data_4IIJ # _model_server_result.job_id uYNH9Xzs8lN_nU_reLpGuQ _model_server_result.datetime_utc '2024-11-26 10:03:47' _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 4iij # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":501}' # _entry.id 4IIJ # _exptl.entry_id 4IIJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 9 _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 90 _cell.entry_id 4IIJ _cell.length_a 103.53 _cell.length_b 155.91 _cell.length_c 181.02 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4IIJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 ? 9 K N N ? 9 R 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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc3 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.695 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc5 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.904 ? metalc ? metalc7 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc9 H MG MG . A MG 502 1_555 U O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc10 H MG MG . A MG 502 1_555 U O HOH . A HOH 610 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc11 H MG MG . A MG 502 1_555 U O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.438 ? metalc ? metalc12 H MG MG . A MG 502 1_555 U O HOH . A HOH 612 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc13 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc14 B OE1 GLU 111 B GLU 113 1_555 M CA CA . B CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? metalc ? metalc17 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc18 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? metalc ? metalc19 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? metalc ? metalc20 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.935 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc22 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc23 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc24 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc25 P MG MG . C MG 502 1_555 W O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc26 R O1A GDP . D GDP 600 1_555 S MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? # _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 4IIJ _atom_sites.fract_transf_matrix[1][1] 0.009659 _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] 0.006414 _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] 0.005524 _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 5 GTP A 1 501 600 GTP GTP . H 6 MG A 1 502 601 MG MG . I 7 CA A 1 503 700 CA CA . J 8 CL A 1 504 800 CL CL . K 9 GDP B 1 501 600 GDP GDP . L 6 MG B 1 502 601 MG MG . M 7 CA B 1 503 700 CA CA . N 10 MES B 1 504 1 MES MES . O 5 GTP C 1 501 600 GTP GTP . P 6 MG C 1 502 601 MG MG . Q 7 CA C 1 503 700 CA CA . R 9 GDP D 1 600 600 GDP GDP . S 6 MG D 1 601 601 MG MG . T 6 MG F 1 401 702 MG MG . U 11 HOH A 1 601 1 HOH HOH . U 11 HOH A 2 602 5 HOH HOH . U 11 HOH A 3 603 18 HOH HOH . U 11 HOH A 4 604 19 HOH HOH . U 11 HOH A 5 605 24 HOH HOH . U 11 HOH A 6 606 32 HOH HOH . U 11 HOH A 7 607 35 HOH HOH . U 11 HOH A 8 608 39 HOH HOH . U 11 HOH A 9 609 43 HOH HOH . U 11 HOH A 10 610 50 HOH HOH . U 11 HOH A 11 611 51 HOH HOH . U 11 HOH A 12 612 52 HOH HOH . U 11 HOH A 13 613 53 HOH HOH . U 11 HOH A 14 614 66 HOH HOH . U 11 HOH A 15 615 76 HOH HOH . U 11 HOH A 16 616 77 HOH HOH . U 11 HOH A 17 617 78 HOH HOH . U 11 HOH A 18 618 79 HOH HOH . U 11 HOH A 19 619 80 HOH HOH . U 11 HOH A 20 620 81 HOH HOH . U 11 HOH A 21 621 82 HOH HOH . U 11 HOH A 22 622 83 HOH HOH . U 11 HOH A 23 623 84 HOH HOH . U 11 HOH A 24 624 85 HOH HOH . U 11 HOH A 25 625 86 HOH HOH . U 11 HOH A 26 626 87 HOH HOH . U 11 HOH A 27 627 89 HOH HOH . U 11 HOH A 28 628 91 HOH HOH . U 11 HOH A 29 629 94 HOH HOH . U 11 HOH A 30 630 95 HOH HOH . U 11 HOH A 31 631 96 HOH HOH . U 11 HOH A 32 632 97 HOH HOH . U 11 HOH A 33 633 98 HOH HOH . V 11 HOH B 1 601 2 HOH HOH . V 11 HOH B 2 602 8 HOH HOH . V 11 HOH B 3 603 23 HOH HOH . V 11 HOH B 4 604 26 HOH HOH . V 11 HOH B 5 605 29 HOH HOH . V 11 HOH B 6 606 33 HOH HOH . V 11 HOH B 7 607 37 HOH HOH . V 11 HOH B 8 608 40 HOH HOH . V 11 HOH B 9 609 46 HOH HOH . V 11 HOH B 10 610 63 HOH HOH . V 11 HOH B 11 611 65 HOH HOH . V 11 HOH B 12 612 88 HOH HOH . V 11 HOH B 13 613 90 HOH HOH . V 11 HOH B 14 614 92 HOH HOH . V 11 HOH B 15 615 99 HOH HOH . W 11 HOH C 1 601 3 HOH HOH . W 11 HOH C 2 602 4 HOH HOH . W 11 HOH C 3 603 6 HOH HOH . W 11 HOH C 4 604 7 HOH HOH . W 11 HOH C 5 605 9 HOH HOH . W 11 HOH C 6 606 12 HOH HOH . W 11 HOH C 7 607 14 HOH HOH . W 11 HOH C 8 608 15 HOH HOH . W 11 HOH C 9 609 16 HOH HOH . W 11 HOH C 10 610 17 HOH HOH . W 11 HOH C 11 611 22 HOH HOH . W 11 HOH C 12 612 25 HOH HOH . W 11 HOH C 13 613 27 HOH HOH . W 11 HOH C 14 614 31 HOH HOH . W 11 HOH C 15 615 34 HOH HOH . W 11 HOH C 16 616 36 HOH HOH . W 11 HOH C 17 617 38 HOH HOH . W 11 HOH C 18 618 41 HOH HOH . W 11 HOH C 19 619 42 HOH HOH . W 11 HOH C 20 620 44 HOH HOH . W 11 HOH C 21 621 48 HOH HOH . W 11 HOH C 22 622 54 HOH HOH . W 11 HOH C 23 623 55 HOH HOH . W 11 HOH C 24 624 56 HOH HOH . W 11 HOH C 25 625 59 HOH HOH . W 11 HOH C 26 626 60 HOH HOH . W 11 HOH C 27 627 61 HOH HOH . W 11 HOH C 28 628 67 HOH HOH . W 11 HOH C 29 629 68 HOH HOH . W 11 HOH C 30 630 69 HOH HOH . X 11 HOH D 1 701 20 HOH HOH . X 11 HOH D 2 702 45 HOH HOH . X 11 HOH D 3 703 47 HOH HOH . X 11 HOH D 4 704 71 HOH HOH . X 11 HOH D 5 705 74 HOH HOH . X 11 HOH D 6 706 75 HOH HOH . Y 11 HOH E 1 201 49 HOH HOH . Y 11 HOH E 2 202 64 HOH HOH . Z 11 HOH F 1 501 13 HOH HOH . Z 11 HOH F 2 502 28 HOH HOH . Z 11 HOH F 3 503 58 HOH HOH . Z 11 HOH F 4 504 70 HOH HOH . Z 11 HOH F 5 505 72 HOH HOH . Z 11 HOH F 6 506 93 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 . . . K 9 18.938 48.445 16.213 1 35.93 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . K 9 19.506 48.944 17.521 1 40.13 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . K 9 18.691 49.57 15.237 1 25.8 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . K 9 19.932 47.484 15.598 1 39.27 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . K 9 17.581 47.627 16.438 1 40.31 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . K 9 16.275 48.142 17.217 1 31.76 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . K 9 15.082 48.132 16.298 1 44.59 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . K 9 16.433 49.503 17.84 1 43.18 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . K 9 16.188 46.966 18.305 1 21.98 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . K 9 15.052 46.117 18.403 1 26.57 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . K 9 14.583 46.131 19.851 1 37.51 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . K 9 14.122 47.44 20.183 1 31.49 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . K 9 13.393 45.238 20.082 1 47.64 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . K 9 13.341 44.911 21.462 1 30.33 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . K 9 12.206 46.107 19.771 1 46.81 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . K 9 11.04 45.653 20.457 1 51 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . K 9 12.695 47.44 20.29 1 38.25 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . K 9 12.201 48.577 19.502 1 41.7 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . K 9 12.491 48.834 18.219 1 33.59 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . K 9 11.884 49.983 17.825 1 39.78 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . K 9 11.208 50.472 18.882 1 40.32 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . K 9 10.362 51.645 19.16 1 41.51 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . K 9 10.132 52.483 18.265 1 50.71 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . K 9 9.853 51.781 20.388 1 39.56 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . K 9 10.086 50.889 21.368 1 47.22 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . K 9 9.53 51.095 22.592 1 25.04 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . K 9 10.854 49.789 21.182 1 35.13 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . K 9 11.428 49.542 19.987 1 39.21 ? C4 GDP 501 B 1 HETATM 29 H H4' GDP . . . K 9 15.407 45.828 20.512 1 45.01 ? H4' GDP 501 B 1 HETATM 30 H H3' GDP . . . K 9 13.424 44.351 19.434 1 57.17 ? H3' GDP 501 B 1 HETATM 31 H HO3' GDP . . . K 9 12.562 44.365 21.634 1 36.39 ? HO3' GDP 501 B 1 HETATM 32 H H2' GDP . . . K 9 12.045 46.157 18.685 1 56.17 ? H2' GDP 501 B 1 HETATM 33 H HO2' GDP . . . K 9 10.799 44.774 20.135 1 61.2 ? HO2' GDP 501 B 1 HETATM 34 H H1' GDP . . . K 9 12.395 47.548 21.342 1 45.9 ? H1' GDP 501 B 1 HETATM 35 H H8 GDP . . . K 9 13.111 48.21 17.586 1 40.31 ? H8 GDP 501 B 1 HETATM 36 H HN1 GDP . . . K 9 9.249 52.603 20.592 1 47.47 ? HN1 GDP 501 B 1 HETATM 37 H HN21 GDP . . . K 9 8.953 51.908 22.754 1 30.04 ? HN21 GDP 501 B 1 HETATM 38 H HN22 GDP . . . K 9 9.698 50.438 23.34 1 30.04 ? HN22 GDP 501 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 24 _model_server_stats.element_count 38 #