data_6KZB # _model_server_result.job_id HvmnQvnoC6VybPG62YHj8g _model_server_result.datetime_utc '2024-12-24 14:03:16' _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 6kzb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":702}' # _entry.id 6KZB # _exptl.entry_id 6KZB _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 3 _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 6KZB _cell.length_a 133.08 _cell.length_b 216.307 _cell.length_c 166.263 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6KZB _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F 1 1,2 B,C,G,H,I,J,K,L 2 1 # 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' 4_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 ? 3 E N N ? 3 I N N ? 3 L 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 230 A CYS 230 1_555 A SG CYS 370 A CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf2 B SG CYS 230 B CYS 230 1_555 B SG CYS 370 B CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 C SG CYS 230 C CYS 230 1_555 C SG CYS 370 C CYS 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? covale ? covale1 B OG SER 482 B SER 482 1_555 I N3 GDP . B GDP 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? metalc ? metalc1 B OD1 ASN 498 B ASN 498 1_555 G CA CA . B CA 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.163 ? # _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 6KZB _atom_sites.fract_transf_matrix[1][1] 0.007514 _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] 0.004623 _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] 0.006015 _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 D 2 CA A 1 701 691 CA CA . E 3 GDP A 1 702 695 GDP GDP . F 2 CA A 1 703 690 CA CA . G 2 CA B 1 701 690 CA CA . H 2 CA B 1 702 691 CA CA . I 3 GDP B 1 703 695 GDP GDP . J 2 CA C 1 701 690 CA CA . K 2 CA C 1 702 691 CA CA . L 3 GDP C 1 703 695 GDP GDP . # 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 . . . E 3 -85.463 -1.585 -2.825 1 104.71 ? PB GDP 702 A 1 HETATM 2 O O1B GDP . . . E 3 -86.308 -1.148 -4.004 1 86.55 ? O1B GDP 702 A 1 HETATM 3 O O2B GDP . . . E 3 -86.253 -2.541 -1.964 1 89.41 ? O2B GDP 702 A 1 HETATM 4 O O3B GDP . . . E 3 -85.104 -0.375 -1.994 1 94.92 ? O3B GDP 702 A 1 HETATM 5 O O3A GDP . . . E 3 -84.153 -2.395 -3.306 1 69.3 ? O3A GDP 702 A 1 HETATM 6 P PA GDP . . . E 3 -82.646 -1.83 -3.198 1 75.34 ? PA GDP 702 A 1 HETATM 7 O O1A GDP . . . E 3 -82.075 -1.57 -4.573 1 80.08 ? O1A GDP 702 A 1 HETATM 8 O O2A GDP . . . E 3 -82.538 -0.595 -2.335 1 85.25 ? O2A GDP 702 A 1 HETATM 9 O O5' GDP . . . E 3 -81.854 -3.033 -2.483 1 61.68 ? O5' GDP 702 A 1 HETATM 10 C C5' GDP . . . E 3 -80.552 -2.773 -1.965 1 60.6 ? C5' GDP 702 A 1 HETATM 11 C C4' GDP . . . E 3 -80.222 -3.739 -0.836 1 56.68 ? C4' GDP 702 A 1 HETATM 12 O O4' GDP . . . E 3 -80.177 -5.073 -1.345 1 65.6 ? O4' GDP 702 A 1 HETATM 13 C C3' GDP . . . E 3 -78.85 -3.437 -0.256 1 60.66 ? C3' GDP 702 A 1 HETATM 14 O O3' GDP . . . E 3 -78.934 -3.284 1.166 1 68.17 ? O3' GDP 702 A 1 HETATM 15 C C2' GDP . . . E 3 -77.995 -4.642 -0.599 1 74.53 ? C2' GDP 702 A 1 HETATM 16 O O2' GDP . . . E 3 -77.122 -4.977 0.483 1 84.3 ? O2' GDP 702 A 1 HETATM 17 C C1' GDP . . . E 3 -79.011 -5.744 -0.859 1 74.01 ? C1' GDP 702 A 1 HETATM 18 N N9 GDP . . . E 3 -78.543 -6.797 -1.81 1 74.44 ? N9 GDP 702 A 1 HETATM 19 C C8 GDP . . . E 3 -77.626 -7.745 -1.534 1 73.31 ? C8 GDP 702 A 1 HETATM 20 N N7 GDP . . . E 3 -77.413 -8.58 -2.579 1 58.8 ? N7 GDP 702 A 1 HETATM 21 C C5 GDP . . . E 3 -78.215 -8.157 -3.566 1 56.38 ? C5 GDP 702 A 1 HETATM 22 C C6 GDP . . . E 3 -78.483 -8.592 -4.947 1 59.03 ? C6 GDP 702 A 1 HETATM 23 O O6 GDP . . . E 3 -77.874 -9.572 -5.414 1 59.29 ? O6 GDP 702 A 1 HETATM 24 N N1 GDP . . . E 3 -79.38 -7.904 -5.665 1 65.67 ? N1 GDP 702 A 1 HETATM 25 C C2 GDP . . . E 3 -80.04 -6.841 -5.16 1 68.73 ? C2 GDP 702 A 1 HETATM 26 N N2 GDP . . . E 3 -80.939 -6.191 -5.942 1 72.77 ? N2 GDP 702 A 1 HETATM 27 N N3 GDP . . . E 3 -79.839 -6.388 -3.895 1 60.47 ? N3 GDP 702 A 1 HETATM 28 C C4 GDP . . . E 3 -78.959 -6.992 -3.064 1 61 ? C4 GDP 702 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #