data_3AP3
#
_model_server_result.job_id            LJv2e5cB9trLX3zIfRpyxQ 
_model_server_result.datetime_utc      '2024-11-12 19:32:40' 
_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          3ap3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1}' 
#
_entry.id    3AP3 
#
_exptl.entry_id    3AP3 
_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    4 
_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            3AP3 
_cell.length_a            71.432 
_cell.length_b            81.326 
_cell.length_c            226.659 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3AP3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 2 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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 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,B,E,F 1 1 
C,D,G,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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H 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
disulf ? disulf1 A SG CYS 74 A CYS 96 1_555 A SG CYS 134 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf2 A SG CYS 203 A CYS 225 1_555 A SG CYS 211 A CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf3 B SG CYS 74 B CYS 96 1_555 B SG CYS 134 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
disulf ? disulf4 B SG CYS 203 B CYS 225 1_555 B SG CYS 211 B CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf5 C SG CYS 74 C CYS 96 1_555 C SG CYS 134 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf6 C SG CYS 203 C CYS 225 1_555 C SG CYS 211 C CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf7 D SG CYS 74 D CYS 96 1_555 D SG CYS 134 D CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf8 D SG CYS 203 D CYS 225 1_555 D SG CYS 211 D CYS 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
#
_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 1 n n 
P1 O2P A3P sing 2 n n 
P1 O3P A3P sing 3 n n 
P1 O3' A3P sing 4 n n 
O2P HOP2 A3P sing 5 n n 
O3P HOP3 A3P sing 6 n n 
P2 O4P A3P doub 7 n n 
P2 O5P A3P sing 8 n n 
P2 O6P A3P sing 9 n n 
P2 O5' A3P sing 10 n n 
O5P HOP5 A3P sing 11 n n 
O6P HOP6 A3P sing 12 n n 
O5' C5' A3P sing 13 n n 
C5' C4' A3P sing 14 n n 
C5' "H5'1" A3P sing 15 n n 
C5' "H5'2" A3P sing 16 n n 
C4' O4' A3P sing 17 n n 
C4' C3' A3P sing 18 n n 
C4' H4' A3P sing 19 n n 
O4' C1' A3P sing 20 n n 
C3' O3' A3P sing 21 n n 
C3' C2' A3P sing 22 n n 
C3' H3' A3P sing 23 n n 
C2' O2' A3P sing 24 n n 
C2' C1' A3P sing 25 n n 
C2' H2' A3P sing 26 n n 
O2' HO2' A3P sing 27 n n 
C1' N9 A3P sing 28 n n 
C1' H1' A3P sing 29 n n 
N9 C8 A3P sing 30 n y 
N9 C4 A3P sing 31 n y 
C8 N7 A3P doub 32 n y 
C8 H8 A3P sing 33 n n 
N7 C5 A3P sing 34 n y 
C5 C6 A3P sing 35 n y 
C5 C4 A3P doub 36 n y 
C6 N6 A3P sing 37 n n 
C6 N1 A3P doub 38 n y 
N6 HN61 A3P sing 39 n n 
N6 HN62 A3P sing 40 n n 
N1 C2 A3P sing 41 n y 
C2 N3 A3P doub 42 n y 
C2 H2 A3P sing 43 n n 
N3 C4 A3P sing 44 n y 
#
_atom_sites.entry_id                     3AP3 
_atom_sites.fract_transf_matrix[1][1]    0.013999 
_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]    0.012296 
_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]    0.004412 
_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
E 2 A3P A 1 1 1 A3P A3P . 
F 2 A3P B 1 1 1 A3P A3P . 
G 2 A3P C 1 1 1 A3P A3P . 
H 2 A3P D 1 1 1 A3P A3P . 
#
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 . . . F 2 -11.694 -25.416 -45.426 1 119.03 ? P1 A3P 1 B 1 
HETATM 2 O O1P A3P . . . F 2 -12.673 -25.277 -44.263 1 116.41 ? O1P A3P 1 B 1 
HETATM 3 O O2P A3P . . . F 2 -11.809 -26.739 -46.163 1 117.67 ? O2P A3P 1 B 1 
HETATM 4 O O3P A3P . . . F 2 -11.707 -24.239 -46.418 1 116.26 ? O3P A3P 1 B 1 
HETATM 5 P P2 A3P . . . F 2 -7.44 -25.541 -39.371 1 118.7 ? P2 A3P 1 B 1 
HETATM 6 O O4P A3P . . . F 2 -8.823 -25.06 -38.936 1 117.45 ? O4P A3P 1 B 1 
HETATM 7 O O5P A3P . . . F 2 -6.378 -24.459 -39.55 1 117.59 ? O5P A3P 1 B 1 
HETATM 8 O O6P A3P . . . F 2 -6.974 -26.753 -38.589 1 118.12 ? O6P A3P 1 B 1 
HETATM 9 O O5' A3P . . . F 2 -7.603 -26.155 -40.85 1 115.86 ? O5' A3P 1 B 1 
HETATM 10 C C5' A3P . . . F 2 -8.881 -26.273 -41.458 1 116.41 ? C5' A3P 1 B 1 
HETATM 11 C C4' A3P . . . F 2 -8.567 -26.254 -42.941 1 117.96 ? C4' A3P 1 B 1 
HETATM 12 O O4' A3P . . . F 2 -7.499 -27.215 -43.13 1 118.97 ? O4' A3P 1 B 1 
HETATM 13 C C3' A3P . . . F 2 -9.764 -26.612 -43.848 1 117.98 ? C3' A3P 1 B 1 
HETATM 14 O O3' A3P . . . F 2 -10.218 -25.508 -44.687 1 117.72 ? O3' A3P 1 B 1 
HETATM 15 C C2' A3P . . . F 2 -9.249 -27.819 -44.638 1 118.24 ? C2' A3P 1 B 1 
HETATM 16 O O2' A3P . . . F 2 -9.54 -27.758 -46.044 1 114.85 ? O2' A3P 1 B 1 
HETATM 17 C C1' A3P . . . F 2 -7.726 -27.885 -44.389 1 120.12 ? C1' A3P 1 B 1 
HETATM 18 N N9 A3P . . . F 2 -7.22 -29.307 -44.538 1 120.51 ? N9 A3P 1 B 1 
HETATM 19 C C8 A3P . . . F 2 -7.298 -30.319 -43.625 1 119.74 ? C8 A3P 1 B 1 
HETATM 20 N N7 A3P . . . F 2 -6.769 -31.476 -44.124 1 119.02 ? N7 A3P 1 B 1 
HETATM 21 C C5 A3P . . . F 2 -6.34 -31.228 -45.391 1 119.4 ? C5 A3P 1 B 1 
HETATM 22 C C6 A3P . . . F 2 -5.685 -31.999 -46.496 1 118.66 ? C6 A3P 1 B 1 
HETATM 23 N N6 A3P . . . F 2 -5.375 -33.307 -46.319 1 118.2 ? N6 A3P 1 B 1 
HETATM 24 N N1 A3P . . . F 2 -5.409 -31.36 -47.672 1 117.21 ? N1 A3P 1 B 1 
HETATM 25 C C2 A3P . . . F 2 -5.713 -30.058 -47.859 1 117.23 ? C2 A3P 1 B 1 
HETATM 26 N N3 A3P . . . F 2 -6.308 -29.293 -46.916 1 118.23 ? N3 A3P 1 B 1 
HETATM 27 C C4 A3P . . . F 2 -6.643 -29.8 -45.675 1 119.88 ? C4 A3P 1 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           280 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#