data_7CV6 # _model_server_result.job_id 26tCXlcuOzC95HiJePkilg _model_server_result.datetime_utc '2024-10-18 15:27:09' _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 7cv6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":503}' # _entry.id 7CV6 # _exptl.entry_id 7CV6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 361.248 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-O-methyladenosine 5'-(dihydrogen phosphate)" _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 7CV6 _cell.length_a 93.821 _cell.length_b 130.022 _cell.length_c 141.322 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7CV6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 D N N # _chem_comp.formula 'C11 H16 N5 O7 P' _chem_comp.formula_weight 361.248 _chem_comp.id A2M _chem_comp.mon_nstd_flag n _chem_comp.name "2'-O-methyladenosine 5'-(dihydrogen phosphate)" _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 P OP1 A2M doub 1 n n P OP3 A2M sing 2 n n P O5' A2M sing 3 n n OP3 HOP3 A2M sing 4 n n O5' C5' A2M sing 5 n n C5' C4' A2M sing 6 n n C5' H5' A2M sing 7 n n C5' "H5''" A2M sing 8 n n C4' O4' A2M sing 9 n n C4' C3' A2M sing 10 n n C4' H4' A2M sing 11 n n O4' C1' A2M sing 12 n n C3' O3' A2M sing 13 n n C3' C2' A2M sing 14 n n C3' H3' A2M sing 15 n n O3' HO3' A2M sing 16 n n C2' O2' A2M sing 17 n n C2' C1' A2M sing 18 n n C2' H2' A2M sing 19 n n O2' CM' A2M sing 20 n n C1' N9 A2M sing 21 n n C1' H1' A2M sing 22 n n CM' "HM'1" A2M sing 23 n n CM' "HM'2" A2M sing 24 n n CM' "HM'3" A2M sing 25 n n N9 C8 A2M sing 26 n y N9 C4 A2M sing 27 n y C8 N7 A2M doub 28 n y C8 H8 A2M sing 29 n n N7 C5 A2M sing 30 n y C5 C6 A2M sing 31 n y C5 C4 A2M doub 32 n y C6 N6 A2M sing 33 n n C6 N1 A2M doub 34 n y N6 H61 A2M sing 35 n n N6 H62 A2M sing 36 n n N1 C2 A2M sing 37 n y C2 N3 A2M doub 38 n y C2 H2 A2M sing 39 n n N3 C4 A2M sing 40 n y P OP2 A2M sing 41 n n OP2 HOP2 A2M sing 42 n n # _atom_sites.entry_id 7CV6 _atom_sites.fract_transf_matrix[1][1] 0.010659 _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] 0.007691 _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] 0.007076 _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 SAH B 1 501 1 SAH SAH . C 3 A2M B 1 502 1 A2M A2M . D 3 A2M B 1 503 2 A2M A2M . E 4 HOH B 1 601 9 HOH HOH . E 4 HOH B 2 602 7 HOH HOH . E 4 HOH B 3 603 12 HOH HOH . E 4 HOH B 4 604 11 HOH HOH . E 4 HOH B 5 605 10 HOH HOH . E 4 HOH B 6 606 18 HOH HOH . E 4 HOH B 7 607 1 HOH HOH . E 4 HOH B 8 608 19 HOH HOH . E 4 HOH B 9 609 6 HOH HOH . E 4 HOH B 10 610 4 HOH HOH . E 4 HOH B 11 611 8 HOH HOH . E 4 HOH B 12 612 13 HOH HOH . E 4 HOH B 13 613 15 HOH HOH . E 4 HOH B 14 614 16 HOH HOH . E 4 HOH B 15 615 3 HOH HOH . E 4 HOH B 16 616 2 HOH HOH . E 4 HOH B 17 617 17 HOH HOH . E 4 HOH B 18 618 5 HOH HOH . E 4 HOH B 19 619 14 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 P A2M . . . D 3 -34.805 -43.688 -39.118 1 202.28 ? P A2M 503 B 1 HETATM 2 O OP1 A2M . . . D 3 -34.494 -45.151 -39.344 1 198.86 ? OP1 A2M 503 B 1 HETATM 3 O OP3 A2M . . . D 3 -35.105 -43.348 -37.678 1 210.33 ? OP3 A2M 503 B 1 HETATM 4 O O5' A2M . . . D 3 -33.42 -42.919 -39.491 1 206.03 ? O5' A2M 503 B 1 HETATM 5 C C5' A2M . . . D 3 -32.926 -41.728 -38.858 1 190.94 ? C5' A2M 503 B 1 HETATM 6 C C4' A2M . . . D 3 -31.68 -42.022 -38.019 1 185.68 ? C4' A2M 503 B 1 HETATM 7 O O4' A2M . . . D 3 -31.366 -40.864 -37.236 1 179 ? O4' A2M 503 B 1 HETATM 8 C C3' A2M . . . D 3 -31.853 -43.156 -37.006 1 183.32 ? C3' A2M 503 B 1 HETATM 9 O O3' A2M . . . D 3 -30.593 -43.785 -36.752 1 182.17 ? O3' A2M 503 B 1 HETATM 10 C C2' A2M . . . D 3 -32.395 -42.436 -35.781 1 175.72 ? C2' A2M 503 B 1 HETATM 11 O O2' A2M . . . D 3 -32.256 -43.151 -34.539 1 154.53 ? O2' A2M 503 B 1 HETATM 12 C C1' A2M . . . D 3 -31.591 -41.144 -35.839 1 175.89 ? C1' A2M 503 B 1 HETATM 13 C CM' A2M . . . D 3 -33.473 -43.331 -33.803 1 137.39 ? CM' A2M 503 B 1 HETATM 14 N N9 A2M . . . D 3 -32.34 -40.077 -35.134 1 166.45 ? N9 A2M 503 B 1 HETATM 15 C C8 A2M . . . D 3 -32.521 -40.027 -33.794 1 162.99 ? C8 A2M 503 B 1 HETATM 16 N N7 A2M . . . D 3 -33.246 -38.938 -33.448 1 155.2 ? N7 A2M 503 B 1 HETATM 17 C C5 A2M . . . D 3 -33.534 -38.285 -34.588 1 149.24 ? C5 A2M 503 B 1 HETATM 18 C C6 A2M . . . D 3 -34.27 -37.055 -34.945 1 139.42 ? C6 A2M 503 B 1 HETATM 19 N N6 A2M . . . D 3 -34.838 -36.324 -33.963 1 128.25 ? N6 A2M 503 B 1 HETATM 20 N N1 A2M . . . D 3 -34.339 -36.707 -36.262 1 134.81 ? N1 A2M 503 B 1 HETATM 21 C C2 A2M . . . D 3 -33.767 -37.443 -37.246 1 133.21 ? C2 A2M 503 B 1 HETATM 22 N N3 A2M . . . D 3 -33.083 -38.577 -36.989 1 136.72 ? N3 A2M 503 B 1 HETATM 23 C C4 A2M . . . D 3 -32.939 -39.035 -35.708 1 151.31 ? C4 A2M 503 B 1 HETATM 24 O OP2 A2M . . . D 3 -35.822 -43.135 -40.085 1 196.37 ? OP2 A2M 503 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 24 #