data_4D5M # _model_server_result.job_id E6gHyCRinjrZkOGIN_MhMw _model_server_result.datetime_utc '2024-10-24 04:27:27' _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 4d5m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1011}' # _entry.id 4D5M # _exptl.entry_id 4D5M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 94.971 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHATE 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 98.83 _cell.angle_gamma 90 _cell.entry_id 4D5M _cell.length_a 84.9 _cell.length_b 27.47 _cell.length_c 13.15 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D5M _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,H 1 1 B,F,I 2 1 C,G,J 3 1 D,K 4 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 ? 2 E N N ? 2 F N N ? 2 G N N # 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 covale ? covale1 A C PCA 1 A PCA 1 1_555 A N HIS 2 A HIS 2 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.413 ? covale ? covale2 A C PCA 1 A PCA 1 1_555 A N HIS 2 A HIS 2 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.381 ? covale ? covale3 A C TYR 5 A TYR 5 1_555 A N DTR 6 A DTR 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale4 A C TYR 5 A TYR 5 1_555 A N DTR 6 A DTR 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale5 A C DTR 6 A DTR 6 1_555 A N LEU 7 A LEU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale6 A C GLY 10 A GLY 10 1_555 A N NH2 11 A NH2 11 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.305 ? covale ? covale7 A C GLY 10 A GLY 10 1_555 A N NH2 11 A NH2 11 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.279 ? covale ? covale8 B C PCA 1 B PCA 1 1_555 B N HIS 2 B HIS 2 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale9 B C PCA 1 B PCA 1 1_555 B N HIS 2 B HIS 2 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.269 ? covale ? covale10 B C TYR 5 B TYR 5 1_555 B N DTR 6 B DTR 6 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 B C TYR 5 B TYR 5 1_555 B N DTR 6 B DTR 6 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale12 B C DTR 6 B DTR 6 1_555 B N LEU 7 B LEU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale13 B C GLY 10 B GLY 10 1_555 B N NH2 11 B NH2 11 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.305 ? covale ? covale14 B C GLY 10 B GLY 10 1_555 B N NH2 11 B NH2 11 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.301 ? covale ? covale15 C C PCA 1 C PCA 1 1_555 C N HIS 2 C HIS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.346 ? covale ? covale16 C C TYR 5 C TYR 5 1_555 C N DTR 6 C DTR 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale17 C C DTR 6 C DTR 6 1_555 C N LEU 7 C LEU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale18 C C GLY 10 C GLY 10 1_555 C N NH2 11 C NH2 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale19 D C PCA 1 D PCA 1 1_555 D N HIS 2 D HIS 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale20 D C TYR 5 D TYR 5 1_555 D N DTR 6 D DTR 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale21 D C DTR 6 D DTR 6 1_555 D N LEU 7 D LEU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale22 D C GLY 10 D GLY 10 1_555 D N NH2 11 D NH2 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? # _chem_comp.formula 'O4 P -3' _chem_comp.formula_weight 94.971 _chem_comp.id PO4 _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHATE ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag P O1 PO4 doub 126 n n P O2 PO4 sing 127 n n P O3 PO4 sing 128 n n P O4 PO4 sing 129 n n # _atom_sites.entry_id 4D5M _atom_sites.fract_transf_matrix[1][1] 0.011779 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00183 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.036403 _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] 0.076958 _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 2 PO4 A 1 1011 1011 PO4 PO4 . F 2 PO4 B 1 1011 1011 PO4 PO4 . G 2 PO4 C 1 1011 1011 PO4 PO4 . H 3 HOH A 1 2001 2001 HOH HOH . H 3 HOH A 2 2003 2003 HOH HOH . H 3 HOH A 3 2004 2004 HOH HOH . H 3 HOH A 4 2005 2005 HOH HOH . H 3 HOH A 5 2006 2006 HOH HOH . H 3 HOH A 6 2007 2007 HOH HOH . H 3 HOH A 7 2008 2008 HOH HOH . H 3 HOH A 8 2009 2009 HOH HOH . H 3 HOH A 9 2010 2010 HOH HOH . H 3 HOH A 10 2011 2011 HOH HOH . H 3 HOH A 11 2012 2012 HOH HOH . H 3 HOH A 12 2013 2013 HOH HOH . H 3 HOH A 13 2014 2014 HOH HOH . H 3 HOH A 14 2015 2015 HOH HOH . H 3 HOH A 15 2016 2016 HOH HOH . H 3 HOH A 16 2017 2017 HOH HOH . I 3 HOH B 1 2001 2001 HOH HOH . I 3 HOH B 2 2002 2002 HOH HOH . I 3 HOH B 3 2003 2003 HOH HOH . I 3 HOH B 4 2004 2004 HOH HOH . I 3 HOH B 5 2005 2005 HOH HOH . I 3 HOH B 6 2006 2006 HOH HOH . I 3 HOH B 7 2007 2007 HOH HOH . I 3 HOH B 8 2008 2008 HOH HOH . I 3 HOH B 9 2009 2009 HOH HOH . I 3 HOH B 10 2010 2010 HOH HOH . J 3 HOH C 1 2001 2001 HOH HOH . J 3 HOH C 2 2002 2002 HOH HOH . J 3 HOH C 3 2003 2003 HOH HOH . J 3 HOH C 4 2004 2004 HOH HOH . J 3 HOH C 5 2005 2005 HOH HOH . J 3 HOH C 6 2008 2008 HOH HOH . J 3 HOH C 7 2010 2010 HOH HOH . J 3 HOH C 8 2011 2011 HOH HOH . J 3 HOH C 9 2012 2012 HOH HOH . J 3 HOH C 10 2013 2013 HOH HOH . J 3 HOH C 11 2014 2014 HOH HOH . J 3 HOH C 12 2015 2015 HOH HOH . J 3 HOH C 13 2016 2016 HOH HOH . K 3 HOH D 1 2001 2001 HOH HOH . K 3 HOH D 2 2003 2003 HOH HOH . K 3 HOH D 3 2004 2004 HOH HOH . K 3 HOH D 4 2005 2005 HOH HOH . K 3 HOH D 5 2007 2007 HOH HOH . K 3 HOH D 6 2008 2008 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P P PO4 . . . F 2 -0.896 0.206 6.08 0.5 0.72 ? P PO4 1011 B 1 HETATM 2 O O1 PO4 . . . F 2 -1.009 1.659 6.497 0.5 1.19 ? O1 PO4 1011 B 1 HETATM 3 O O2 PO4 . . . F 2 -0.764 0.312 4.518 0.5 1.86 ? O2 PO4 1011 B 1 HETATM 4 O O3 PO4 . . . F 2 -2.19 -0.478 6.439 0.5 1.75 ? O3 PO4 1011 B 1 HETATM 5 O O4 PO4 . . . F 2 0.296 -0.574 6.594 0.5 1.95 ? O4 PO4 1011 B 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 5 #