data_3VNV # _model_server_result.job_id 8dpAE9TYfuyBEW5xod0L0A _model_server_result.datetime_utc '2024-11-26 19:58:59' _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 3vnv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2501}' # _entry.id 3VNV # _exptl.entry_id 3VNV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE" _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 3VNV _cell.length_a 139.73 _cell.length_b 256.04 _cell.length_c 101.72 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3VNV _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 4 _struct_asym.id D _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 OD2 ASP 968 A ASP 968 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc2 A OD2 ASP 968 A ASP 968 1_555 F CA CA . A CA 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc3 A O LEU 969 A LEU 969 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc4 A OD2 ASP 1053 A ASP 1053 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? metalc ? metalc5 A OD1 ASP 1053 A ASP 1053 1_555 F CA CA . A CA 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.882 ? metalc ? metalc6 A OD2 ASP 1054 A ASP 1054 1_555 F CA CA . A CA 2503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc7 D O3G CH1 . A CH1 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc8 D O2A CH1 . A CH1 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc9 D O2B CH1 . A CH1 2501 1_555 E CA CA . A CA 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.644 ? metalc ? metalc10 F CA CA . A CA 2503 1_555 B O3' C 7 G C 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? hydrog 'C-G PAIR' hydrog1 B N4 C 1 G C 2001 1_555 C O6 G 8 T G 2108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N3 C 2 G C 2002 1_555 C N1 G 7 T G 2107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N4 C 2 G C 2002 1_555 C O6 G 7 T G 2107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B O2 C 2 G C 2002 1_555 C N2 G 7 T G 2107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog5 B N4 C 3 G C 2003 1_555 C O6 G 6 T G 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog6 B N3 U 4 G U 2004 1_555 C N1 A 5 T A 2105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N1 A 5 G A 2005 1_555 C N3 U 4 T U 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N6 A 5 G A 2005 1_555 C O4 U 4 T U 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N3 C 6 G C 2006 1_555 C N1 G 3 T G 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N4 C 6 G C 2006 1_555 C O6 G 3 T G 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B O2 C 6 G C 2006 1_555 C N2 G 3 T G 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'C-G PAIR' hydrog12 B O2 C 7 G C 2007 1_555 C N2 G 2 T G 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id CH1 _chem_comp.mon_nstd_flag . _chem_comp.name "3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 N1 C2 CH1 sing 145 n n N1 C6 CH1 sing 146 n n N1 C1' CH1 sing 147 n n C2 N3 CH1 sing 148 n n C2 O2 CH1 doub 149 n n N3 C4 CH1 doub 150 n n C4 C5 CH1 sing 151 n n C4 N4 CH1 sing 152 n n C5 C6 CH1 doub 153 n n C5 H5 CH1 sing 154 n n C6 H6 CH1 sing 155 n n N4 HN41 CH1 sing 156 n n N4 HN42 CH1 sing 157 n n C1' C2' CH1 sing 158 n n C1' O4' CH1 sing 159 n n C1' H1' CH1 sing 160 n n C2' O2' CH1 sing 161 n n C2' C3' CH1 sing 162 n n C2' H2' CH1 sing 163 n n O2' HO2' CH1 sing 164 n n C3' C4' CH1 sing 165 n n C3' "H3'2" CH1 sing 166 n n C3' H3' CH1 sing 167 n n C4' O4' CH1 sing 168 n n C4' C5' CH1 sing 169 n n C4' H4' CH1 sing 170 n n C5' O5' CH1 sing 171 n n C5' "H5'1" CH1 sing 172 n n C5' "H5'2" CH1 sing 173 n n O5' PA CH1 sing 174 n n PA O1A CH1 doub 175 n n PA O2A CH1 sing 176 n n PA O3A CH1 sing 177 n n O2A HOA2 CH1 sing 178 n n O3A PB CH1 sing 179 n n PB O1B CH1 doub 180 n n PB O2B CH1 sing 181 n n PB O3B CH1 sing 182 n n O2B HOB2 CH1 sing 183 n n O3B PG CH1 sing 184 n n PG O1G CH1 doub 185 n n PG O2G CH1 sing 186 n n PG O3G CH1 sing 187 n n O2G HOG2 CH1 sing 188 n n O3G HOG3 CH1 sing 189 n n # _atom_sites.entry_id 3VNV _atom_sites.fract_transf_matrix[1][1] 0.007157 _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] 0.009831 _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 4 CH1 A 1 2501 2501 CH1 CTP . E 5 CA A 1 2502 3001 CA CA . F 5 CA A 1 2503 3002 CA CA . G 6 HOH A 1 3501 3501 HOH HOH . G 6 HOH A 2 3502 3502 HOH HOH . G 6 HOH A 3 3503 3503 HOH HOH . G 6 HOH A 4 3504 3504 HOH HOH . G 6 HOH A 5 3505 3505 HOH HOH . G 6 HOH A 6 3506 3506 HOH HOH . G 6 HOH A 7 3507 3507 HOH HOH . G 6 HOH A 8 3508 3508 HOH HOH . G 6 HOH A 9 3509 3509 HOH HOH . G 6 HOH A 10 3510 3510 HOH HOH . G 6 HOH A 11 3511 3511 HOH HOH . G 6 HOH A 12 3512 3512 HOH HOH . G 6 HOH A 13 3513 3513 HOH HOH . G 6 HOH A 14 3514 3514 HOH HOH . G 6 HOH A 15 3515 3515 HOH HOH . G 6 HOH A 16 3516 3516 HOH HOH . G 6 HOH A 17 3517 3517 HOH HOH . G 6 HOH A 18 3518 3518 HOH HOH . G 6 HOH A 19 3519 3519 HOH HOH . G 6 HOH A 20 3520 3520 HOH HOH . G 6 HOH A 21 3521 3521 HOH HOH . G 6 HOH A 22 3522 3522 HOH HOH . G 6 HOH A 23 3523 3523 HOH HOH . G 6 HOH A 24 3524 3524 HOH HOH . G 6 HOH A 25 3525 3525 HOH HOH . G 6 HOH A 26 3526 3526 HOH HOH . G 6 HOH A 27 3527 3527 HOH HOH . G 6 HOH A 28 3528 3528 HOH HOH . G 6 HOH A 29 3529 3529 HOH HOH . G 6 HOH A 30 3530 3530 HOH HOH . G 6 HOH A 31 3531 3531 HOH HOH . G 6 HOH A 32 3532 3532 HOH HOH . G 6 HOH A 33 3533 3533 HOH HOH . G 6 HOH A 34 3534 3534 HOH HOH . G 6 HOH A 35 3535 3535 HOH HOH . G 6 HOH A 36 3536 3536 HOH HOH . G 6 HOH A 37 3537 3537 HOH HOH . G 6 HOH A 38 3538 3538 HOH HOH . G 6 HOH A 39 3539 3539 HOH HOH . G 6 HOH A 40 3540 3540 HOH HOH . G 6 HOH A 41 3541 3541 HOH HOH . G 6 HOH A 42 3542 3542 HOH HOH . G 6 HOH A 43 3543 3543 HOH HOH . G 6 HOH A 44 3544 3544 HOH HOH . G 6 HOH A 45 3545 3545 HOH HOH . G 6 HOH A 46 3546 3546 HOH HOH . G 6 HOH A 47 3547 3547 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 N N1 CH1 . . . D 4 53.895 63.694 -0.389 1 49.82 ? N1 CH1 2501 A 1 HETATM 2 C C2 CH1 . . . D 4 54.183 63.424 -1.696 1 55.3 ? C2 CH1 2501 A 1 HETATM 3 N N3 CH1 . . . D 4 53.225 63.578 -2.663 1 53.46 ? N3 CH1 2501 A 1 HETATM 4 C C4 CH1 . . . D 4 51.986 64.002 -2.331 1 52.19 ? C4 CH1 2501 A 1 HETATM 5 C C5 CH1 . . . D 4 51.708 64.273 -0.985 1 48.36 ? C5 CH1 2501 A 1 HETATM 6 C C6 CH1 . . . D 4 52.681 64.106 -0.033 1 49.31 ? C6 CH1 2501 A 1 HETATM 7 O O2 CH1 . . . D 4 55.318 63.04 -1.996 1 51.79 ? O2 CH1 2501 A 1 HETATM 8 N N4 CH1 . . . D 4 50.918 64.175 -3.354 1 40.23 ? N4 CH1 2501 A 1 HETATM 9 C C1' CH1 . . . D 4 54.959 63.526 0.67 1 50.7 ? C1' CH1 2501 A 1 HETATM 10 C C2' CH1 . . . D 4 55.997 64.502 0.684 1 49.85 ? C2' CH1 2501 A 1 HETATM 11 O O2' CH1 . . . D 4 57.236 63.848 0.682 1 45.02 ? O2' CH1 2501 A 1 HETATM 12 C C3' CH1 . . . D 4 55.812 65.306 1.902 1 47.48 ? C3' CH1 2501 A 1 HETATM 13 C C4' CH1 . . . D 4 54.835 64.645 2.681 1 49.93 ? C4' CH1 2501 A 1 HETATM 14 O O4' CH1 . . . D 4 54.406 63.512 1.967 1 57.36 ? O4' CH1 2501 A 1 HETATM 15 C C5' CH1 . . . D 4 53.666 65.539 2.924 1 44.87 ? C5' CH1 2501 A 1 HETATM 16 O O5' CH1 . . . D 4 53.651 66.727 2.223 1 43.16 ? O5' CH1 2501 A 1 HETATM 17 P PA CH1 . . . D 4 52.324 67.525 2.366 1 42.39 ? PA CH1 2501 A 1 HETATM 18 O O1A CH1 . . . D 4 51.174 66.825 1.716 1 44.1 ? O1A CH1 2501 A 1 HETATM 19 O O2A CH1 . . . D 4 52.049 67.6 3.875 1 49.44 ? O2A CH1 2501 A 1 HETATM 20 O O3A CH1 . . . D 4 52.519 69.008 1.877 1 48.64 ? O3A CH1 2501 A 1 HETATM 21 P PB CH1 . . . D 4 53.86 69.83 1.8 1 42.96 ? PB CH1 2501 A 1 HETATM 22 O O1B CH1 . . . D 4 54.641 69.45 0.617 1 42.65 ? O1B CH1 2501 A 1 HETATM 23 O O2B CH1 . . . D 4 54.824 69.669 2.989 1 35.64 ? O2B CH1 2501 A 1 HETATM 24 O O3B CH1 . . . D 4 53.302 71.348 1.569 1 46.36 ? O3B CH1 2501 A 1 HETATM 25 P PG CH1 . . . D 4 52.124 72.067 2.443 1 53.21 ? PG CH1 2501 A 1 HETATM 26 O O1G CH1 . . . D 4 50.865 72.054 1.621 1 48.62 ? O1G CH1 2501 A 1 HETATM 27 O O2G CH1 . . . D 4 52.479 73.552 2.661 1 41.79 ? O2G CH1 2501 A 1 HETATM 28 O O3G CH1 . . . D 4 51.816 71.448 3.801 1 43.09 ? O3G CH1 2501 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #