data_3QVV
#
_model_server_result.job_id            JnhIz52lhARDzbRDYHS7lA 
_model_server_result.datetime_utc      '2024-11-08 16:46:35' 
_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          3qvv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":2001}' 
#
_entry.id    3QVV 
#
_exptl.entry_id    3QVV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-3'-5'-DIPHOSPHATE" 
_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            3QVV 
_cell.length_a            71.79 
_cell.length_b            71.91 
_cell.length_c            122.59 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3QVV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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
? 2 C N N 
? 2 E N N 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                A3P 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-3'-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
P1 O1P A3P doub 21 n n 
P1 O2P A3P sing 22 n n 
P1 O3P A3P sing 23 n n 
P1 O3' A3P sing 24 n n 
O2P HOP2 A3P sing 25 n n 
O3P HOP3 A3P sing 26 n n 
P2 O4P A3P doub 27 n n 
P2 O5P A3P sing 28 n n 
P2 O6P A3P sing 29 n n 
P2 O5' A3P sing 30 n n 
O5P HOP5 A3P sing 31 n n 
O6P HOP6 A3P sing 32 n n 
O5' C5' A3P sing 33 n n 
C5' C4' A3P sing 34 n n 
C5' "H5'1" A3P sing 35 n n 
C5' "H5'2" A3P sing 36 n n 
C4' O4' A3P sing 37 n n 
C4' C3' A3P sing 38 n n 
C4' H4' A3P sing 39 n n 
O4' C1' A3P sing 40 n n 
C3' O3' A3P sing 41 n n 
C3' C2' A3P sing 42 n n 
C3' H3' A3P sing 43 n n 
C2' O2' A3P sing 44 n n 
C2' C1' A3P sing 45 n n 
C2' H2' A3P sing 46 n n 
O2' HO2' A3P sing 47 n n 
C1' N9 A3P sing 48 n n 
C1' H1' A3P sing 49 n n 
N9 C8 A3P sing 50 n y 
N9 C4 A3P sing 51 n y 
C8 N7 A3P doub 52 n y 
C8 H8 A3P sing 53 n n 
N7 C5 A3P sing 54 n y 
C5 C6 A3P sing 55 n y 
C5 C4 A3P doub 56 n y 
C6 N6 A3P sing 57 n n 
C6 N1 A3P doub 58 n y 
N6 HN61 A3P sing 59 n n 
N6 HN62 A3P sing 60 n n 
N1 C2 A3P sing 61 n y 
C2 N3 A3P doub 62 n y 
C2 H2 A3P sing 63 n n 
N3 C4 A3P sing 64 n y 
#
_atom_sites.entry_id                     3QVV 
_atom_sites.fract_transf_matrix[1][1]    0.01393 
_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]    0.013906 
_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]    0.008157 
_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 2 A3P A 1 2001 2001 A3P A3P . 
D 3 3QV A 1 296 2 3QV 3QV . 
E 2 A3P B 1 2001 2001 A3P A3P . 
F 3 3QV B 1 296 2 3QV 3QV . 
G 4 HOH A 1 297 6 HOH HOH . 
G 4 HOH A 2 298 16 HOH HOH . 
G 4 HOH A 3 299 24 HOH HOH . 
G 4 HOH A 4 300 31 HOH HOH . 
G 4 HOH A 5 301 37 HOH HOH . 
G 4 HOH A 6 302 61 HOH HOH . 
G 4 HOH A 7 303 70 HOH HOH . 
G 4 HOH A 8 304 74 HOH HOH . 
G 4 HOH A 9 305 139 HOH HOH . 
G 4 HOH A 10 306 140 HOH HOH . 
G 4 HOH A 11 307 265 HOH HOH . 
G 4 HOH A 12 308 266 HOH HOH . 
G 4 HOH A 13 309 271 HOH HOH . 
G 4 HOH A 14 310 272 HOH HOH . 
G 4 HOH A 15 311 273 HOH HOH . 
G 4 HOH A 16 312 274 HOH HOH . 
G 4 HOH A 17 313 275 HOH HOH . 
H 4 HOH B 1 297 1 HOH HOH . 
H 4 HOH B 2 298 4 HOH HOH . 
H 4 HOH B 3 299 8 HOH HOH . 
H 4 HOH B 4 300 9 HOH HOH . 
H 4 HOH B 5 301 18 HOH HOH . 
H 4 HOH B 6 302 22 HOH HOH . 
H 4 HOH B 7 303 45 HOH HOH . 
H 4 HOH B 8 304 47 HOH HOH . 
H 4 HOH B 9 305 48 HOH HOH . 
H 4 HOH B 10 306 115 HOH HOH . 
H 4 HOH B 11 307 137 HOH HOH . 
H 4 HOH B 12 308 194 HOH HOH . 
H 4 HOH B 13 309 253 HOH HOH . 
H 4 HOH B 14 310 256 HOH HOH . 
H 4 HOH B 15 311 258 HOH HOH . 
H 4 HOH B 16 312 264 HOH HOH . 
H 4 HOH B 17 313 267 HOH HOH . 
H 4 HOH B 18 314 268 HOH HOH . 
H 4 HOH B 19 315 270 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 P1 A3P . . . C 2 4.272 16.376 24.022 1 57.04 ? P1 A3P 2001 A 1 
HETATM 2 O O1P A3P . . . C 2 5.202 15.395 23.354 1 56.02 ? O1P A3P 2001 A 1 
HETATM 3 O O2P A3P . . . C 2 3.359 15.76 25.055 1 60.63 ? O2P A3P 2001 A 1 
HETATM 4 O O3P A3P . . . C 2 4.925 17.659 24.465 1 56.55 ? O3P A3P 2001 A 1 
HETATM 5 P P2 A3P . . . C 2 1.065 16.151 17.117 1 54.94 ? P2 A3P 2001 A 1 
HETATM 6 O O4P A3P . . . C 2 2.027 14.999 16.996 1 56.73 ? O4P A3P 2001 A 1 
HETATM 7 O O5P A3P . . . C 2 -0.386 15.74 17.133 1 58.21 ? O5P A3P 2001 A 1 
HETATM 8 O O6P A3P . . . C 2 1.386 17.334 16.235 1 58.18 ? O6P A3P 2001 A 1 
HETATM 9 O O5' A3P . . . C 2 1.317 16.756 18.58 1 57.26 ? O5' A3P 2001 A 1 
HETATM 10 C C5' A3P . . . C 2 1.795 15.954 19.651 1 56.33 ? C5' A3P 2001 A 1 
HETATM 11 C C4' A3P . . . C 2 2.095 16.864 20.832 1 58.68 ? C4' A3P 2001 A 1 
HETATM 12 O O4' A3P . . . C 2 0.936 17.641 21.165 1 59.83 ? O4' A3P 2001 A 1 
HETATM 13 C C3' A3P . . . C 2 2.437 16.059 22.07 1 58.57 ? C3' A3P 2001 A 1 
HETATM 14 O O3' A3P . . . C 2 3.29 16.887 22.854 1 58.18 ? O3' A3P 2001 A 1 
HETATM 15 C C2' A3P . . . C 2 1.09 15.92 22.736 1 57.97 ? C2' A3P 2001 A 1 
HETATM 16 O O2' A3P . . . C 2 1.213 15.642 24.127 1 59.98 ? O2' A3P 2001 A 1 
HETATM 17 C C1' A3P . . . C 2 0.505 17.299 22.486 1 60.47 ? C1' A3P 2001 A 1 
HETATM 18 N N9 A3P . . . C 2 -0.973 17.356 22.637 1 60.83 ? N9 A3P 2001 A 1 
HETATM 19 C C8 A3P . . . C 2 -1.877 16.472 22.173 1 60.63 ? C8 A3P 2001 A 1 
HETATM 20 N N7 A3P . . . C 2 -3.14 16.846 22.505 1 59.13 ? N7 A3P 2001 A 1 
HETATM 21 C C5 A3P . . . C 2 -3.051 17.994 23.201 1 61.95 ? C5 A3P 2001 A 1 
HETATM 22 C C6 A3P . . . C 2 -3.994 18.934 23.853 1 62.58 ? C6 A3P 2001 A 1 
HETATM 23 N N6 A3P . . . C 2 -5.329 18.718 23.829 1 63.6 ? N6 A3P 2001 A 1 
HETATM 24 N N1 A3P . . . C 2 -3.477 20.019 24.473 1 63.82 ? N1 A3P 2001 A 1 
HETATM 25 C C2 A3P . . . C 2 -2.153 20.255 24.511 1 64.76 ? C2 A3P 2001 A 1 
HETATM 26 N N3 A3P . . . C 2 -1.245 19.445 23.941 1 64.96 ? N3 A3P 2001 A 1 
HETATM 27 C C4 A3P . . . C 2 -1.622 18.322 23.284 1 62.64 ? C4 A3P 2001 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           216 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#