data_3AVY # _model_server_result.job_id NyA9LjqK7e3SMmXP0EJ-kg _model_server_result.datetime_utc '2024-11-28 12:17:20' _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 3avy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":2501}' # _entry.id 3AVY # _exptl.entry_id 3AVY _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 3AVY _cell.length_a 140.07 _cell.length_b 257.22 _cell.length_c 101.31 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3AVY _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,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 # _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 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc2 A OD1 ASP 968 A ASP 968 1_555 E CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? metalc ? metalc3 A OD2 ASP 968 A ASP 968 1_555 F CA CA . A CA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.793 ? metalc ? metalc4 A O LEU 969 A LEU 969 1_555 E CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc5 A OD1 ASP 1053 A ASP 1053 1_555 E CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc6 A OD2 ASP 1053 A ASP 1053 1_555 F CA CA . A CA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc7 A OD1 ASP 1054 A ASP 1054 1_555 F CA CA . A CA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.117 ? metalc ? metalc8 D O2G CH1 . A CH1 2501 1_555 E CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc9 D O3A CH1 . A CH1 2501 1_555 E CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.008 ? metalc ? metalc10 D O1A CH1 . A CH1 2501 1_555 E CA CA . A CA 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.032 ? metalc ? metalc11 D O1A CH1 . A CH1 2501 1_555 F CA CA . A CA 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.807 ? hydrog 'C-G PAIR' hydrog1 B N3 C 6 G C 2006 1_555 C N1 G 13 T G 2113 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog2 B O4 U 8 G U 2008 1_555 C N6 A 10 T A 2110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog3 B N1 A 9 G A 2009 1_555 C N3 U 9 T U 2109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog4 B N1 A 10 G A 2010 1_555 C N3 U 8 T U 2108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'A-U PAIR' hydrog5 B N1 A 11 G A 2011 1_555 C N3 U 7 T U 2107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'U-A PAIR' hydrog6 B N3 U 13 G U 2013 1_555 C N1 A 5 T A 2105 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 3AVY _atom_sites.fract_transf_matrix[1][1] 0.007139 _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] 0.003888 _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] 0.009871 _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 CH1 . E 5 CA A 1 3001 3001 CA CA . F 5 CA A 1 3002 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 3510 3510 HOH HOH . G 6 HOH A 10 3511 3511 HOH HOH . G 6 HOH A 11 3512 3512 HOH HOH . G 6 HOH A 12 3513 3513 HOH HOH . G 6 HOH A 13 3514 3514 HOH HOH . G 6 HOH A 14 3515 3515 HOH HOH . G 6 HOH A 15 3516 3516 HOH HOH . G 6 HOH A 16 3517 3517 HOH HOH . G 6 HOH A 17 3518 3518 HOH HOH . G 6 HOH A 18 3519 3519 HOH HOH . G 6 HOH A 19 3520 3520 HOH HOH . G 6 HOH A 20 3521 3521 HOH HOH . G 6 HOH A 21 3522 3522 HOH HOH . G 6 HOH A 22 3523 3523 HOH HOH . G 6 HOH A 23 3524 3524 HOH HOH . G 6 HOH A 24 3525 3525 HOH HOH . G 6 HOH A 25 3526 3526 HOH HOH . G 6 HOH A 26 3527 3527 HOH HOH . G 6 HOH A 27 3529 3529 HOH HOH . G 6 HOH A 28 3530 3530 HOH HOH . G 6 HOH A 29 3531 3531 HOH HOH . G 6 HOH A 30 3532 3532 HOH HOH . G 6 HOH A 31 3533 3533 HOH HOH . G 6 HOH A 32 3534 3534 HOH HOH . G 6 HOH A 33 3535 3535 HOH HOH . G 6 HOH A 34 3536 3536 HOH HOH . G 6 HOH A 35 3537 3537 HOH HOH . G 6 HOH A 36 3538 3538 HOH HOH . G 6 HOH A 37 3539 3539 HOH HOH . G 6 HOH A 38 3540 3540 HOH HOH . G 6 HOH A 39 3541 3541 HOH HOH . G 6 HOH A 40 3542 3542 HOH HOH . G 6 HOH A 41 3543 3543 HOH HOH . G 6 HOH A 42 3544 3544 HOH HOH . G 6 HOH A 43 3545 3545 HOH HOH . G 6 HOH A 44 3546 3546 HOH HOH . G 6 HOH A 45 3547 3547 HOH HOH . G 6 HOH A 46 3548 3548 HOH HOH . G 6 HOH A 47 3549 3549 HOH HOH . G 6 HOH A 48 3550 3550 HOH HOH . G 6 HOH A 49 3551 3551 HOH HOH . G 6 HOH A 50 3552 3552 HOH HOH . G 6 HOH A 51 3553 3553 HOH HOH . G 6 HOH A 52 3554 3554 HOH HOH . G 6 HOH A 53 3555 3555 HOH HOH . G 6 HOH A 54 3556 3556 HOH HOH . G 6 HOH A 55 3557 3557 HOH HOH . G 6 HOH A 56 3558 3558 HOH HOH . G 6 HOH A 57 3559 3559 HOH HOH . G 6 HOH A 58 3560 3560 HOH HOH . G 6 HOH A 59 3561 3561 HOH HOH . G 6 HOH A 60 3562 3562 HOH HOH . G 6 HOH A 61 3563 3563 HOH HOH . G 6 HOH A 62 3564 3564 HOH HOH . G 6 HOH A 63 3565 3565 HOH HOH . G 6 HOH A 64 3566 3566 HOH HOH . G 6 HOH A 65 3567 3567 HOH HOH . G 6 HOH A 66 3568 3568 HOH HOH . G 6 HOH A 67 3569 3569 HOH HOH . G 6 HOH A 68 3571 3571 HOH HOH . G 6 HOH A 69 3572 3572 HOH HOH . G 6 HOH A 70 3573 3573 HOH HOH . G 6 HOH A 71 3574 3574 HOH HOH . G 6 HOH A 72 3575 3575 HOH HOH . G 6 HOH A 73 3576 3576 HOH HOH . G 6 HOH A 74 3577 3577 HOH HOH . G 6 HOH A 75 3578 3578 HOH HOH . G 6 HOH A 76 3579 3579 HOH HOH . G 6 HOH A 77 3580 3580 HOH HOH . G 6 HOH A 78 3581 3581 HOH HOH . G 6 HOH A 79 3582 3582 HOH HOH . G 6 HOH A 80 3583 3583 HOH HOH . G 6 HOH A 81 3584 3584 HOH HOH . G 6 HOH A 82 3585 3585 HOH HOH . G 6 HOH A 83 3586 3586 HOH HOH . G 6 HOH A 84 3587 3587 HOH HOH . G 6 HOH A 85 3588 3588 HOH HOH . H 6 HOH T 1 3509 3509 HOH HOH . H 6 HOH T 2 3528 3528 HOH HOH . H 6 HOH T 3 3570 3570 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 -14.798 -63.242 1.209 1 79.82 ? N1 CH1 2501 A 1 HETATM 2 C C2 CH1 . . . D 4 -14.066 -62.319 1.895 1 76.73 ? C2 CH1 2501 A 1 HETATM 3 N N3 CH1 . . . D 4 -14.177 -62.253 3.247 1 83.04 ? N3 CH1 2501 A 1 HETATM 4 C C4 CH1 . . . D 4 -14.999 -63.094 3.931 1 77.1 ? C4 CH1 2501 A 1 HETATM 5 C C5 CH1 . . . D 4 -15.733 -64.045 3.231 1 69.7 ? C5 CH1 2501 A 1 HETATM 6 C C6 CH1 . . . D 4 -15.614 -64.107 1.858 1 76.08 ? C6 CH1 2501 A 1 HETATM 7 O O2 CH1 . . . D 4 -13.312 -61.54 1.314 1 60.46 ? O2 CH1 2501 A 1 HETATM 8 N N4 CH1 . . . D 4 -15.074 -62.96 5.369 1 74.26 ? N4 CH1 2501 A 1 HETATM 9 C C1' CH1 . . . D 4 -14.61 -63.29 -0.25 1 69.35 ? C1' CH1 2501 A 1 HETATM 10 C C2' CH1 . . . D 4 -13.347 -63.944 -0.455 1 61.28 ? C2' CH1 2501 A 1 HETATM 11 O O2' CH1 . . . D 4 -12.285 -63.01 -0.337 1 55.58 ? O2' CH1 2501 A 1 HETATM 12 C C3' CH1 . . . D 4 -13.439 -64.586 -1.771 1 55.73 ? C3' CH1 2501 A 1 HETATM 13 C C4' CH1 . . . D 4 -14.825 -64.567 -2.128 1 62.47 ? C4' CH1 2501 A 1 HETATM 14 O O4' CH1 . . . D 4 -15.524 -64.074 -0.985 1 77.59 ? O4' CH1 2501 A 1 HETATM 15 C C5' CH1 . . . D 4 -15.316 -65.919 -2.613 1 55.31 ? C5' CH1 2501 A 1 HETATM 16 O O5' CH1 . . . D 4 -16.202 -66.697 -1.853 1 57.85 ? O5' CH1 2501 A 1 HETATM 17 P PA CH1 . . . D 4 -17.574 -67.196 -2.428 1 50.23 ? PA CH1 2501 A 1 HETATM 18 O O1A CH1 . . . D 4 -17.572 -66.853 -3.88 1 52.24 ? O1A CH1 2501 A 1 HETATM 19 O O2A CH1 . . . D 4 -18.728 -66.517 -1.78 1 60.48 ? O2A CH1 2501 A 1 HETATM 20 O O3A CH1 . . . D 4 -17.655 -68.772 -2.308 1 52.9 ? O3A CH1 2501 A 1 HETATM 21 P PB CH1 . . . D 4 -16.47 -69.689 -1.756 1 64.37 ? PB CH1 2501 A 1 HETATM 22 O O1B CH1 . . . D 4 -16.497 -69.532 -0.245 1 61.41 ? O1B CH1 2501 A 1 HETATM 23 O O2B CH1 . . . D 4 -15.094 -69.295 -2.267 1 33.16 ? O2B CH1 2501 A 1 HETATM 24 O O3B CH1 . . . D 4 -16.766 -71.242 -2.049 1 55.16 ? O3B CH1 2501 A 1 HETATM 25 P PG CH1 . . . D 4 -18.139 -71.917 -2.554 1 65.16 ? PG CH1 2501 A 1 HETATM 26 O O1G CH1 . . . D 4 -19.206 -71.552 -1.524 1 47.31 ? O1G CH1 2501 A 1 HETATM 27 O O2G CH1 . . . D 4 -18.603 -71.349 -3.909 1 53.13 ? O2G CH1 2501 A 1 HETATM 28 O O3G CH1 . . . D 4 -17.988 -73.425 -2.737 1 50.88 ? O3G CH1 2501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 28 #