data_6XAF # _model_server_result.job_id eup3xoMddz2bAMrLETJSbg _model_server_result.datetime_utc '2024-11-16 10:32:35' _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 6xaf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1602}' # _entry.id 6XAF # _exptl.entry_id 6XAF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 101.38 _cell.angle_gamma 90 _cell.entry_id 6XAF _cell.length_a 44.497 _cell.length_b 101.785 _cell.length_c 44.527 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XAF _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 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 _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 ? 3 D N N ? 3 F 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 OG1 THR 34 A THR 1348 1_555 C MG MG . A MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc2 C MG MG . A MG 1601 1_555 D O3B GDP . A GDP 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc3 C MG MG . A MG 1601 1_555 G O HOH . A HOH 1713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc4 C MG MG . A MG 1601 1_555 G O HOH . A HOH 1720 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 C MG MG . A MG 1601 1_555 G O HOH . A HOH 1741 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc6 C MG MG . A MG 1601 1_555 H O HOH . B HOH 1707 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc7 G O HOH . A HOH 1704 1_555 E MG MG . B MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc8 B OG1 THR 34 B THR 1348 1_555 E MG MG . B MG 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc9 E MG MG . B MG 1601 1_555 F O1B GDP . B GDP 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc10 E MG MG . B MG 1601 1_555 H O HOH . B HOH 1721 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? metalc ? metalc11 E MG MG . B MG 1601 1_555 H O HOH . B HOH 1725 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc12 E MG MG . B MG 1601 1_555 H O HOH . B HOH 1745 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? # _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 6XAF _atom_sites.fract_transf_matrix[1][1] 0.022473 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004523 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009825 _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] 0.022909 _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 MG A 1 1601 2 MG MG . D 3 GDP A 1 1602 2 GDP GDP . E 2 MG B 1 1601 1 MG MG . F 3 GDP B 1 1602 1 GDP GDP . G 4 HOH A 1 1701 48 HOH HOH . G 4 HOH A 2 1702 15 HOH HOH . G 4 HOH A 3 1703 17 HOH HOH . G 4 HOH A 4 1704 10 HOH HOH . G 4 HOH A 5 1705 50 HOH HOH . G 4 HOH A 6 1706 11 HOH HOH . G 4 HOH A 7 1707 95 HOH HOH . G 4 HOH A 8 1708 44 HOH HOH . G 4 HOH A 9 1709 80 HOH HOH . G 4 HOH A 10 1710 25 HOH HOH . G 4 HOH A 11 1711 60 HOH HOH . G 4 HOH A 12 1712 86 HOH HOH . G 4 HOH A 13 1713 98 HOH HOH . G 4 HOH A 14 1714 70 HOH HOH . G 4 HOH A 15 1715 1 HOH HOH . G 4 HOH A 16 1716 118 HOH HOH . G 4 HOH A 17 1717 35 HOH HOH . G 4 HOH A 18 1718 107 HOH HOH . G 4 HOH A 19 1719 42 HOH HOH . G 4 HOH A 20 1720 117 HOH HOH . G 4 HOH A 21 1721 4 HOH HOH . G 4 HOH A 22 1722 127 HOH HOH . G 4 HOH A 23 1723 51 HOH HOH . G 4 HOH A 24 1724 14 HOH HOH . G 4 HOH A 25 1725 66 HOH HOH . G 4 HOH A 26 1726 88 HOH HOH . G 4 HOH A 27 1727 28 HOH HOH . G 4 HOH A 28 1728 23 HOH HOH . G 4 HOH A 29 1729 46 HOH HOH . G 4 HOH A 30 1730 120 HOH HOH . G 4 HOH A 31 1731 129 HOH HOH . G 4 HOH A 32 1732 22 HOH HOH . G 4 HOH A 33 1733 56 HOH HOH . G 4 HOH A 34 1734 113 HOH HOH . G 4 HOH A 35 1735 100 HOH HOH . G 4 HOH A 36 1736 103 HOH HOH . G 4 HOH A 37 1737 68 HOH HOH . G 4 HOH A 38 1738 31 HOH HOH . G 4 HOH A 39 1739 53 HOH HOH . G 4 HOH A 40 1740 112 HOH HOH . G 4 HOH A 41 1741 76 HOH HOH . G 4 HOH A 42 1742 83 HOH HOH . G 4 HOH A 43 1743 21 HOH HOH . G 4 HOH A 44 1744 73 HOH HOH . G 4 HOH A 45 1745 61 HOH HOH . G 4 HOH A 46 1746 116 HOH HOH . G 4 HOH A 47 1747 125 HOH HOH . G 4 HOH A 48 1748 67 HOH HOH . G 4 HOH A 49 1749 123 HOH HOH . G 4 HOH A 50 1750 119 HOH HOH . G 4 HOH A 51 1751 65 HOH HOH . G 4 HOH A 52 1752 49 HOH HOH . G 4 HOH A 53 1753 97 HOH HOH . G 4 HOH A 54 1754 57 HOH HOH . G 4 HOH A 55 1755 38 HOH HOH . G 4 HOH A 56 1756 64 HOH HOH . G 4 HOH A 57 1757 91 HOH HOH . G 4 HOH A 58 1758 110 HOH HOH . G 4 HOH A 59 1759 74 HOH HOH . G 4 HOH A 60 1760 75 HOH HOH . G 4 HOH A 61 1761 90 HOH HOH . G 4 HOH A 62 1762 45 HOH HOH . G 4 HOH A 63 1763 109 HOH HOH . G 4 HOH A 64 1764 63 HOH HOH . G 4 HOH A 65 1765 69 HOH HOH . G 4 HOH A 66 1766 77 HOH HOH . H 4 HOH B 1 1701 43 HOH HOH . H 4 HOH B 2 1702 128 HOH HOH . H 4 HOH B 3 1703 71 HOH HOH . H 4 HOH B 4 1704 26 HOH HOH . H 4 HOH B 5 1705 18 HOH HOH . H 4 HOH B 6 1706 89 HOH HOH . H 4 HOH B 7 1707 2 HOH HOH . H 4 HOH B 8 1708 37 HOH HOH . H 4 HOH B 9 1709 5 HOH HOH . H 4 HOH B 10 1710 32 HOH HOH . H 4 HOH B 11 1711 3 HOH HOH . H 4 HOH B 12 1712 106 HOH HOH . H 4 HOH B 13 1713 105 HOH HOH . H 4 HOH B 14 1714 16 HOH HOH . H 4 HOH B 15 1715 84 HOH HOH . H 4 HOH B 16 1716 13 HOH HOH . H 4 HOH B 17 1717 19 HOH HOH . H 4 HOH B 18 1718 54 HOH HOH . H 4 HOH B 19 1719 8 HOH HOH . H 4 HOH B 20 1720 124 HOH HOH . H 4 HOH B 21 1721 7 HOH HOH . H 4 HOH B 22 1722 24 HOH HOH . H 4 HOH B 23 1723 9 HOH HOH . H 4 HOH B 24 1724 101 HOH HOH . H 4 HOH B 25 1725 134 HOH HOH . H 4 HOH B 26 1726 39 HOH HOH . H 4 HOH B 27 1727 27 HOH HOH . H 4 HOH B 28 1728 36 HOH HOH . H 4 HOH B 29 1729 94 HOH HOH . H 4 HOH B 30 1730 126 HOH HOH . H 4 HOH B 31 1731 55 HOH HOH . H 4 HOH B 32 1732 104 HOH HOH . H 4 HOH B 33 1733 12 HOH HOH . H 4 HOH B 34 1734 30 HOH HOH . H 4 HOH B 35 1735 108 HOH HOH . H 4 HOH B 36 1736 6 HOH HOH . H 4 HOH B 37 1737 29 HOH HOH . H 4 HOH B 38 1738 47 HOH HOH . H 4 HOH B 39 1739 20 HOH HOH . H 4 HOH B 40 1740 72 HOH HOH . H 4 HOH B 41 1741 111 HOH HOH . H 4 HOH B 42 1742 40 HOH HOH . H 4 HOH B 43 1743 34 HOH HOH . H 4 HOH B 44 1744 59 HOH HOH . H 4 HOH B 45 1745 99 HOH HOH . H 4 HOH B 46 1746 102 HOH HOH . H 4 HOH B 47 1747 79 HOH HOH . H 4 HOH B 48 1748 93 HOH HOH . H 4 HOH B 49 1749 133 HOH HOH . H 4 HOH B 50 1750 58 HOH HOH . H 4 HOH B 51 1751 122 HOH HOH . H 4 HOH B 52 1752 121 HOH HOH . H 4 HOH B 53 1753 33 HOH HOH . H 4 HOH B 54 1754 81 HOH HOH . H 4 HOH B 55 1755 132 HOH HOH . H 4 HOH B 56 1756 92 HOH HOH . H 4 HOH B 57 1757 52 HOH HOH . H 4 HOH B 58 1758 62 HOH HOH . H 4 HOH B 59 1759 82 HOH HOH . H 4 HOH B 60 1760 78 HOH HOH . H 4 HOH B 61 1761 130 HOH HOH . H 4 HOH B 62 1762 85 HOH HOH . H 4 HOH B 63 1763 114 HOH HOH . H 4 HOH B 64 1764 41 HOH HOH . H 4 HOH B 65 1765 96 HOH HOH . H 4 HOH B 66 1766 115 HOH HOH . H 4 HOH B 67 1767 131 HOH HOH . H 4 HOH B 68 1768 87 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 . . . F 3 4.258 -6.611 24.437 1 24.57 ? PB GDP 1602 B 1 HETATM 2 O O1B GDP . . . F 3 5.436 -7.125 23.648 1 23.85 ? O1B GDP 1602 B 1 HETATM 3 O O2B GDP . . . F 3 2.994 -7.248 23.883 1 23.91 ? O2B GDP 1602 B 1 HETATM 4 O O3B GDP . . . F 3 4.149 -5.097 24.525 1 24.04 ? O3B GDP 1602 B 1 HETATM 5 O O3A GDP . . . F 3 4.329 -7.145 25.976 1 24.39 ? O3A GDP 1602 B 1 HETATM 6 P PA GDP . . . F 3 5.674 -7.548 26.808 1 27.66 ? PA GDP 1602 B 1 HETATM 7 O O1A GDP . . . F 3 6.167 -8.888 26.325 1 26.46 ? O1A GDP 1602 B 1 HETATM 8 O O2A GDP . . . F 3 6.659 -6.412 26.743 1 28.2 ? O2A GDP 1602 B 1 HETATM 9 O O5' GDP . . . F 3 5.157 -7.752 28.335 1 26.01 ? O5' GDP 1602 B 1 HETATM 10 C C5' GDP . . . F 3 4.54 -6.709 29.034 1 33.54 ? C5' GDP 1602 B 1 HETATM 11 C C4' GDP . . . F 3 4.456 -7.095 30.476 1 33.38 ? C4' GDP 1602 B 1 HETATM 12 O O4' GDP . . . F 3 3.598 -8.066 30.663 1 33.77 ? O4' GDP 1602 B 1 HETATM 13 C C3' GDP . . . F 3 5.917 -7.653 31.037 1 28.06 ? C3' GDP 1602 B 1 HETATM 14 O O3' GDP . . . F 3 5.973 -7.13 32.421 1 28.27 ? O3' GDP 1602 B 1 HETATM 15 C C2' GDP . . . F 3 5.812 -8.896 30.997 1 28.88 ? C2' GDP 1602 B 1 HETATM 16 O O2' GDP . . . F 3 6.638 -9.59 32.017 1 26.11 ? O2' GDP 1602 B 1 HETATM 17 C C1' GDP . . . F 3 4.28 -9.198 31.394 1 33.34 ? C1' GDP 1602 B 1 HETATM 18 N N9 GDP . . . F 3 3.832 -10.348 30.902 1 30.02 ? N9 GDP 1602 B 1 HETATM 19 C C8 GDP . . . F 3 3.719 -10.863 29.659 1 28.31 ? C8 GDP 1602 B 1 HETATM 20 N N7 GDP . . . F 3 3.151 -12.08 29.735 1 25.89 ? N7 GDP 1602 B 1 HETATM 21 C C5 GDP . . . F 3 2.9 -12.334 31.007 1 27.01 ? C5 GDP 1602 B 1 HETATM 22 C C6 GDP . . . F 3 2.266 -13.549 31.704 1 31.49 ? C6 GDP 1602 B 1 HETATM 23 O O6 GDP . . . F 3 1.878 -14.508 31.12 1 27.43 ? O6 GDP 1602 B 1 HETATM 24 N N1 GDP . . . F 3 2.126 -13.548 33.115 1 27.96 ? N1 GDP 1602 B 1 HETATM 25 C C2 GDP . . . F 3 2.57 -12.409 33.86 1 30.53 ? C2 GDP 1602 B 1 HETATM 26 N N2 GDP . . . F 3 2.4 -12.413 35.283 1 29.09 ? N2 GDP 1602 B 1 HETATM 27 N N3 GDP . . . F 3 3.154 -11.26 33.203 1 26.9 ? N3 GDP 1602 B 1 HETATM 28 C C4 GDP . . . F 3 3.317 -11.247 31.738 1 25.46 ? C4 GDP 1602 B 1 # _model_server_stats.io_time_ms 74 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #