data_3RB5 # _model_server_result.job_id Qnm0hW7etWkZHRff-sZr1A _model_server_result.datetime_utc '2024-12-26 19:15:03' _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 3rb5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":4984}' # _entry.id 3RB5 # _exptl.entry_id 3RB5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 118.174 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (4S)-2-METHYL-2,4-PENTANEDIOL _entity.pdbx_number_of_molecules 1 _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 3RB5 _cell.length_a 63.091 _cell.length_b 63.091 _cell.length_c 227.499 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RB5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 78 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,S 1 1 B,K,L,M,N,O,P,Q,R,T 2 1 B,K,L,M,N,O,P,Q,R,T 3 1 A,C,D,E,F,G,H,I,J,S 3 2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -y,x,z-1/4 0 -1 0 1 0 0 0 0 1 0 0 -56.87475 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 C CA CA . A CA 1 1_555 A OD1 ASP 58 A ASP 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? metalc ? metalc2 C CA CA . A CA 1 1_555 A OD2 ASP 58 A ASP 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc3 C CA CA . A CA 1 1_555 A OE2 GLU 88 A GLU 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc4 C CA CA . A CA 1 1_555 A OE1 GLU 91 A GLU 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc5 C CA CA . A CA 1 1_555 A OE2 GLU 91 A GLU 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc6 D CA CA . A CA 2 1_555 A OE2 GLU 23 A GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? metalc ? metalc7 D CA CA . A CA 2 1_555 A OD2 ASP 83 A ASP 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc8 D CA CA . A CA 2 1_555 A O ASP 84 A ASP 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.709 ? metalc ? metalc9 D CA CA . A CA 2 1_555 A OD1 ASP 119 A ASP 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc10 D CA CA . A CA 2 1_555 A OD1 ASP 120 A ASP 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc11 D CA CA . A CA 2 1_555 A OD2 ASP 120 A ASP 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.856 ? metalc ? metalc12 E CA CA . A CA 3 1_555 A OE2 GLU 23 A GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc13 E CA CA . A CA 3 1_555 A OE1 GLU 23 A GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc14 E CA CA . A CA 3 1_555 A OD2 ASP 84 A ASP 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.72 ? metalc ? metalc15 E CA CA . A CA 3 1_555 A O VAL 86 A VAL 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc16 E CA CA . A CA 3 1_555 A OE1 GLU 88 A GLU 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc17 E CA CA . A CA 3 1_555 A OD1 ASP 118 A ASP 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.857 ? metalc ? metalc18 E CA CA . A CA 3 1_555 A OD2 ASP 118 A ASP 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.186 ? metalc ? metalc19 E CA CA . A CA 3 1_555 A OD2 ASP 120 A ASP 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc20 F CA CA . A CA 4 1_555 S O HOH . A HOH 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.885 ? metalc ? metalc21 F CA CA . A CA 4 1_555 A OE1 GLU 23 A GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc22 F CA CA . A CA 4 1_555 A OD2 ASP 58 A ASP 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc23 F CA CA . A CA 4 1_555 A OE1 GLU 88 A GLU 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc24 F CA CA . A CA 4 1_555 A OE2 GLU 88 A GLU 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? metalc ? metalc25 K CA CA . B CA 1 1_555 B OD2 ASP 58 B ASP 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc26 K CA CA . B CA 1 1_555 B OD1 ASP 58 B ASP 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc27 K CA CA . B CA 1 1_555 B OE2 GLU 88 B GLU 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.141 ? metalc ? metalc28 K CA CA . B CA 1 1_555 B OE2 GLU 91 B GLU 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc29 L CA CA . B CA 2 1_555 B OE2 GLU 23 B GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? metalc ? metalc30 L CA CA . B CA 2 1_555 B OD2 ASP 83 B ASP 515 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc31 L CA CA . B CA 2 1_555 B O ASP 84 B ASP 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc32 L CA CA . B CA 2 1_555 B OD1 ASP 119 B ASP 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc33 L CA CA . B CA 2 1_555 B OD1 ASP 120 B ASP 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.563 ? metalc ? metalc34 L CA CA . B CA 2 1_555 B OD2 ASP 120 B ASP 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc35 M CA CA . B CA 3 1_555 B OE1 GLU 23 B GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.63 ? metalc ? metalc36 M CA CA . B CA 3 1_555 B OE2 GLU 23 B GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.632 ? metalc ? metalc37 M CA CA . B CA 3 1_555 B OD2 ASP 84 B ASP 516 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? metalc ? metalc38 M CA CA . B CA 3 1_555 B O VAL 86 B VAL 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc39 M CA CA . B CA 3 1_555 B OE1 GLU 88 B GLU 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.933 ? metalc ? metalc40 M CA CA . B CA 3 1_555 B OD1 ASP 118 B ASP 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? metalc ? metalc41 M CA CA . B CA 3 1_555 B OD2 ASP 120 B ASP 552 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? metalc ? metalc42 N CA CA . B CA 4 1_555 B OE1 GLU 23 B GLU 455 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc43 N CA CA . B CA 4 1_555 B OD2 ASP 58 B ASP 490 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc44 N CA CA . B CA 4 1_555 B OE2 GLU 88 B GLU 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.853 ? # _chem_comp.formula 'C6 H14 O2' _chem_comp.formula_weight 118.174 _chem_comp.id MPD _chem_comp.mon_nstd_flag . _chem_comp.name (4S)-2-METHYL-2,4-PENTANEDIOL _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 C1 C2 MPD sing 237 n n C1 H11 MPD sing 238 n n C1 H12 MPD sing 239 n n C1 H13 MPD sing 240 n n C2 O2 MPD sing 241 n n C2 CM MPD sing 242 n n C2 C3 MPD sing 243 n n O2 HO2 MPD sing 244 n n CM HM1 MPD sing 245 n n CM HM2 MPD sing 246 n n CM HM3 MPD sing 247 n n C3 C4 MPD sing 248 n n C3 H31 MPD sing 249 n n C3 H32 MPD sing 250 n n C4 O4 MPD sing 251 n n C4 C5 MPD sing 252 n n C4 H4 MPD sing 253 n n O4 HO4 MPD sing 254 n n C5 H51 MPD sing 255 n n C5 H52 MPD sing 256 n n C5 H53 MPD sing 257 n n # _atom_sites.entry_id 3RB5 _atom_sites.fract_transf_matrix[1][1] 0.01585 _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] 0.01585 _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] 0.004396 _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 C 2 CA A 1 1 1 CA CA . D 2 CA A 1 2 2 CA CA . E 2 CA A 1 3 3 CA CA . F 2 CA A 1 4 4 CA CA . G 3 MPD A 1 4984 4984 MPD MPD . H 4 SO4 A 1 731 731 SO4 SO4 . I 4 SO4 A 1 732 732 SO4 SO4 . J 4 SO4 A 1 7 7 SO4 SO4 . K 2 CA B 1 1 1 CA CA . L 2 CA B 1 2 2 CA CA . M 2 CA B 1 3 3 CA CA . N 2 CA B 1 4 4 CA CA . O 4 SO4 B 1 731 731 SO4 SO4 . P 4 SO4 B 1 6 6 SO4 SO4 . Q 4 SO4 B 1 5 5 SO4 SO4 . R 4 SO4 B 1 8 8 SO4 SO4 . S 5 HOH A 1 10 10 HOH HOH . S 5 HOH A 2 11 11 HOH HOH . S 5 HOH A 3 12 12 HOH HOH . S 5 HOH A 4 13 13 HOH HOH . S 5 HOH A 5 14 14 HOH HOH . S 5 HOH A 6 16 16 HOH HOH . S 5 HOH A 7 17 17 HOH HOH . S 5 HOH A 8 18 18 HOH HOH . S 5 HOH A 9 19 19 HOH HOH . S 5 HOH A 10 20 20 HOH HOH . S 5 HOH A 11 21 21 HOH HOH . S 5 HOH A 12 22 22 HOH HOH . S 5 HOH A 13 33 33 HOH HOH . S 5 HOH A 14 34 34 HOH HOH . S 5 HOH A 15 37 37 HOH HOH . S 5 HOH A 16 38 38 HOH HOH . S 5 HOH A 17 39 39 HOH HOH . S 5 HOH A 18 40 40 HOH HOH . S 5 HOH A 19 41 41 HOH HOH . S 5 HOH A 20 42 42 HOH HOH . S 5 HOH A 21 733 733 HOH HOH . T 5 HOH B 1 7 7 HOH HOH . T 5 HOH B 2 9 9 HOH HOH . T 5 HOH B 3 15 15 HOH HOH . T 5 HOH B 4 23 23 HOH HOH . T 5 HOH B 5 24 24 HOH HOH . T 5 HOH B 6 27 27 HOH HOH . T 5 HOH B 7 28 28 HOH HOH . T 5 HOH B 8 29 29 HOH HOH . T 5 HOH B 9 30 30 HOH HOH . T 5 HOH B 10 31 31 HOH HOH . T 5 HOH B 11 32 32 HOH HOH . T 5 HOH B 12 35 35 HOH HOH . T 5 HOH B 13 36 36 HOH HOH . T 5 HOH B 14 43 43 HOH HOH . T 5 HOH B 15 44 44 HOH HOH . T 5 HOH B 16 45 45 HOH HOH . T 5 HOH B 17 46 46 HOH HOH . T 5 HOH B 18 47 47 HOH HOH . T 5 HOH B 19 732 732 HOH HOH . T 5 HOH B 20 733 733 HOH HOH . T 5 HOH B 21 734 734 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 C C1 MPD . . . G 3 -9.757 22.774 23.667 1 56.93 ? C1 MPD 4984 A 1 HETATM 2 C C2 MPD . . . G 3 -8.915 24.015 23.939 1 59.95 ? C2 MPD 4984 A 1 HETATM 3 O O2 MPD . . . G 3 -9.251 25.012 22.927 1 55.19 ? O2 MPD 4984 A 1 HETATM 4 C CM MPD . . . G 3 -9.259 24.554 25.33 1 53.86 ? CM MPD 4984 A 1 HETATM 5 C C3 MPD . . . G 3 -7.421 23.656 23.894 1 52.31 ? C3 MPD 4984 A 1 HETATM 6 C C4 MPD . . . G 3 -6.821 23.539 22.494 1 49.93 ? C4 MPD 4984 A 1 HETATM 7 O O4 MPD . . . G 3 -5.784 24.487 22.375 1 47.89 ? O4 MPD 4984 A 1 HETATM 8 C C5 MPD . . . G 3 -6.267 22.139 22.24 1 38.56 ? C5 MPD 4984 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 8 #