data_1NY6
#
_model_server_result.job_id            Z-4APi04cbjezkrCjN-7AA 
_model_server_result.datetime_utc      '2024-11-07 21:47:57' 
_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          1ny6 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"AA","auth_seq_id":12}' 
#
_entry.id    1NY6 
#
_exptl.entry_id    1NY6 
_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-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    14 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         70.25 
_cell.angle_beta          85.9 
_cell.angle_gamma         73.27 
_cell.entry_id            1NY6 
_cell.length_a            106.788 
_cell.length_b            108.265 
_cell.length_c            110.02 
_cell.Z_PDB               14 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1NY6 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 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
? heptameric 7 author_defined_assembly 1 
? heptameric 7 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,O,P,Q,R,S,T,U 1 1 
H,I,J,K,L,M,N,V,W,X,Y,Z,AA,BA 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 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X N N 
? 2 Y N N 
? 2 Z N N 
? 2 AA N N 
? 2 BA 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                     1NY6 
_atom_sites.fract_transf_matrix[1][1]    0.009364 
_atom_sites.fract_transf_matrix[1][2]    -0.002814 
_atom_sites.fract_transf_matrix[1][3]    0.00028 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009645 
_atom_sites.fract_transf_matrix[2][3]    -0.003396 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.009661 
_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
O 2 ADP A 1 6 6 ADP ADP . 
P 2 ADP B 1 7 7 ADP ADP . 
Q 2 ADP C 1 1 1 ADP ADP . 
R 2 ADP D 1 2 2 ADP ADP . 
S 2 ADP E 1 3 3 ADP ADP . 
T 2 ADP F 1 4 4 ADP ADP . 
U 2 ADP G 1 5 5 ADP ADP . 
V 2 ADP H 1 14 14 ADP ADP . 
W 2 ADP I 1 8 8 ADP ADP . 
X 2 ADP J 1 9 9 ADP ADP . 
Y 2 ADP K 1 10 10 ADP ADP . 
Z 2 ADP L 1 11 11 ADP ADP . 
AA 2 ADP M 1 12 12 ADP ADP . 
BA 2 ADP N 1 13 13 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 . . . AA 2 122.91 142.166 35.937 1 83.52 ? PB ADP 12 M 1 
HETATM 2 O O1B ADP . . . AA 2 123.032 143.387 36.769 1 75.81 ? O1B ADP 12 M 1 
HETATM 3 O O2B ADP . . . AA 2 123.68 140.946 36.626 1 86.8 ? O2B ADP 12 M 1 
HETATM 4 O O3B ADP . . . AA 2 121.485 141.809 35.695 1 75.39 ? O3B ADP 12 M 1 
HETATM 5 P PA ADP . . . AA 2 125.15 142.078 34.23 1 86.86 ? PA ADP 12 M 1 
HETATM 6 O O1A ADP . . . AA 2 125.994 142.417 35.363 1 75.51 ? O1A ADP 12 M 1 
HETATM 7 O O2A ADP . . . AA 2 125.322 140.675 33.879 1 87.52 ? O2A ADP 12 M 1 
HETATM 8 O O3A ADP . . . AA 2 123.661 142.358 34.591 1 83.38 ? O3A ADP 12 M 1 
HETATM 9 O O5' ADP . . . AA 2 125.536 142.924 32.968 1 83.09 ? O5' ADP 12 M 1 
HETATM 10 C C5' ADP . . . AA 2 124.697 143.794 32.237 1 78.07 ? C5' ADP 12 M 1 
HETATM 11 C C4' ADP . . . AA 2 125.566 144.4 31.095 1 73.58 ? C4' ADP 12 M 1 
HETATM 12 O O4' ADP . . . AA 2 126.045 145.648 31.563 1 66.18 ? O4' ADP 12 M 1 
HETATM 13 C C3' ADP . . . AA 2 126.834 143.609 30.633 1 71.96 ? C3' ADP 12 M 1 
HETATM 14 O O3' ADP . . . AA 2 126.847 143.389 29.211 1 73.77 ? O3' ADP 12 M 1 
HETATM 15 C C2' ADP . . . AA 2 128.052 144.416 31.11 1 67.24 ? C2' ADP 12 M 1 
HETATM 16 O O2' ADP . . . AA 2 129.163 144.436 30.185 1 67.85 ? O2' ADP 12 M 1 
HETATM 17 C C1' ADP . . . AA 2 127.462 145.767 31.39 1 62.34 ? C1' ADP 12 M 1 
HETATM 18 N N9 ADP . . . AA 2 128.035 146.453 32.581 1 57.55 ? N9 ADP 12 M 1 
HETATM 19 C C8 ADP . . . AA 2 127.401 146.694 33.751 1 62.72 ? C8 ADP 12 M 1 
HETATM 20 N N7 ADP . . . AA 2 128.213 147.342 34.559 1 60.95 ? N7 ADP 12 M 1 
HETATM 21 C C5 ADP . . . AA 2 129.334 147.549 33.939 1 52.08 ? C5 ADP 12 M 1 
HETATM 22 C C6 ADP . . . AA 2 130.546 148.147 34.254 1 53.09 ? C6 ADP 12 M 1 
HETATM 23 N N6 ADP . . . AA 2 130.712 148.722 35.43 1 58.13 ? N6 ADP 12 M 1 
HETATM 24 N N1 ADP . . . AA 2 131.565 148.172 33.313 1 55.04 ? N1 ADP 12 M 1 
HETATM 25 C C2 ADP . . . AA 2 131.434 147.605 32.085 1 60.46 ? C2 ADP 12 M 1 
HETATM 26 N N3 ADP . . . AA 2 130.255 147.004 31.774 1 51.91 ? N3 ADP 12 M 1 
HETATM 27 C C4 ADP . . . AA 2 129.22 146.966 32.652 1 52.22 ? C4 ADP 12 M 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#