data_4FMB # _model_server_result.job_id YfiV3xxRKdhWoJzKYHAQlg _model_server_result.datetime_utc '2024-11-16 10:39:14' _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 4fmb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":202}' # _entry.id 4FMB # _exptl.entry_id 4FMB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 94.45 _cell.angle_gamma 90 _cell.entry_id 4FMB _cell.length_a 186.118 _cell.length_b 127.311 _cell.length_c 107.325 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FMB _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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dodecameric 12 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,B,G,H,I,P 1 1 C,D,J,K,L,Q,R 2 1 E,F,M,N,O,S,T 3 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T 4 1,2 # 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' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 K N N ? 4 N 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 disulf ? disulf1 A SG CYS 214 A CYS 253 1_555 E SG CYS 316 E CYS 355 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 316 A CYS 355 1_555 C SG CYS 214 C CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf3 C SG CYS 316 C CYS 355 1_555 E SG CYS 214 E CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc1 B OG SER 20 B SER 25 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 B OG1 THR 38 B THR 43 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc3 G AL AF3 . B AF3 201 1_555 H O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc4 G AL AF3 . B AF3 201 1_555 P O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc5 H O3B GDP . B GDP 202 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc6 I MG MG . B MG 203 1_555 P O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc7 I MG MG . B MG 203 1_555 P O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? metalc ? metalc8 Q O HOH . C HOH 501 1_555 J AL AF3 . D AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc9 D OG SER 20 D SER 25 1_555 L MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc10 D OG1 THR 38 D THR 43 1_555 L MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc11 J AL AF3 . D AF3 201 1_555 K O1B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc12 K O3B GDP . D GDP 202 1_555 L MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc13 L MG MG . D MG 203 1_555 R O HOH . D HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc14 L MG MG . D MG 203 1_555 R O HOH . D HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc15 S O HOH . E HOH 501 1_555 M AL AF3 . F AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc16 F OG SER 20 F SER 25 1_555 O MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc17 F OG1 THR 38 F THR 43 1_555 O MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc18 M AL AF3 . F AF3 201 1_555 N O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc19 N O3B GDP . F GDP 202 1_555 O MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc20 N O1B GDP . F GDP 202 1_555 O MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? metalc ? metalc21 O MG MG . F MG 203 1_555 T O HOH . F HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc22 O MG MG . F MG 203 1_555 T O HOH . F HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 4FMB _atom_sites.fract_transf_matrix[1][1] 0.005373 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000418 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007855 _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] 0.009346 _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 G 3 AF3 B 1 201 505 AF3 AF3 . H 4 GDP B 1 202 501 GDP GDP . I 5 MG B 1 203 502 MG MG . J 3 AF3 D 1 201 505 AF3 AF3 . K 4 GDP D 1 202 501 GDP GDP . L 5 MG D 1 203 502 MG MG . M 3 AF3 F 1 201 505 AF3 AF3 . N 4 GDP F 1 202 501 GDP GDP . O 5 MG F 1 203 502 MG MG . P 6 HOH B 1 301 504 HOH HOH . P 6 HOH B 2 302 503 HOH HOH . P 6 HOH B 3 303 1 HOH HOH . Q 6 HOH C 1 501 504 HOH HOH . R 6 HOH D 1 301 503 HOH HOH . R 6 HOH D 2 302 2 HOH HOH . S 6 HOH E 1 501 504 HOH HOH . T 6 HOH F 1 301 503 HOH HOH . T 6 HOH F 2 302 3 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 PB GDP . . . H 4 -29.677 -24.668 48.328 1 72.97 ? PB GDP 202 B 1 HETATM 2 O O1B GDP . . . H 4 -28.981 -24.873 46.907 1 72.97 ? O1B GDP 202 B 1 HETATM 3 O O2B GDP . . . H 4 -29.335 -25.779 49.288 1 72.97 ? O2B GDP 202 B 1 HETATM 4 O O3B GDP . . . H 4 -29.383 -23.238 48.702 1 72.97 ? O3B GDP 202 B 1 HETATM 5 O O3A GDP . . . H 4 -31.265 -24.89 48.09 1 72.97 ? O3A GDP 202 B 1 HETATM 6 P PA GDP . . . H 4 -32.379 -23.896 47.409 1 72.97 ? PA GDP 202 B 1 HETATM 7 O O1A GDP . . . H 4 -32.977 -23.068 48.528 1 72.97 ? O1A GDP 202 B 1 HETATM 8 O O2A GDP . . . H 4 -31.989 -23.182 46.119 1 72.97 ? O2A GDP 202 B 1 HETATM 9 O O5' GDP . . . H 4 -33.454 -25.087 46.997 1 72.97 ? O5' GDP 202 B 1 HETATM 10 C C5' GDP . . . H 4 -33.456 -25.814 45.745 1 72.97 ? C5' GDP 202 B 1 HETATM 11 C C4' GDP . . . H 4 -34.896 -26.194 45.492 1 72.97 ? C4' GDP 202 B 1 HETATM 12 O O4' GDP . . . H 4 -35.392 -26.512 46.758 1 72.97 ? O4' GDP 202 B 1 HETATM 13 C C3' GDP . . . H 4 -35.868 -25.047 45.245 1 72.97 ? C3' GDP 202 B 1 HETATM 14 O O3' GDP . . . H 4 -35.841 -24.287 44.027 1 72.97 ? O3' GDP 202 B 1 HETATM 15 C C2' GDP . . . H 4 -37.219 -25.661 45.502 1 72.97 ? C2' GDP 202 B 1 HETATM 16 O O2' GDP . . . H 4 -37.812 -26.456 44.426 1 72.97 ? O2' GDP 202 B 1 HETATM 17 C C1' GDP . . . H 4 -36.815 -26.503 46.691 1 72.97 ? C1' GDP 202 B 1 HETATM 18 N N9 GDP . . . H 4 -37.37 -25.892 47.901 1 72.97 ? N9 GDP 202 B 1 HETATM 19 C C8 GDP . . . H 4 -36.79 -25.036 48.722 1 72.97 ? C8 GDP 202 B 1 HETATM 20 N N7 GDP . . . H 4 -37.671 -24.727 49.715 1 72.97 ? N7 GDP 202 B 1 HETATM 21 C C5 GDP . . . H 4 -38.797 -25.407 49.494 1 72.97 ? C5 GDP 202 B 1 HETATM 22 C C6 GDP . . . H 4 -40.108 -25.513 50.189 1 72.97 ? C6 GDP 202 B 1 HETATM 23 O O6 GDP . . . H 4 -40.414 -24.836 51.334 1 72.97 ? O6 GDP 202 B 1 HETATM 24 N N1 GDP . . . H 4 -41.035 -26.333 49.641 1 72.97 ? N1 GDP 202 B 1 HETATM 25 C C2 GDP . . . H 4 -40.78 -27.039 48.49 1 72.97 ? C2 GDP 202 B 1 HETATM 26 N N2 GDP . . . H 4 -41.739 -27.866 47.947 1 72.97 ? N2 GDP 202 B 1 HETATM 27 N N3 GDP . . . H 4 -39.564 -26.923 47.873 1 72.97 ? N3 GDP 202 B 1 HETATM 28 C C4 GDP . . . H 4 -38.586 -26.13 48.348 1 72.97 ? C4 GDP 202 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 83 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #