SG CYS 141 D CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf8 D SG CYS 189 D CYS 189 1_555 D SG CYS 190 D CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf9 E SG CYS 127 E CYS 127 1_555 E SG CYS 141 E CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf10 E SG CYS 189 E CYS 189 1_555 E SG CYS 190 E CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 23 A ASN 23 1_555 L C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 67 A ASN 67 1_555 K C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale3 A ND2 ASN 110 A ASN 110 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 B ND2 ASN 23 B ASN 23 1_555 R C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale5 B ND2 ASN 67 B ASN 67 1_555 Q C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 110 B ASN 110 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale7 C ND2 ASN 23 C ASN 23 1_555 W C1 NAG . C NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 C ND2 ASN 67 C ASN 67 1_555 V C1 NAG . C NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 C ND2 ASN 110 C ASN 110 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale10 D ND2 ASN 23 D ASN 23 1_555 BA C1 NAG . D NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale11 D ND2 ASN 67 D ASN 67 1_555 AA C1 NAG . D NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale12 D ND2 ASN 110 D ASN 110 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 E ND2 ASN 23 E ASN 23 1_555 FA C1 NAG . E NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale14 E ND2 ASN 67 E ASN 67 1_555 EA C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale15 E ND2 ASN 110 E ASN 110 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale17 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale18 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale19 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale20 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? metalc ? metalc1 B O VAL 42 B VAL 42 1_555 P CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.494 ? metalc ? metalc2 B OE1 GLU 44 B GLU 44 1_555 P CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc3 B OE2 GLU 44 B GLU 44 1_555 P CA CA . B CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.189 ? metalc ? metalc4 C OE2 GLU 172 C GLU 172 1_555 U CA CA . C CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.914 ? metalc ? metalc5 C OH TYR 210 C TYR 210 1_555 U CA CA . C CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.052 ? metalc ? metalc6 D OE1 GLU 44 D GLU 44 1_555 Z CA CA . D CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.831 ? metalc ? metalc7 D OE2 GLU 44 D GLU 44 1_555 Z CA CA . D CA 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.655 ? # _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 8V8D _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 K 3 NAG A 1 601 512 NAG NAG . L 3 NAG A 1 602 510 NAG NAG . M 4 EPJ A 1 603 609 EPJ EPJ . N 5 I34 A 1 604 600 I34 I34 . O 5 I34 B 1 601 600 I34 I34 . P 6 CA B 1 602 504 CA CA . Q 3 NAG B 1 603 512 NAG NAG . R 3 NAG B 1 604 510 NAG NAG . S 4 EPJ B 1 605 609 EPJ EPJ . T 5 I34 C 1 601 600 I34 I34 . U 6 CA C 1 602 504 CA CA . V 3 NAG C 1 603 512 NAG NAG . W 3 NAG C 1 604 510 NAG NAG . X 4 EPJ C 1 605 609 EPJ EPJ . Y 5 I34 D 1 601 600 I34 I34 . Z 6 CA D 1 602 504 CA CA . AA 3 NAG D 1 603 512 NAG NAG . BA 3 NAG D 1 604 510 NAG NAG . CA 4 EPJ D 1 605 609 EPJ EPJ . DA 5 I34 D 1 606 600 I34 I34 . EA 3 NAG E 1 601 512 NAG NAG . FA 3 NAG E 1 602 510 NAG NAG . GA 4 EPJ E 1 603 609 EPJ EPJ . # _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 Z _atom_site.label_entity_id 6 _atom_site.Cartn_x 133.898 _atom_site.Cartn_y 124.116 _atom_site.Cartn_z 142.879 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 81.19 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 602 _atom_site.auth_asym_id D _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 81 _model_server_stats.query_time_ms 224 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #