data_6RVD # _model_server_result.job_id pufkJIXvSqQCPBeNCxF0Iw _model_server_result.datetime_utc '2025-07-03 23:15:17' _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 6rvd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":204}' # _entry.id 6RVD # _exptl.entry_id 6RVD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 40.078 _entity.id 8 _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 6RVD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RVD _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 ? 8 R N N ? 8 S N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _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 3 n D NAG 1 D 1 NAG G 1805 NAG 3 n D NAG 2 D 2 NAG G 1806 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 234 A CYS 234 1_555 A SG CYS 327 A CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 A SG CYS 296 A CYS 296 1_555 A SG CYS 304 A CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 B SG CYS 203 B CYS 203 1_555 B SG CYS 226 B CYS 226 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 B SG CYS 234 B CYS 234 1_555 B SG CYS 327 B CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf5 B SG CYS 296 B CYS 296 1_555 B SG CYS 304 B CYS 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? covale ? covale1 A ND2 ASN 141 A ASN 141 1_555 J C1 NAG . A NAG 1508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 312 A ASN 312 1_555 F C1 NAG . A NAG 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale3 A ND2 ASN 349 A ASN 349 1_555 G C1 NAG . A NAG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? covale ? covale4 A ND2 ASN 414 A ASN 414 1_555 H C1 NAG . A NAG 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 A ND2 ASN 875 A ASN 875 1_555 I C1 NAG . A NAG 1505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale6 A ND2 ASN 1000 A ASN 1000 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale7 B ND2 ASN 414 B ASN 414 1_555 M C1 NAG . B NAG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale8 B ND2 ASN 1000 B ASN 1000 1_555 N C1 NAG . B NAG 1504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale9 C N CYS 1 C CYS 24 1_555 O C1 PLM . C PLM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.511 ? covale ? covale10 C C GLY 174 C GLY 197 1_555 P O1 CLR . C CLR 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.374 ? covale ? covale11 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 C OE1 GLU 66 C GLU 89 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc2 C OE2 GLU 66 C GLU 89 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc3 C OE2 GLU 67 C GLU 90 1_555 R CA CA . C CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc4 C OE1 GLU 67 C GLU 90 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc5 C OE2 GLU 67 C GLU 90 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc6 C OD1 ASP 72 C ASP 95 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc7 C OD2 ASP 72 C ASP 95 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? metalc ? metalc8 C O THR 102 C THR 125 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc9 C OE1 GLU 103 C GLU 126 1_555 R CA CA . C CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc10 C OE2 GLU 103 C GLU 126 1_555 R CA CA . C CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc11 C OE2 GLU 103 C GLU 126 1_555 S CA CA . C CA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc12 C OD1 ASP 106 C ASP 129 1_555 R CA CA . C CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc13 C OD2 ASP 108 C ASP 131 1_555 R CA CA . C CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc14 C NE2 HIS 117 C HIS 140 1_555 Q ZN ZN . C ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc15 C OD1 ASP 124 C ASP 147 1_555 Q ZN ZN . C ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc16 C OD2 ASP 124 C ASP 147 1_555 Q ZN ZN . C ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc17 C OE1 GLU 153 C GLU 176 1_555 Q ZN ZN . C ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc18 C ND1 HIS 159 C HIS 182 1_555 Q ZN ZN . C ZN 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? # _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 6RVD _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 E 4 CLR A 1 1501 3 CLR CLR . F 5 NAG A 1 1502 1801 NAG NAG . G 5 NAG A 1 1503 1802 NAG NAG . H 5 NAG A 1 1504 1803 NAG NAG . I 5 NAG A 1 1505 1804 NAG NAG . J 5 NAG A 1 1508 1807 NAG NAG . K 4 CLR B 1 1501 1 CLR CLR . L 4 CLR B 1 1502 2 CLR CLR . M 5 NAG B 1 1503 1808 NAG NAG . N 5 NAG B 1 1504 1809 NAG NAG . O 6 PLM C 1 201 23 PLM PLM . P 4 CLR C 1 202 198 CLR CLR . Q 7 ZN C 1 203 1 ZN ZN . R 8 CA C 1 204 1 CA CA . S 8 CA C 1 205 2 CA CA . # _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 8 _atom_site.Cartn_x 75.109 _atom_site.Cartn_y 151.812 _atom_site.Cartn_z 127.891 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 97.67 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 204 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 62 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 1 #