data_3VKF # _model_server_result.job_id NFpEmuR6fEg4resjpn8V8A _model_server_result.datetime_utc '2025-03-04 09:05:34' _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 3vkf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":2001}' # _entry.id 3VKF # _exptl.entry_id 3VKF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 5 _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 108.62 _cell.angle_gamma 90 _cell.entry_id 3VKF _cell.length_a 81.261 _cell.length_b 95.186 _cell.length_c 120.396 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VKF _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? tetrameric 4 author_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 PISA monomeric 1 software_defined_assembly 4 PISA monomeric 1 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I 1 1 A,E,F 2 1 B,G 3 1 C,H 4 1 D,I 5 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 H N N ? 5 I N N # _pdbx_entity_branch.entity_id 3 _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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . 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 E NAG 1 E 1 NAG A 2002 NAG 3 n E NAG 2 E 2 NAG A 2003 NAG 3 n E BMA 3 E 3 BMA A 2004 BMA # 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 73 A CYS 117 1_555 A SG CYS 109 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf2 A SG CYS 128 A CYS 172 1_555 A SG CYS 137 A CYS 181 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 289 A CYS 342 1_555 A SG CYS 300 A CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 459 A CYS 512 1_555 A SG CYS 493 A CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf5 B SG CYS 73 B CYS 117 1_555 B SG CYS 109 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 B SG CYS 289 B CYS 342 1_555 B SG CYS 300 B CYS 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 B SG CYS 459 B CYS 512 1_555 B SG CYS 493 B CYS 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 290 A ASN 343 1_555 F C1 NAG . A NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 494 A ASN 547 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? covale ? covale3 B ND2 ASN 290 B ASN 343 1_555 G C1 NAG . B NAG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? metalc ? metalc1 C OD2 ASP 56 C ASP 136 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc2 C O VAL 73 C VAL 153 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc3 C O ILE 125 C ILE 235 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc4 C OD1 ASN 127 C ASN 237 1_555 H CA CA . C CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? metalc ? metalc5 D OD2 ASP 56 D ASP 136 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc6 D O VAL 73 D VAL 153 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc7 D O ILE 125 D ILE 235 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? metalc ? metalc8 D OD1 ASN 127 D ASN 237 1_555 I CA CA . D CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? # _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 3VKF _atom_sites.fract_transf_matrix[1][1] 0.012306 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004146 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010506 _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] 0.008765 _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 F 4 NAG A 1 2001 2001 NAG NAG . G 4 NAG B 1 2001 2001 NAG NAG . H 5 CA C 1 2001 2001 CA CA . I 5 CA D 1 2001 2001 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 H _atom_site.label_entity_id 5 _atom_site.Cartn_x -34.149 _atom_site.Cartn_y -9.023 _atom_site.Cartn_z 42.005 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 68.48 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 2001 _atom_site.auth_asym_id C _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 29 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 1 #