data_1NY6
#
_model_server_result.job_id            HXspDkcbmdz2-D28rm5CvA 
_model_server_result.datetime_utc      '2024-11-07 21:59:51' 
_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":"Q","auth_seq_id":1}' 
#
_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 . . . Q 2 33.943 105.219 -3.236 1 70.04 ? PB ADP 1 C 1 
HETATM 2 O O1B ADP . . . Q 2 34.267 103.901 -3.839 1 64.38 ? O1B ADP 1 C 1 
HETATM 3 O O2B ADP . . . Q 2 32.959 105.036 -1.983 1 66.43 ? O2B ADP 1 C 1 
HETATM 4 O O3B ADP . . . Q 2 35.19 105.928 -2.824 1 54.99 ? O3B ADP 1 C 1 
HETATM 5 P PA ADP . . . Q 2 31.917 107.085 -4.15 1 71.82 ? PA ADP 1 C 1 
HETATM 6 O O1A ADP . . . Q 2 30.664 106.347 -3.95 1 62.4 ? O1A ADP 1 C 1 
HETATM 7 O O2A ADP . . . Q 2 32.117 108.041 -3.061 1 60.59 ? O2A ADP 1 C 1 
HETATM 8 O O3A ADP . . . Q 2 33.136 106.094 -4.26 1 72.3 ? O3A ADP 1 C 1 
HETATM 9 O O5' ADP . . . Q 2 31.856 107.91 -5.471 1 74.54 ? O5' ADP 1 C 1 
HETATM 10 C C5' ADP . . . Q 2 32.684 107.89 -6.634 1 71.94 ? C5' ADP 1 C 1 
HETATM 11 C C4' ADP . . . Q 2 32.017 108.968 -7.554 1 68.76 ? C4' ADP 1 C 1 
HETATM 12 O O4' ADP . . . Q 2 31.452 108.233 -8.632 1 67.3 ? O4' ADP 1 C 1 
HETATM 13 C C3' ADP . . . Q 2 30.834 109.71 -6.896 1 66.84 ? C3' ADP 1 C 1 
HETATM 14 O O3' ADP . . . Q 2 30.844 111.119 -7.162 1 66.18 ? O3' ADP 1 C 1 
HETATM 15 C C2' ADP . . . Q 2 29.564 109.02 -7.397 1 67.26 ? C2' ADP 1 C 1 
HETATM 16 O O2' ADP . . . Q 2 28.429 109.893 -7.46 1 73.52 ? O2' ADP 1 C 1 
HETATM 17 C C1' ADP . . . Q 2 30.017 108.395 -8.725 1 66.58 ? C1' ADP 1 C 1 
HETATM 18 N N9 ADP . . . Q 2 29.492 107.004 -8.968 1 70.28 ? N9 ADP 1 C 1 
HETATM 19 C C8 ADP . . . Q 2 30.026 105.886 -8.416 1 75.91 ? C8 ADP 1 C 1 
HETATM 20 N N7 ADP . . . Q 2 29.371 104.827 -8.814 1 77.8 ? N7 ADP 1 C 1 
HETATM 21 C C5 ADP . . . Q 2 28.42 105.2 -9.612 1 75.05 ? C5 ADP 1 C 1 
HETATM 22 C C6 ADP . . . Q 2 27.424 104.539 -10.333 1 76.88 ? C6 ADP 1 C 1 
HETATM 23 N N6 ADP . . . Q 2 27.326 103.212 -10.257 1 79.94 ? N6 ADP 1 C 1 
HETATM 24 N N1 ADP . . . Q 2 26.54 105.263 -11.121 1 77.83 ? N1 ADP 1 C 1 
HETATM 25 C C2 ADP . . . Q 2 26.611 106.623 -11.225 1 79.41 ? C2 ADP 1 C 1 
HETATM 26 N N3 ADP . . . Q 2 27.582 107.285 -10.523 1 77.75 ? N3 ADP 1 C 1 
HETATM 27 C C4 ADP . . . Q 2 28.49 106.623 -9.732 1 73.94 ? C4 ADP 1 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#