data_6LS4 # _model_server_result.job_id mH7zld2ovoRgcVFBlKQrOQ _model_server_result.datetime_utc '2024-10-20 19:11:37' _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 6ls4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":501}' # _entry.id 6LS4 # _exptl.entry_id 6LS4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 107.42 _cell.angle_gamma 90 _cell.entry_id 6LS4 _cell.length_a 82.68 _cell.length_b 102.2 _cell.length_c 131.5 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6LS4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id I _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 A OD1 ASP 39 A ASP 39 1_555 H MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc2 A O THR 41 A THR 41 1_555 H MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 H MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 H MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 H MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 H MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.648 ? metalc ? metalc7 F O1G GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc8 F O1B GTP . A GTP 501 1_555 G MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc9 G MG MG . A MG 502 1_555 T O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc10 G MG MG . A MG 502 1_555 T O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc11 G MG MG . A MG 502 1_555 T O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc12 U O HOH . B HOH 601 1_555 P MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc13 U O HOH . B HOH 602 1_555 P MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc14 U O HOH . B HOH 605 1_555 P MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 O MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 O MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc17 C O THR 41 C THR 41 1_555 O MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 O MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc19 C O GLY 44 C GLY 44 1_555 O MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 O MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.971 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 O MG MG . C MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc22 C O ASN 249 C ASN 249 1_555 P MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.721 ? metalc ? metalc23 C OD1 ASN 249 C ASN 249 1_555 P MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc24 C OE2 GLU 254 C GLU 254 1_555 P MG MG . C MG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc25 M O1G GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc26 M O1B GTP . C GTP 501 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc27 N MG MG . C MG 502 1_555 V O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? metalc ? metalc28 N MG MG . C MG 502 1_555 V O HOH . C HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc29 N MG MG . C MG 502 1_555 V O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc30 Q O3G GTP . D GTP 501 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.605 ? metalc ? metalc31 Q O1B GTP . D GTP 501 1_555 R MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? metalc ? metalc32 R MG MG . D MG 502 1_555 W O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc33 R MG MG . D MG 502 1_555 W O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 6LS4 _atom_sites.fract_transf_matrix[1][1] 0.012095 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003795 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009785 _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] 0.00797 _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 GTP A 1 501 501 GTP GTP . G 5 MG A 1 502 505 MG MG . H 5 MG A 1 503 506 MG MG . I 6 GDP B 1 501 501 GDP GDP . J 7 MES B 1 502 601 MES MES . K 8 GOL B 1 503 701 GOL GOL . L 9 S40 B 1 504 1 S40 S40 . M 4 GTP C 1 501 501 GTP GTP . N 5 MG C 1 502 505 MG MG . O 5 MG C 1 503 506 MG MG . P 5 MG C 1 504 507 MG MG . Q 4 GTP D 1 501 501 GTP GTP . R 5 MG D 1 502 505 MG MG . S 9 S40 D 1 503 2 S40 S40 . T 10 HOH A 1 601 12 HOH HOH . T 10 HOH A 2 602 24 HOH HOH . T 10 HOH A 3 603 10 HOH HOH . T 10 HOH A 4 604 13 HOH HOH . U 10 HOH B 1 601 1 HOH HOH . U 10 HOH B 2 602 4 HOH HOH . U 10 HOH B 3 603 19 HOH HOH . U 10 HOH B 4 604 9 HOH HOH . U 10 HOH B 5 605 3 HOH HOH . U 10 HOH B 6 606 21 HOH HOH . U 10 HOH B 7 607 23 HOH HOH . V 10 HOH C 1 601 7 HOH HOH . V 10 HOH C 2 602 20 HOH HOH . V 10 HOH C 3 603 22 HOH HOH . V 10 HOH C 4 604 8 HOH HOH . V 10 HOH C 5 605 6 HOH HOH . W 10 HOH D 1 601 17 HOH HOH . W 10 HOH D 2 602 14 HOH HOH . W 10 HOH D 3 603 15 HOH HOH . W 10 HOH D 4 604 18 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 . . . I 6 2.861 23.692 39.486 1 69.78 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . I 6 1.729 24.078 38.595 1 56.95 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . I 6 4.117 24.024 38.844 1 66.79 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . I 6 2.719 24.472 40.757 1 65.14 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . I 6 2.831 22.158 39.836 1 61.41 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . I 6 2.857 20.901 38.812 1 69.33 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . I 6 4.148 20.231 38.837 1 67.11 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . I 6 2.558 21.382 37.462 1 64.15 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . I 6 1.652 20.062 39.416 1 59.8 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . I 6 1.728 18.768 40.015 1 57.99 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . I 6 0.688 17.927 39.309 1 70.53 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . I 6 0.987 17.928 37.91 1 63.3 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . I 6 0.816 16.494 39.771 1 62.88 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . I 6 -0.499 15.94 39.673 1 71.44 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . I 6 1.778 15.865 38.776 1 60 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . I 6 1.512 14.468 38.608 1 62.97 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . I 6 1.413 16.607 37.517 1 65.69 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . I 6 2.486 16.814 36.529 1 66.73 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . I 6 3.602 17.541 36.702 1 68.59 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . I 6 4.324 17.569 35.557 1 70.16 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . I 6 3.668 16.856 34.638 1 70.52 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . I 6 3.884 16.494 33.224 1 75.05 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . I 6 4.898 16.919 32.652 1 73.69 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . I 6 2.973 15.739 32.614 1 68.14 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . I 6 1.868 15.302 33.251 1 67.12 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . I 6 0.964 14.531 32.599 1 72.57 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . I 6 1.611 15.606 34.547 1 68.94 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . I 6 2.451 16.368 35.271 1 66.93 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 120 _model_server_stats.query_time_ms 455 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #