data_7EVL # _model_server_result.job_id 00BDKaWij8lZ35u3ctpOOA _model_server_result.datetime_utc '2025-01-31 02:43:06' _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 7evl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 7EVL # _exptl.entry_id 7EVL _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 1 _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 7EVL _cell.length_a 40.166 _cell.length_b 79.515 _cell.length_c 90.892 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7EVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _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 O ASN 247 B ASN 247 1_555 E NA NA . B NA 504 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc2 A OE1 GLU 252 B GLU 252 1_555 E NA NA . B NA 504 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc3 A OE2 GLU 252 B GLU 252 1_555 E NA NA . B NA 504 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc4 B O2G GTP . B GTP 501 1_555 D NA NA . B NA 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc5 B O3G GTP . B GTP 501 1_555 D NA NA . B NA 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.109 ? metalc ? metalc6 B O2B GTP . B GTP 501 1_555 D NA NA . B NA 503 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.465 ? metalc ? metalc7 B O2G GTP . B GTP 501 1_555 E NA NA . B NA 504 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.512 ? metalc ? metalc8 C O2B GDP . B GDP 502 1_555 D NA NA . B NA 503 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc9 D NA NA . B NA 503 1_555 F O HOH . B HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.908 ? metalc ? metalc10 D NA NA . B NA 503 1_555 F O HOH . B HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc11 D NA NA . B NA 503 1_555 F O HOH . B HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc12 D NA NA . B NA 503 1_555 F O HOH . B HOH 622 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc13 E NA NA . B NA 504 1_555 F O HOH . B HOH 619 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc14 E NA NA . B NA 504 1_555 F O HOH . B HOH 622 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.802 ? metalc ? metalc15 E NA NA . B NA 504 1_555 F O HOH . B HOH 626 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? # _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 7EVL _atom_sites.fract_transf_matrix[1][1] 0.024897 _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] 0.012576 _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] 0.011002 _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 B 2 GTP B 1 501 501 GTP GTP . C 3 GDP B 1 502 501 GDP GDP . D 4 NA B 1 503 1 NA NA . E 4 NA B 1 504 2 NA NA . F 5 HOH B 1 601 22 HOH HOH . F 5 HOH B 2 602 26 HOH HOH . F 5 HOH B 3 603 13 HOH HOH . F 5 HOH B 4 604 30 HOH HOH . F 5 HOH B 5 605 27 HOH HOH . F 5 HOH B 6 606 5 HOH HOH . F 5 HOH B 7 607 25 HOH HOH . F 5 HOH B 8 608 1 HOH HOH . F 5 HOH B 9 609 21 HOH HOH . F 5 HOH B 10 610 19 HOH HOH . F 5 HOH B 11 611 18 HOH HOH . F 5 HOH B 12 612 6 HOH HOH . F 5 HOH B 13 613 3 HOH HOH . F 5 HOH B 14 614 10 HOH HOH . F 5 HOH B 15 615 9 HOH HOH . F 5 HOH B 16 616 4 HOH HOH . F 5 HOH B 17 617 15 HOH HOH . F 5 HOH B 18 618 11 HOH HOH . F 5 HOH B 19 619 28 HOH HOH . F 5 HOH B 20 620 7 HOH HOH . F 5 HOH B 21 621 20 HOH HOH . F 5 HOH B 22 622 24 HOH HOH . F 5 HOH B 23 623 12 HOH HOH . F 5 HOH B 24 624 2 HOH HOH . F 5 HOH B 25 625 17 HOH HOH . F 5 HOH B 26 626 29 HOH HOH . F 5 HOH B 27 627 23 HOH HOH . F 5 HOH B 28 628 14 HOH HOH . F 5 HOH B 29 629 16 HOH HOH . F 5 HOH B 30 630 8 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 . B . C 3 1.683 1.378 -14.031 0.39 37.01 ? PB GDP 502 B 1 HETATM 2 O O1B GDP . B . C 3 1.208 0.502 -15.164 0.39 39.28 ? O1B GDP 502 B 1 HETATM 3 O O2B GDP . B . C 3 1.205 2.791 -14.269 0.39 41.09 ? O2B GDP 502 B 1 HETATM 4 O O3B GDP . B . C 3 3.191 1.339 -13.979 0.39 41.42 ? O3B GDP 502 B 1 HETATM 5 O O3A GDP . B . C 3 1.03 0.816 -12.67 0.39 39.47 ? O3A GDP 502 B 1 HETATM 6 P PA GDP . B . C 3 1.773 0.848 -11.242 0.39 36.69 ? PA GDP 502 B 1 HETATM 7 O O1A GDP . B . C 3 3.082 1.599 -11.291 0.39 40.1 ? O1A GDP 502 B 1 HETATM 8 O O2A GDP . B . C 3 0.866 1.45 -10.196 0.39 40.27 ? O2A GDP 502 B 1 HETATM 9 O O5' GDP . B . C 3 2.014 -0.709 -10.918 0.39 38.96 ? O5' GDP 502 B 1 HETATM 10 C C5' GDP . B . C 3 1.304 -1.313 -9.844 0.39 37.11 ? C5' GDP 502 B 1 HETATM 11 C C4' GDP . B . C 3 2.287 -1.856 -8.822 0.39 36.77 ? C4' GDP 502 B 1 HETATM 12 O O4' GDP . B . C 3 3.337 -0.903 -8.644 0.39 35.12 ? O4' GDP 502 B 1 HETATM 13 C C3' GDP . B . C 3 1.594 -2.02 -7.483 0.39 38.6 ? C3' GDP 502 B 1 HETATM 14 O O3' GDP . B . C 3 1.805 -3.35 -6.999 0.39 39.14 ? O3' GDP 502 B 1 HETATM 15 C C2' GDP . B . C 3 2.239 -1.014 -6.55 0.39 38.18 ? C2' GDP 502 B 1 HETATM 16 O O2' GDP . B . C 3 2.549 -1.626 -5.295 0.39 40.19 ? O2' GDP 502 B 1 HETATM 17 C C1' GDP . B . C 3 3.506 -0.572 -7.264 0.39 35.79 ? C1' GDP 502 B 1 HETATM 18 N N9 GDP . B . C 3 3.717 0.891 -7.137 0.39 33.65 ? N9 GDP 502 B 1 HETATM 19 C C8 GDP . B . C 3 2.952 1.852 -7.692 0.39 32.66 ? C8 GDP 502 B 1 HETATM 20 N N7 GDP . B . C 3 3.427 3.088 -7.392 0.39 31.38 ? N7 GDP 502 B 1 HETATM 21 C C5 GDP . B . C 3 4.528 2.924 -6.636 0.39 31.98 ? C5 GDP 502 B 1 HETATM 22 C C6 GDP . B . C 3 5.515 3.813 -5.984 0.39 33.49 ? C6 GDP 502 B 1 HETATM 23 O O6 GDP . B . C 3 5.418 5.056 -6.079 0.39 32.96 ? O6 GDP 502 B 1 HETATM 24 N N1 GDP . B . C 3 6.509 3.244 -5.288 0.39 35.14 ? N1 GDP 502 B 1 HETATM 25 C C2 GDP . B . C 3 6.635 1.907 -5.172 0.39 35.17 ? C2 GDP 502 B 1 HETATM 26 N N2 GDP . B . C 3 7.67 1.41 -4.453 0.39 33.81 ? N2 GDP 502 B 1 HETATM 27 N N3 GDP . B . C 3 5.768 1.032 -5.745 0.39 35.14 ? N3 GDP 502 B 1 HETATM 28 C C4 GDP . B . C 3 4.717 1.475 -6.474 0.39 33.78 ? C4 GDP 502 B 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 830 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 28 #