data_4IZ5
#
_model_server_result.job_id            YQEXmGe5jZ6065dzhwme5w 
_model_server_result.datetime_utc      '2024-12-22 03:05:25' 
_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          4iz5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":900}' 
#
_entry.id    4IZ5 
#
_exptl.entry_id    4IZ5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_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          90.41 
_cell.angle_gamma         90 
_cell.entry_id            4IZ5 
_cell.length_a            80.801 
_cell.length_b            149.129 
_cell.length_c            98.869 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4IZ5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,I,J,K,L,M 1 1 
B,H,N,O,P,Q,R 2 1 
C,F,S,T,U,V,W 3 1 
D,E,X,Y,Z,AA,BA 4 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
? 3 I N N 
? 3 N N N 
? 3 S N N 
? 3 X 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                     4IZ5 
_atom_sites.fract_transf_matrix[1][1]    0.012376 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000088 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006706 
_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]    0.010115 
_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
I 3 ADP A 1 900 900 ADP ADP . 
J 4 SO4 A 1 901 901 SO4 SO4 . 
K 4 SO4 A 1 902 902 SO4 SO4 . 
L 4 SO4 A 1 903 903 SO4 SO4 . 
M 4 SO4 A 1 904 904 SO4 SO4 . 
N 3 ADP B 1 900 900 ADP ADP . 
O 4 SO4 B 1 901 901 SO4 SO4 . 
P 4 SO4 B 1 902 902 SO4 SO4 . 
Q 4 SO4 B 1 903 903 SO4 SO4 . 
R 4 SO4 B 1 904 904 SO4 SO4 . 
S 3 ADP C 1 900 900 ADP ADP . 
T 4 SO4 C 1 901 901 SO4 SO4 . 
U 4 SO4 C 1 902 902 SO4 SO4 . 
V 4 SO4 C 1 903 903 SO4 SO4 . 
W 4 SO4 C 1 904 904 SO4 SO4 . 
X 3 ADP D 1 900 900 ADP ADP . 
Y 4 SO4 D 1 901 901 SO4 SO4 . 
Z 4 SO4 D 1 902 902 SO4 SO4 . 
AA 4 SO4 D 1 903 903 SO4 SO4 . 
BA 4 SO4 D 1 904 904 SO4 SO4 . 
#
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 . . . N 3 -10.949 16.181 -9.762 1 100.66 ? PB ADP 900 B 1 
HETATM 2 O O1B ADP . . . N 3 -10.257 15.267 -8.838 1 99.73 ? O1B ADP 900 B 1 
HETATM 3 O O2B ADP . . . N 3 -9.907 17.391 -10.184 1 101.29 ? O2B ADP 900 B 1 
HETATM 4 O O3B ADP . . . N 3 -12.236 16.868 -8.988 1 97.55 ? O3B ADP 900 B 1 
HETATM 5 P PA ADP . . . N 3 -12.718 14.386 -10.986 1 95.72 ? PA ADP 900 B 1 
HETATM 6 O O1A ADP . . . N 3 -13.491 14.642 -9.768 1 94.23 ? O1A ADP 900 B 1 
HETATM 7 O O2A ADP . . . N 3 -13.753 14.656 -12.247 1 93.93 ? O2A ADP 900 B 1 
HETATM 8 O O3A ADP . . . N 3 -11.406 15.392 -11.153 1 96.82 ? O3A ADP 900 B 1 
HETATM 9 O O5' ADP . . . N 3 -12.203 12.809 -11.013 1 95.81 ? O5' ADP 900 B 1 
HETATM 10 C C5' ADP . . . N 3 -11.248 12.599 -9.957 1 93.88 ? C5' ADP 900 B 1 
HETATM 11 C C4' ADP . . . N 3 -10.229 11.494 -10.28 1 90.94 ? C4' ADP 900 B 1 
HETATM 12 O O4' ADP . . . N 3 -10.752 10.619 -11.288 1 91.01 ? O4' ADP 900 B 1 
HETATM 13 C C3' ADP . . . N 3 -8.911 12.072 -10.815 1 89.68 ? C3' ADP 900 B 1 
HETATM 14 O O3' ADP . . . N 3 -7.798 11.319 -10.324 1 88.36 ? O3' ADP 900 B 1 
HETATM 15 C C2' ADP . . . N 3 -9.043 11.924 -12.33 1 89.72 ? C2' ADP 900 B 1 
HETATM 16 O O2' ADP . . . N 3 -7.775 11.727 -12.964 1 92.33 ? O2' ADP 900 B 1 
HETATM 17 C C1' ADP . . . N 3 -9.9 10.663 -12.441 1 89.27 ? C1' ADP 900 B 1 
HETATM 18 N N9 ADP . . . N 3 -10.702 10.671 -13.66 1 84.65 ? N9 ADP 900 B 1 
HETATM 19 C C8 ADP . . . N 3 -11.705 11.515 -13.979 1 81.01 ? C8 ADP 900 B 1 
HETATM 20 N N7 ADP . . . N 3 -12.186 11.182 -15.192 1 80.43 ? N7 ADP 900 B 1 
HETATM 21 C C5 ADP . . . N 3 -11.49 10.119 -15.65 1 83.13 ? C5 ADP 900 B 1 
HETATM 22 C C6 ADP . . . N 3 -11.54 9.349 -16.817 1 84.04 ? C6 ADP 900 B 1 
HETATM 23 N N6 ADP . . . N 3 -12.426 9.615 -17.789 1 83.48 ? N6 ADP 900 B 1 
HETATM 24 N N1 ADP . . . N 3 -10.67 8.321 -16.955 1 85.37 ? N1 ADP 900 B 1 
HETATM 25 C C2 ADP . . . N 3 -9.767 8.03 -15.993 1 85.17 ? C2 ADP 900 B 1 
HETATM 26 N N3 ADP . . . N 3 -9.699 8.756 -14.861 1 84.01 ? N3 ADP 900 B 1 
HETATM 27 C C4 ADP . . . N 3 -10.546 9.793 -14.67 1 84.15 ? C4 ADP 900 B 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    48 
_model_server_stats.query_time_ms           222 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#