data_2J3F # _model_server_result.job_id 1rNzR2cSCt4wZBOoMjw5xg _model_server_result.datetime_utc '2024-11-26 21:00:14' _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 2j3f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":1290}' # _entry.id 2J3F # _exptl.entry_id 2J3F _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 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 120 _cell.entry_id 2J3F _cell.length_a 96.825 _cell.length_b 96.825 _cell.length_c 141.898 _cell.Z_PDB 15 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J3F _symmetry.cell_setting ? _symmetry.Int_Tables_number 145 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS trimeric 3 author_and_software_defined_assembly 1 PQS trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,I,J,K,L,M,N,U,V,W 1 1 D,E,F,H,O,P,Q,R,S,T,X,Y,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 I N N ? 5 K N N ? 5 N N N ? 5 P N N ? 5 T N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 4 ? 3 5 1 FUC NAG C1 O1 . O6 HO6 . sing 5 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 4 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 G NAG 1 G 1 NAG B 1291 NAG 3 n G NAG 2 G 2 NAG B 1292 NAG 3 n G BMA 3 G 3 BMA B 1294 BMA 3 n G MAN 4 G 4 MAN B 1295 MAN 3 n G FUC 5 G 5 FUC B 1293 FUC 4 n H NAG 1 H 1 NAG E 1291 NAG 4 n H NAG 2 H 2 NAG E 1292 NAG 4 n H BMA 3 H 3 BMA E 1293 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 4 A CYS 73 1_555 A SG CYS 32 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf2 A SG CYS 11 A CYS 80 1_555 A SG CYS 39 A CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 163 A CYS 232 1_555 A SG CYS 176 A CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? disulf ? disulf4 B SG CYS 4 B CYS 73 1_555 B SG CYS 32 B CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf5 B SG CYS 11 B CYS 80 1_555 B SG CYS 39 B CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 163 B CYS 232 1_555 B SG CYS 176 B CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf7 C SG CYS 11 C CYS 80 1_555 C SG CYS 39 C CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 C SG CYS 163 C CYS 232 1_555 C SG CYS 176 C CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf9 D SG CYS 4 D CYS 73 1_555 D SG CYS 32 D CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? disulf ? disulf10 D SG CYS 11 D CYS 80 1_555 D SG CYS 39 D CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf11 D SG CYS 163 D CYS 232 1_555 D SG CYS 176 D CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf12 E SG CYS 4 E CYS 73 1_555 E SG CYS 32 E CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf13 E SG CYS 11 E CYS 80 1_555 E SG CYS 39 E CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf14 E SG CYS 163 E CYS 232 1_555 E SG CYS 176 E CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf15 F SG CYS 4 F CYS 73 1_555 F SG CYS 32 F CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf16 F SG CYS 11 F CYS 80 1_555 F SG CYS 39 F CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf17 F SG CYS 163 F CYS 232 1_555 F SG CYS 176 F CYS 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? covale ? covale1 B ND2 ASN 146 B ASN 215 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale2 E ND2 ASN 146 E ASN 215 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale3 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 G O6 NAG . G NAG 1 1_555 G C1 FUC . G FUC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale6 G O6 BMA . G BMA 3 1_555 G C1 MAN . G MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? covale ? covale8 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? metalc ? metalc1 A OD1 ASP 155 A ASP 224 1_555 I CA CA . A CA 1289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc2 A OD1 ASP 157 A ASP 226 1_555 I CA CA . A CA 1289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc3 A O ASN 159 A ASN 228 1_555 I CA CA . A CA 1289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? metalc ? metalc4 A O GLY 161 A GLY 230 1_555 I CA CA . A CA 1289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.062 ? metalc ? metalc5 B OD2 ASP 155 B ASP 224 1_555 K CA CA . B CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc6 B OD1 ASP 155 B ASP 224 1_555 K CA CA . B CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc7 B OD1 ASP 157 B ASP 226 1_555 K CA CA . B CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc8 B O ASN 159 B ASN 228 1_555 K CA CA . B CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc9 B O GLY 161 B GLY 230 1_555 K CA CA . B CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? metalc ? metalc10 K CA CA . B CA 1290 1_555 V O HOH . B HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc11 C OD1 ASP 155 C ASP 224 1_555 N CA CA . C CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.556 ? metalc ? metalc12 C OD2 ASP 155 C ASP 224 1_555 N CA CA . C CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc13 C OD1 ASP 157 C ASP 226 1_555 N CA CA . C CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc14 C O ASN 159 C ASN 228 1_555 N CA CA . C CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc15 C O GLY 161 C GLY 230 1_555 N CA CA . C CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc16 E OD1 ASP 155 E ASP 224 1_555 P CA CA . E CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc17 E OD2 ASP 155 E ASP 224 1_555 P CA CA . E CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc18 E OD1 ASP 157 E ASP 226 1_555 P CA CA . E CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc19 E O ASN 159 E ASN 228 1_555 P CA CA . E CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc20 E O GLY 161 E GLY 230 1_555 P CA CA . E CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc21 P CA CA . E CA 1290 1_555 Y O HOH . E HOH 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.674 ? metalc ? metalc22 F OD1 ASP 155 F ASP 224 1_555 T CA CA . F CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc23 F OD2 ASP 155 F ASP 224 1_555 T CA CA . F CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc24 F OD1 ASP 157 F ASP 226 1_555 T CA CA . F CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc25 F O ASN 159 F ASN 228 1_555 T CA CA . F CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc26 F O GLY 161 F GLY 230 1_555 T CA CA . F CA 1290 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? # _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 2J3F _atom_sites.fract_transf_matrix[1][1] 0.010328 _atom_sites.fract_transf_matrix[1][2] 0.005963 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011926 _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] 0.007047 _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 5 CA A 1 1289 1289 CA CA . J 6 A2G B 1 1289 1289 A2G A2G . K 5 CA B 1 1290 1290 CA CA . L 7 P4C B 1 1296 1296 P4C P4C . M 6 A2G C 1 1289 1289 A2G A2G . N 5 CA C 1 1290 1290 CA CA . O 6 A2G E 1 1289 1289 A2G A2G . P 5 CA E 1 1290 1290 CA CA . Q 7 P4C E 1 1294 1294 P4C P4C . R 8 EPE E 1 1295 1295 EPE EPE . S 6 A2G F 1 1289 1289 A2G A2G . T 5 CA F 1 1290 1290 CA CA . U 9 HOH A 1 2001 2001 HOH HOH . U 9 HOH A 2 2002 2002 HOH HOH . U 9 HOH A 3 2003 2003 HOH HOH . U 9 HOH A 4 2004 2004 HOH HOH . U 9 HOH A 5 2005 2005 HOH HOH . U 9 HOH A 6 2006 2006 HOH HOH . V 9 HOH B 1 2001 2001 HOH HOH . V 9 HOH B 2 2002 2002 HOH HOH . V 9 HOH B 3 2003 2003 HOH HOH . V 9 HOH B 4 2004 2004 HOH HOH . V 9 HOH B 5 2005 2005 HOH HOH . V 9 HOH B 6 2006 2006 HOH HOH . V 9 HOH B 7 2007 2007 HOH HOH . V 9 HOH B 8 2008 2008 HOH HOH . V 9 HOH B 9 2009 2009 HOH HOH . V 9 HOH B 10 2010 2010 HOH HOH . V 9 HOH B 11 2011 2011 HOH HOH . V 9 HOH B 12 2012 2012 HOH HOH . V 9 HOH B 13 2013 2013 HOH HOH . W 9 HOH C 1 2001 2001 HOH HOH . W 9 HOH C 2 2002 2002 HOH HOH . W 9 HOH C 3 2003 2003 HOH HOH . W 9 HOH C 4 2004 2004 HOH HOH . W 9 HOH C 5 2005 2005 HOH HOH . W 9 HOH C 6 2006 2006 HOH HOH . W 9 HOH C 7 2007 2007 HOH HOH . W 9 HOH C 8 2008 2008 HOH HOH . W 9 HOH C 9 2009 2009 HOH HOH . W 9 HOH C 10 2010 2010 HOH HOH . W 9 HOH C 11 2011 2011 HOH HOH . W 9 HOH C 12 2012 2012 HOH HOH . X 9 HOH D 1 2001 2001 HOH HOH . X 9 HOH D 2 2002 2002 HOH HOH . X 9 HOH D 3 2003 2003 HOH HOH . X 9 HOH D 4 2004 2004 HOH HOH . X 9 HOH D 5 2005 2005 HOH HOH . Y 9 HOH E 1 2001 2001 HOH HOH . Y 9 HOH E 2 2002 2002 HOH HOH . Y 9 HOH E 3 2003 2003 HOH HOH . Y 9 HOH E 4 2004 2004 HOH HOH . Y 9 HOH E 5 2005 2005 HOH HOH . Y 9 HOH E 6 2006 2006 HOH HOH . Y 9 HOH E 7 2007 2007 HOH HOH . Y 9 HOH E 8 2008 2008 HOH HOH . Y 9 HOH E 9 2009 2009 HOH HOH . Y 9 HOH E 10 2010 2010 HOH HOH . Z 9 HOH F 1 2001 2001 HOH HOH . Z 9 HOH F 2 2002 2002 HOH HOH . Z 9 HOH F 3 2003 2003 HOH HOH . Z 9 HOH F 4 2004 2004 HOH HOH . Z 9 HOH F 5 2005 2005 HOH HOH . Z 9 HOH F 6 2006 2006 HOH HOH . Z 9 HOH F 7 2007 2007 HOH HOH . # _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 P _atom_site.label_entity_id 5 _atom_site.Cartn_x 30.458 _atom_site.Cartn_y 52.422 _atom_site.Cartn_z 123.328 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 33.67 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 1290 _atom_site.auth_asym_id E _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 1085 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #