data_3AVT # _model_server_result.job_id cEP3CHesN0xCpC5TEuf07g _model_server_result.datetime_utc '2024-11-15 03:59:09' _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 3avt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2501}' # _entry.id 3AVT # _exptl.entry_id 3AVT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE" _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 3AVT _cell.length_a 139.12 _cell.length_b 255.99 _cell.length_c 101.37 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AVT _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 C 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 OD1 ASP 968 A ASP 968 1_555 D CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc2 A OD2 ASP 968 A ASP 968 1_555 D CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.019 ? metalc ? metalc3 A OD2 ASP 968 A ASP 968 1_555 E CA CA . A CA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc4 A O LEU 969 A LEU 969 1_555 D CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc5 A OD1 ASP 1053 A ASP 1053 1_555 E CA CA . A CA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.179 ? metalc ? metalc6 A OD2 ASP 1054 A ASP 1054 1_555 E CA CA . A CA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc7 C O3A GH3 . A GH3 2502 1_555 D CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc8 C O2G GH3 . A GH3 2502 1_555 D CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id GH3 _chem_comp.mon_nstd_flag n _chem_comp.name "3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE" _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 PG O1G GH3 doub 198 n n PG O2G GH3 sing 199 n n PG O3G GH3 sing 200 n n PG O3B GH3 sing 201 n n O2G HOG2 GH3 sing 202 n n O3G HOG3 GH3 sing 203 n n O3B PB GH3 sing 204 n n PB O1B GH3 doub 205 n n PB O2B GH3 sing 206 n n PB O3A GH3 sing 207 n n O2B HOB2 GH3 sing 208 n n O3A PA GH3 sing 209 n n PA O1A GH3 doub 210 n n PA O2A GH3 sing 211 n n PA O5' GH3 sing 212 n n O2A HOA2 GH3 sing 213 n n O5' C5' GH3 sing 214 n n C5' C4' GH3 sing 215 n n C5' H5' GH3 sing 216 n n C5' "H5''" GH3 sing 217 n n C4' O4' GH3 sing 218 n n C4' C3' GH3 sing 219 n n C4' H4' GH3 sing 220 n n O4' C1' GH3 sing 221 n n C3' C2' GH3 sing 222 n n C3' "H3'2" GH3 sing 223 n n C3' H3' GH3 sing 224 n n C2' O2' GH3 sing 225 n n C2' C1' GH3 sing 226 n n C2' H2' GH3 sing 227 n n O2' HO2' GH3 sing 228 n n C1' N9 GH3 sing 229 n n C1' H1' GH3 sing 230 n n N9 C8 GH3 sing 231 n y N9 C4 GH3 sing 232 n y C8 N7 GH3 doub 233 n y C8 H8 GH3 sing 234 n n N7 C5 GH3 sing 235 n y C5 C6 GH3 sing 236 n n C5 C4 GH3 doub 237 n y C6 O6 GH3 doub 238 n n C6 N1 GH3 sing 239 n n N1 C2 GH3 sing 240 n n N1 HN1 GH3 sing 241 n n C2 N2 GH3 sing 242 n n C2 N3 GH3 doub 243 n n N2 HN21 GH3 sing 244 n n N2 HN22 GH3 sing 245 n n N3 C4 GH3 sing 246 n n # _atom_sites.entry_id 3AVT _atom_sites.fract_transf_matrix[1][1] 0.007188 _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] 0.003906 _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] 0.009865 _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 GH3 A 1 2502 2502 GH3 GH3 . D 4 CA A 1 3001 3001 CA CA . E 4 CA A 1 3002 3002 CA CA . F 3 GH3 T 1 2501 2501 GH3 GH3 . G 5 HOH A 1 3501 3501 HOH HOH . G 5 HOH A 2 3502 3502 HOH HOH . G 5 HOH A 3 3503 3503 HOH HOH . G 5 HOH A 4 3505 3505 HOH HOH . G 5 HOH A 5 3506 3506 HOH HOH . G 5 HOH A 6 3507 3507 HOH HOH . G 5 HOH A 7 3508 3508 HOH HOH . G 5 HOH A 8 3509 3509 HOH HOH . G 5 HOH A 9 3510 3510 HOH HOH . G 5 HOH A 10 3512 3512 HOH HOH . G 5 HOH A 11 3513 3513 HOH HOH . G 5 HOH A 12 3514 3514 HOH HOH . G 5 HOH A 13 3515 3515 HOH HOH . G 5 HOH A 14 3516 3516 HOH HOH . G 5 HOH A 15 3517 3517 HOH HOH . G 5 HOH A 16 3518 3518 HOH HOH . G 5 HOH A 17 3519 3519 HOH HOH . G 5 HOH A 18 3520 3520 HOH HOH . G 5 HOH A 19 3521 3521 HOH HOH . G 5 HOH A 20 3522 3522 HOH HOH . G 5 HOH A 21 3523 3523 HOH HOH . G 5 HOH A 22 3524 3524 HOH HOH . G 5 HOH A 23 3525 3525 HOH HOH . G 5 HOH A 24 3526 3526 HOH HOH . G 5 HOH A 25 3527 3527 HOH HOH . G 5 HOH A 26 3528 3528 HOH HOH . G 5 HOH A 27 3529 3529 HOH HOH . G 5 HOH A 28 3530 3530 HOH HOH . G 5 HOH A 29 3531 3531 HOH HOH . G 5 HOH A 30 3532 3532 HOH HOH . G 5 HOH A 31 3533 3533 HOH HOH . G 5 HOH A 32 3534 3534 HOH HOH . G 5 HOH A 33 3535 3535 HOH HOH . G 5 HOH A 34 3536 3536 HOH HOH . G 5 HOH A 35 3537 3537 HOH HOH . G 5 HOH A 36 3538 3538 HOH HOH . G 5 HOH A 37 3539 3539 HOH HOH . G 5 HOH A 38 3540 3540 HOH HOH . G 5 HOH A 39 3541 3541 HOH HOH . G 5 HOH A 40 3542 3542 HOH HOH . G 5 HOH A 41 3544 3544 HOH HOH . G 5 HOH A 42 3545 3545 HOH HOH . G 5 HOH A 43 3546 3546 HOH HOH . G 5 HOH A 44 3547 3547 HOH HOH . G 5 HOH A 45 3548 3548 HOH HOH . G 5 HOH A 46 3549 3549 HOH HOH . G 5 HOH A 47 3550 3550 HOH HOH . G 5 HOH A 48 3551 3551 HOH HOH . G 5 HOH A 49 3552 3552 HOH HOH . G 5 HOH A 50 3553 3553 HOH HOH . G 5 HOH A 51 3554 3554 HOH HOH . G 5 HOH A 52 3555 3555 HOH HOH . G 5 HOH A 53 3556 3556 HOH HOH . G 5 HOH A 54 3557 3557 HOH HOH . G 5 HOH A 55 3558 3558 HOH HOH . G 5 HOH A 56 3559 3559 HOH HOH . H 5 HOH T 1 3504 3504 HOH HOH . H 5 HOH T 2 3511 3511 HOH HOH . H 5 HOH T 3 3543 3543 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 PG GH3 . . . F 3 44.223 59.638 2.737 1 127.76 ? PG GH3 2501 T 1 HETATM 2 O O1G GH3 . . . F 3 42.731 59.868 2.537 1 101.55 ? O1G GH3 2501 T 1 HETATM 3 O O2G GH3 . . . F 3 44.907 59.403 1.407 1 128.77 ? O2G GH3 2501 T 1 HETATM 4 O O3G GH3 . . . F 3 44.45 58.376 3.567 1 87.3 ? O3G GH3 2501 T 1 HETATM 5 O O3B GH3 . . . F 3 44.86 60.866 3.449 1 96.27 ? O3B GH3 2501 T 1 HETATM 6 P PB GH3 . . . F 3 46.224 61.605 3.134 1 109.54 ? PB GH3 2501 T 1 HETATM 7 O O1B GH3 . . . F 3 47.226 61.185 4.223 1 81.54 ? O1B GH3 2501 T 1 HETATM 8 O O2B GH3 . . . F 3 46.76 61.14 1.783 1 107.7 ? O2B GH3 2501 T 1 HETATM 9 O O3A GH3 . . . F 3 45.991 63.229 3.119 1 102.09 ? O3A GH3 2501 T 1 HETATM 10 P PA GH3 . . . F 3 46.371 64.475 4.146 1 103.4 ? PA GH3 2501 T 1 HETATM 11 O O1A GH3 . . . F 3 46.085 65.841 3.407 1 86.97 ? O1A GH3 2501 T 1 HETATM 12 O O2A GH3 . . . F 3 45.569 64.448 5.432 1 88.79 ? O2A GH3 2501 T 1 HETATM 13 O O5' GH3 . . . F 3 47.936 64.5 4.445 1 92.87 ? O5' GH3 2501 T 1 HETATM 14 C C5' GH3 . . . F 3 48.478 63.746 5.484 1 80.78 ? C5' GH3 2501 T 1 HETATM 15 C C4' GH3 . . . F 3 49.846 63.178 5.398 1 75.63 ? C4' GH3 2501 T 1 HETATM 16 O O4' GH3 . . . F 3 49.909 61.908 4.669 1 82.07 ? O4' GH3 2501 T 1 HETATM 17 C C3' GH3 . . . F 3 50.77 64.103 4.723 1 76.7 ? C3' GH3 2501 T 1 HETATM 18 C C2' GH3 . . . F 3 51.642 63.247 3.924 1 83.18 ? C2' GH3 2501 T 1 HETATM 19 O O2' GH3 . . . F 3 52.731 62.866 4.69 1 65.97 ? O2' GH3 2501 T 1 HETATM 20 C C1' GH3 . . . F 3 50.795 62.068 3.58 1 89.01 ? C1' GH3 2501 T 1 HETATM 21 N N9 GH3 . . . F 3 50.19 62.238 2.294 1 98.1 ? N9 GH3 2501 T 1 HETATM 22 C C8 GH3 . . . F 3 49.139 62.761 1.743 1 94.15 ? C8 GH3 2501 T 1 HETATM 23 N N7 GH3 . . . F 3 49.152 62.584 0.511 1 95.13 ? N7 GH3 2501 T 1 HETATM 24 C C5 GH3 . . . F 3 50.219 61.92 0.081 1 96.67 ? C5 GH3 2501 T 1 HETATM 25 C C6 GH3 . . . F 3 50.726 61.472 -1.128 1 94.78 ? C6 GH3 2501 T 1 HETATM 26 O O6 GH3 . . . F 3 50.016 61.721 -2.293 1 90.59 ? O6 GH3 2501 T 1 HETATM 27 N N1 GH3 . . . F 3 51.92 60.792 -1.137 1 93.88 ? N1 GH3 2501 T 1 HETATM 28 C C2 GH3 . . . F 3 52.629 60.544 0.018 1 91.14 ? C2 GH3 2501 T 1 HETATM 29 N N2 GH3 . . . F 3 53.922 59.807 -0.007 1 73.65 ? N2 GH3 2501 T 1 HETATM 30 N N3 GH3 . . . F 3 52.174 60.959 1.217 1 93.89 ? N3 GH3 2501 T 1 HETATM 31 C C4 GH3 . . . F 3 51.007 61.63 1.28 1 99.06 ? C4 GH3 2501 T 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #