data_6RA9 # _model_server_result.job_id PPCGLEr41ZMLDzbDK0Ms8w _model_server_result.datetime_utc '2024-11-16 01:54:49' _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 6ra9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":502}' # _entry.id 6RA9 # _exptl.entry_id 6RA9 _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 2 _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 6RA9 _cell.length_a 133.52 _cell.length_b 133.52 _cell.length_c 305.44 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RA9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,X,Y,Z _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 E 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 covale ? covale1 A C GLY 265 A GLY 265 1_555 A N POK 266 A POK 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale2 A C POK 266 A POK 266 1_555 A N VAL 267 A VAL 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale3 A C LEU 299 A LEU 299 1_555 A N SEP 300 A SEP 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale4 A C SEP 300 A SEP 300 1_555 A N GLU 301 A GLU 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A CD GLU 301 A GLU 301 1_555 D N GPE . A GPE 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale6 A CD GLU 374 A GLU 374 1_555 C N GPE . A GPE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.485 ? covale ? covale7 B C GLY 265 B GLY 265 1_555 B N POK 266 B POK 266 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 B C POK 266 B POK 266 1_555 B N VAL 267 B VAL 267 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale9 B CD GLU 374 B GLU 374 1_555 M N GPE . B GPE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.487 ? # _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 6RA9 _atom_sites.fract_transf_matrix[1][1] 0.00749 _atom_sites.fract_transf_matrix[1][2] 0.004324 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008648 _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] 0.003274 _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 3 GPE A 1 501 374 GPE EF1 . D 3 GPE A 1 502 301 GPE EF1 . E 4 GDP A 1 503 501 GDP GDP . F 5 GOL A 1 504 502 GOL GOL . G 5 GOL A 1 505 503 GOL GOL . H 6 SO4 A 1 506 1 SO4 SO4 . I 6 SO4 A 1 507 2 SO4 SO4 . J 6 SO4 A 1 508 4 SO4 SO4 . K 6 SO4 A 1 509 9 SO4 SO4 . L 6 SO4 A 1 510 13 SO4 SO4 . M 3 GPE B 1 501 374 GPE EF1 . N 4 GDP B 1 502 501 GDP GDP . O 5 GOL B 1 503 502 GOL GOL . P 5 GOL B 1 504 503 GOL GOL . Q 5 GOL B 1 505 504 GOL GOL . R 5 GOL B 1 506 505 GOL GOL . S 6 SO4 B 1 507 5 SO4 SO4 . T 6 SO4 B 1 508 6 SO4 SO4 . U 6 SO4 B 1 509 8 SO4 SO4 . V 6 SO4 B 1 510 10 SO4 SO4 . W 6 SO4 B 1 511 11 SO4 SO4 . X 6 SO4 B 1 512 12 SO4 SO4 . Y 7 HOH A 1 601 87 HOH HOH . Y 7 HOH A 2 602 96 HOH HOH . Y 7 HOH A 3 603 24 HOH HOH . Y 7 HOH A 4 604 84 HOH HOH . Y 7 HOH A 5 605 4 HOH HOH . Y 7 HOH A 6 606 102 HOH HOH . Y 7 HOH A 7 607 82 HOH HOH . Y 7 HOH A 8 608 29 HOH HOH . Y 7 HOH A 9 609 104 HOH HOH . Y 7 HOH A 10 610 39 HOH HOH . Y 7 HOH A 11 611 16 HOH HOH . Y 7 HOH A 12 612 117 HOH HOH . Y 7 HOH A 13 613 50 HOH HOH . Y 7 HOH A 14 614 40 HOH HOH . Y 7 HOH A 15 615 110 HOH HOH . Y 7 HOH A 16 616 9 HOH HOH . Y 7 HOH A 17 617 33 HOH HOH . Y 7 HOH A 18 618 103 HOH HOH . Y 7 HOH A 19 619 13 HOH HOH . Y 7 HOH A 20 620 123 HOH HOH . Y 7 HOH A 21 621 83 HOH HOH . Y 7 HOH A 22 622 114 HOH HOH . Y 7 HOH A 23 623 21 HOH HOH . Y 7 HOH A 24 624 95 HOH HOH . Y 7 HOH A 25 625 18 HOH HOH . Y 7 HOH A 26 626 67 HOH HOH . Y 7 HOH A 27 627 99 HOH HOH . Y 7 HOH A 28 628 112 HOH HOH . Y 7 HOH A 29 629 25 HOH HOH . Y 7 HOH A 30 630 10 HOH HOH . Y 7 HOH A 31 631 46 HOH HOH . Y 7 HOH A 32 632 85 HOH HOH . Y 7 HOH A 33 633 5 HOH HOH . Y 7 HOH A 34 634 17 HOH HOH . Y 7 HOH A 35 635 120 HOH HOH . Y 7 HOH A 36 636 101 HOH HOH . Y 7 HOH A 37 637 56 HOH HOH . Y 7 HOH A 38 638 53 HOH HOH . Y 7 HOH A 39 639 119 HOH HOH . Y 7 HOH A 40 640 20 HOH HOH . Y 7 HOH A 41 641 1 HOH HOH . Y 7 HOH A 42 642 93 HOH HOH . Y 7 HOH A 43 643 6 HOH HOH . Y 7 HOH A 44 644 100 HOH HOH . Y 7 HOH A 45 645 54 HOH HOH . Y 7 HOH A 46 646 7 HOH HOH . Y 7 HOH A 47 647 12 HOH HOH . Y 7 HOH A 48 648 44 HOH HOH . Y 7 HOH A 49 649 45 HOH HOH . Y 7 HOH A 50 650 75 HOH HOH . Y 7 HOH A 51 651 125 HOH HOH . Y 7 HOH A 52 652 57 HOH HOH . Y 7 HOH A 53 653 78 HOH HOH . Y 7 HOH A 54 654 94 HOH HOH . Y 7 HOH A 55 655 121 HOH HOH . Y 7 HOH A 56 656 8 HOH HOH . Y 7 HOH A 57 657 98 HOH HOH . Y 7 HOH A 58 658 59 HOH HOH . Y 7 HOH A 59 659 73 HOH HOH . Y 7 HOH A 60 660 42 HOH HOH . Y 7 HOH A 61 661 14 HOH HOH . Y 7 HOH A 62 662 68 HOH HOH . Y 7 HOH A 63 663 47 HOH HOH . Z 7 HOH B 1 601 38 HOH HOH . Z 7 HOH B 2 602 122 HOH HOH . Z 7 HOH B 3 603 88 HOH HOH . Z 7 HOH B 4 604 34 HOH HOH . Z 7 HOH B 5 605 48 HOH HOH . Z 7 HOH B 6 606 31 HOH HOH . Z 7 HOH B 7 607 43 HOH HOH . Z 7 HOH B 8 608 91 HOH HOH . Z 7 HOH B 9 609 62 HOH HOH . Z 7 HOH B 10 610 89 HOH HOH . Z 7 HOH B 11 611 105 HOH HOH . Z 7 HOH B 12 612 116 HOH HOH . Z 7 HOH B 13 613 52 HOH HOH . Z 7 HOH B 14 614 70 HOH HOH . Z 7 HOH B 15 615 30 HOH HOH . Z 7 HOH B 16 616 11 HOH HOH . Z 7 HOH B 17 617 86 HOH HOH . Z 7 HOH B 18 618 51 HOH HOH . Z 7 HOH B 19 619 113 HOH HOH . Z 7 HOH B 20 620 26 HOH HOH . Z 7 HOH B 21 621 97 HOH HOH . Z 7 HOH B 22 622 22 HOH HOH . Z 7 HOH B 23 623 74 HOH HOH . Z 7 HOH B 24 624 79 HOH HOH . Z 7 HOH B 25 625 81 HOH HOH . Z 7 HOH B 26 626 15 HOH HOH . Z 7 HOH B 27 627 72 HOH HOH . Z 7 HOH B 28 628 77 HOH HOH . Z 7 HOH B 29 629 3 HOH HOH . Z 7 HOH B 30 630 19 HOH HOH . Z 7 HOH B 31 631 118 HOH HOH . Z 7 HOH B 32 632 106 HOH HOH . Z 7 HOH B 33 633 108 HOH HOH . Z 7 HOH B 34 634 27 HOH HOH . Z 7 HOH B 35 635 76 HOH HOH . Z 7 HOH B 36 636 63 HOH HOH . Z 7 HOH B 37 637 111 HOH HOH . Z 7 HOH B 38 638 49 HOH HOH . Z 7 HOH B 39 639 28 HOH HOH . Z 7 HOH B 40 640 37 HOH HOH . Z 7 HOH B 41 641 90 HOH HOH . Z 7 HOH B 42 642 124 HOH HOH . Z 7 HOH B 43 643 58 HOH HOH . Z 7 HOH B 44 644 61 HOH HOH . Z 7 HOH B 45 645 23 HOH HOH . Z 7 HOH B 46 646 115 HOH HOH . Z 7 HOH B 47 647 80 HOH HOH . Z 7 HOH B 48 648 107 HOH HOH . Z 7 HOH B 49 649 60 HOH HOH . Z 7 HOH B 50 650 64 HOH HOH . Z 7 HOH B 51 651 66 HOH HOH . Z 7 HOH B 52 652 35 HOH HOH . Z 7 HOH B 53 653 41 HOH HOH . Z 7 HOH B 54 654 71 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 . . . N 4 44.263 46.328 -20.31 1 41.27 ? PB GDP 502 B 1 HETATM 2 O O1B GDP . . . N 4 44.674 46.787 -21.684 1 56.98 ? O1B GDP 502 B 1 HETATM 3 O O2B GDP . . . N 4 42.777 46.095 -20.305 1 44.46 -1 O2B GDP 502 B 1 HETATM 4 O O3B GDP . . . N 4 45.07 45.179 -19.772 1 43.19 ? O3B GDP 502 B 1 HETATM 5 O O3A GDP . . . N 4 44.483 47.713 -19.343 1 40.73 ? O3A GDP 502 B 1 HETATM 6 P PA GDP . . . N 4 45.623 47.982 -18.289 1 44.82 ? PA GDP 502 B 1 HETATM 7 O O1A GDP . . . N 4 46.921 47.437 -18.75 1 71.32 ? O1A GDP 502 B 1 HETATM 8 O O2A GDP . . . N 4 45.159 47.682 -16.912 1 47.15 -1 O2A GDP 502 B 1 HETATM 9 O O5' GDP . . . N 4 45.754 49.611 -18.38 1 39.12 ? O5' GDP 502 B 1 HETATM 10 C C5' GDP . . . N 4 44.667 50.464 -18.586 1 36.31 ? C5' GDP 502 B 1 HETATM 11 C C4' GDP . . . N 4 45.105 51.851 -18.169 1 41.81 ? C4' GDP 502 B 1 HETATM 12 O O4' GDP . . . N 4 44.179 52.369 -17.218 1 54.11 ? O4' GDP 502 B 1 HETATM 13 C C3' GDP . . . N 4 46.461 51.901 -17.465 1 50.09 ? C3' GDP 502 B 1 HETATM 14 O O3' GDP . . . N 4 47.006 53.183 -17.642 1 57.92 ? O3' GDP 502 B 1 HETATM 15 C C2' GDP . . . N 4 46.066 51.687 -16.004 1 55 ? C2' GDP 502 B 1 HETATM 16 O O2' GDP . . . N 4 46.962 52.237 -15.079 1 51.83 ? O2' GDP 502 B 1 HETATM 17 C C1' GDP . . . N 4 44.728 52.423 -15.938 1 53.92 ? C1' GDP 502 B 1 HETATM 18 N N9 GDP . . . N 4 43.793 51.863 -14.992 1 45.87 ? N9 GDP 502 B 1 HETATM 19 C C8 GDP . . . N 4 43.516 50.528 -14.796 1 46.04 ? C8 GDP 502 B 1 HETATM 20 N N7 GDP . . . N 4 42.603 50.331 -13.85 1 37.43 ? N7 GDP 502 B 1 HETATM 21 C C5 GDP . . . N 4 42.283 51.606 -13.421 1 43.51 ? C5 GDP 502 B 1 HETATM 22 C C6 GDP . . . N 4 41.376 52.082 -12.433 1 47.69 ? C6 GDP 502 B 1 HETATM 23 O O6 GDP . . . N 4 40.664 51.399 -11.732 1 45.22 ? O6 GDP 502 B 1 HETATM 24 N N1 GDP . . . N 4 41.289 53.387 -12.248 1 48.85 ? N1 GDP 502 B 1 HETATM 25 C C2 GDP . . . N 4 42.076 54.202 -13.018 1 46.54 ? C2 GDP 502 B 1 HETATM 26 N N2 GDP . . . N 4 41.949 55.521 -12.791 1 47.46 ? N2 GDP 502 B 1 HETATM 27 N N3 GDP . . . N 4 42.929 53.865 -13.94 1 44.93 ? N3 GDP 502 B 1 HETATM 28 C C4 GDP . . . N 4 43.005 52.534 -14.115 1 41.35 ? C4 GDP 502 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #