data_3A5C
#
_model_server_result.job_id            fk3d_LTsHsv-jTqxmnf41Q 
_model_server_result.datetime_utc      '2025-04-25 16:20:02' 
_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          3a5c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"T","auth_seq_id":600}' 
#
_entry.id    3A5C 
#
_exptl.entry_id    3A5C 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-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         120 
_cell.entry_id            3A5C 
_cell.length_a            381.578 
_cell.length_b            381.578 
_cell.length_c            147.672 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3A5C 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? octameric 8 author_defined_assembly 1 
? octameric 8 author_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,C,D,E,F,G,H,Q,R 1 1 
I,J,K,L,M,N,O,P,S,T 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
? 5 Q N N 
? 5 R N N 
? 5 S N N 
? 5 T N N 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                ADP 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-5'-DIPHOSPHATE" 
_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
PB O1B ADP doub 1 n n 
PB O2B ADP sing 2 n n 
PB O3B ADP sing 3 n n 
PB O3A ADP sing 4 n n 
O2B HOB2 ADP sing 5 n n 
O3B HOB3 ADP sing 6 n n 
PA O1A ADP doub 7 n n 
PA O2A ADP sing 8 n n 
PA O3A ADP sing 9 n n 
PA O5' ADP sing 10 n n 
O2A HOA2 ADP sing 11 n n 
O5' C5' ADP sing 12 n n 
C5' C4' ADP sing 13 n n 
C5' "H5'1" ADP sing 14 n n 
C5' "H5'2" ADP sing 15 n n 
C4' O4' ADP sing 16 n n 
C4' C3' ADP sing 17 n n 
C4' H4' ADP sing 18 n n 
O4' C1' ADP sing 19 n n 
C3' O3' ADP sing 20 n n 
C3' C2' ADP sing 21 n n 
C3' H3' ADP sing 22 n n 
O3' HO3' ADP sing 23 n n 
C2' O2' ADP sing 24 n n 
C2' C1' ADP sing 25 n n 
C2' H2' ADP sing 26 n n 
O2' HO2' ADP sing 27 n n 
C1' N9 ADP sing 28 n n 
C1' H1' ADP sing 29 n n 
N9 C8 ADP sing 30 n y 
N9 C4 ADP sing 31 n y 
C8 N7 ADP doub 32 n y 
C8 H8 ADP sing 33 n n 
N7 C5 ADP sing 34 n y 
C5 C6 ADP sing 35 n y 
C5 C4 ADP doub 36 n y 
C6 N6 ADP sing 37 n n 
C6 N1 ADP doub 38 n y 
N6 HN61 ADP sing 39 n n 
N6 HN62 ADP sing 40 n n 
N1 C2 ADP sing 41 n y 
C2 N3 ADP doub 42 n y 
C2 H2 ADP sing 43 n n 
N3 C4 ADP sing 44 n y 
#
_atom_sites.entry_id                     3A5C 
_atom_sites.fract_transf_matrix[1][1]    0.002621 
_atom_sites.fract_transf_matrix[1][2]    0.001513 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.003026 
_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]    0.006772 
_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
Q 5 ADP A 1 600 600 ADP ADP . 
R 5 ADP C 1 600 600 ADP ADP . 
S 5 ADP I 1 600 600 ADP ADP . 
T 5 ADP K 1 600 600 ADP ADP . 
#
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 PB ADP . . . T 5 168.391 53.466 -14.215 1 112.18 ? PB ADP 600 K 1 
HETATM 2 O O1B ADP . . . T 5 167.447 53.697 -15.377 1 112.18 ? O1B ADP 600 K 1 
HETATM 3 O O2B ADP . . . T 5 167.743 53.729 -12.945 1 112.18 ? O2B ADP 600 K 1 
HETATM 4 O O3B ADP . . . T 5 169.05 52.145 -14.367 1 112.18 ? O3B ADP 600 K 1 
HETATM 5 P PA ADP . . . T 5 169.871 55.863 -13.603 1 112.18 ? PA ADP 600 K 1 
HETATM 6 O O1A ADP . . . T 5 168.657 56.58 -13.417 1 112.18 ? O1A ADP 600 K 1 
HETATM 7 O O2A ADP . . . T 5 170.542 55.617 -12.246 1 112.18 ? O2A ADP 600 K 1 
HETATM 8 O O3A ADP . . . T 5 169.653 54.446 -14.336 1 112.18 ? O3A ADP 600 K 1 
HETATM 9 O O5' ADP . . . T 5 170.982 56.541 -14.523 1 112.18 ? O5' ADP 600 K 1 
HETATM 10 C C5' ADP . . . T 5 172.287 55.941 -14.821 1 112.18 ? C5' ADP 600 K 1 
HETATM 11 C C4' ADP . . . T 5 173.239 57.041 -15.304 1 112.18 ? C4' ADP 600 K 1 
HETATM 12 O O4' ADP . . . T 5 172.678 57.656 -16.506 1 112.18 ? O4' ADP 600 K 1 
HETATM 13 C C3' ADP . . . T 5 173.343 58.256 -14.372 1 112.18 ? C3' ADP 600 K 1 
HETATM 14 O O3' ADP . . . T 5 174.244 57.995 -13.312 1 112.18 ? O3' ADP 600 K 1 
HETATM 15 C C2' ADP . . . T 5 173.894 59.309 -15.345 1 112.18 ? C2' ADP 600 K 1 
HETATM 16 O O2' ADP . . . T 5 175.281 59.173 -15.592 1 112.18 ? O2' ADP 600 K 1 
HETATM 17 C C1' ADP . . . T 5 173.024 59.033 -16.586 1 112.18 ? C1' ADP 600 K 1 
HETATM 18 N N9 ADP . . . T 5 171.756 59.791 -16.484 1 112.18 ? N9 ADP 600 K 1 
HETATM 19 C C8 ADP . . . T 5 170.523 59.346 -16.16 1 112.18 ? C8 ADP 600 K 1 
HETATM 20 N N7 ADP . . . T 5 169.626 60.313 -16.061 1 112.18 ? N7 ADP 600 K 1 
HETATM 21 C C5 ADP . . . T 5 170.332 61.462 -16.354 1 112.18 ? C5 ADP 600 K 1 
HETATM 22 C C6 ADP . . . T 5 169.945 62.812 -16.476 1 112.18 ? C6 ADP 600 K 1 
HETATM 23 N N6 ADP . . . T 5 168.696 63.255 -16.268 1 112.18 ? N6 ADP 600 K 1 
HETATM 24 N N1 ADP . . . T 5 170.903 63.692 -16.799 1 112.18 ? N1 ADP 600 K 1 
HETATM 25 C C2 ADP . . . T 5 172.174 63.248 -17.037 1 112.18 ? C2 ADP 600 K 1 
HETATM 26 N N3 ADP . . . T 5 172.637 62.024 -16.952 1 112.18 ? N3 ADP 600 K 1 
HETATM 27 C C4 ADP . . . T 5 171.653 61.16 -16.605 1 112.18 ? C4 ADP 600 K 1 
#
_model_server_stats.io_time_ms              109 
_model_server_stats.parse_time_ms           37 
_model_server_stats.create_model_time_ms    77 
_model_server_stats.query_time_ms           674 
_model_server_stats.encode_time_ms          28 
_model_server_stats.element_count           27 
#