data_4Z8X
#
_model_server_result.job_id            wUvuWLAuxKkNUOW4XglPkQ 
_model_server_result.datetime_utc      '2025-04-17 01:35:45' 
_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          4z8x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":702}' 
#
_entry.id    4Z8X 
#
_exptl.entry_id    4Z8X 
_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    2 
_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            4Z8X 
_cell.length_a            127.86 
_cell.length_b            188.48 
_cell.length_c            206.22 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Z8X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 J 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
metalc ? metalc1 A NE2 HIS 281 A HIS 418 1_555 D ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc2 A NE2 HIS 285 A HIS 422 1_555 D ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc3 A OD2 ASP 359 A ASP 496 1_555 D ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc4 D ZN ZN . A ZN 701 1_555 L O HOH . A HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
metalc ? metalc5 B NE2 HIS 281 B HIS 418 1_555 G ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc6 B NE2 HIS 285 B HIS 422 1_555 G ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.108 ? 
metalc ? metalc7 B OD2 ASP 359 B ASP 496 1_555 G ZN ZN . B ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc8 G ZN ZN . B ZN 701 1_555 M O HOH . B HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
metalc ? metalc9 C NE2 HIS 281 C HIS 418 1_555 I ZN ZN . C ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? 
metalc ? metalc10 C NE2 HIS 285 C HIS 422 1_555 I ZN ZN . C ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc11 C OD2 ASP 359 C ASP 496 1_555 I ZN ZN . C ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc12 I ZN ZN . C ZN 701 1_555 N O HOH . C HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
#
_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                     4Z8X 
_atom_sites.fract_transf_matrix[1][1]    0.007821 
_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]    0.005306 
_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]    0.004849 
_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
D 2 ZN A 1 701 900 ZN ZN . 
E 3 ADP A 1 702 999 ADP ADP . 
F 4 SO4 A 1 703 1 SO4 SO4 . 
G 2 ZN B 1 701 900 ZN ZN . 
H 4 SO4 B 1 702 3 SO4 SO4 . 
I 2 ZN C 1 701 900 ZN ZN . 
J 3 ADP C 1 702 999 ADP ADP . 
K 4 SO4 C 1 703 2 SO4 SO4 . 
L 5 HOH A 1 901 901 HOH HOH . 
M 5 HOH B 1 901 901 HOH HOH . 
N 5 HOH C 1 901 901 HOH HOH . 
#
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 . . . J 3 -39.956 -4.069 -84.978 1 300 ? PB ADP 702 C 1 
HETATM 2 O O1B ADP . . . J 3 -39.982 -3.154 -86.19 1 300 ? O1B ADP 702 C 1 
HETATM 3 O O2B ADP . . . J 3 -38.826 -5.089 -85.164 1 300 ? O2B ADP 702 C 1 
HETATM 4 O O3B ADP . . . J 3 -39.835 -3.308 -83.696 1 300 ? O3B ADP 702 C 1 
HETATM 5 P PA ADP . . . J 3 -42.402 -5.154 -86.164 1 300 ? PA ADP 702 C 1 
HETATM 6 O O1A ADP . . . J 3 -41.65 -5.51 -87.456 1 299.96 ? O1A ADP 702 C 1 
HETATM 7 O O2A ADP . . . J 3 -43.215 -3.932 -86.371 1 299.81 ? O2A ADP 702 C 1 
HETATM 8 O O3A ADP . . . J 3 -41.318 -4.897 -85.022 1 300 ? O3A ADP 702 C 1 
HETATM 9 O O5' ADP . . . J 3 -43.299 -6.415 -85.716 1 300 ? O5' ADP 702 C 1 
HETATM 10 C C5' ADP . . . J 3 -43.695 -7.519 -86.56 1 300 ? C5' ADP 702 C 1 
HETATM 11 C C4' ADP . . . J 3 -45.193 -7.704 -86.493 1 300 ? C4' ADP 702 C 1 
HETATM 12 O O4' ADP . . . J 3 -45.679 -7.399 -85.168 1 300 ? O4' ADP 702 C 1 
HETATM 13 C C3' ADP . . . J 3 -46.022 -6.885 -87.483 1 299.77 ? C3' ADP 702 C 1 
HETATM 14 O O3' ADP . . . J 3 -46.921 -7.702 -88.224 1 299.67 ? O3' ADP 702 C 1 
HETATM 15 C C2' ADP . . . J 3 -46.721 -5.84 -86.604 1 299.68 ? C2' ADP 702 C 1 
HETATM 16 O O2' ADP . . . J 3 -48.041 -5.568 -87.059 1 299.42 ? O2' ADP 702 C 1 
HETATM 17 C C1' ADP . . . J 3 -46.789 -6.528 -85.24 1 299.99 ? C1' ADP 702 C 1 
HETATM 18 N N9 ADP . . . J 3 -46.729 -5.596 -84.114 1 300 ? N9 ADP 702 C 1 
HETATM 19 C C8 ADP . . . J 3 -45.613 -5.215 -83.415 1 300 ? C8 ADP 702 C 1 
HETATM 20 N N7 ADP . . . J 3 -45.837 -4.296 -82.507 1 299.97 ? N7 ADP 702 C 1 
HETATM 21 C C5 ADP . . . J 3 -47.199 -4.056 -82.611 1 299.81 ? C5 ADP 702 C 1 
HETATM 22 C C6 ADP . . . J 3 -48.06 -3.158 -81.946 1 299.46 ? C6 ADP 702 C 1 
HETATM 23 N N6 ADP . . . J 3 -47.662 -2.322 -80.984 1 299.08 ? N6 ADP 702 C 1 
HETATM 24 N N1 ADP . . . J 3 -49.365 -3.15 -82.309 1 299.73 ? N1 ADP 702 C 1 
HETATM 25 C C2 ADP . . . J 3 -49.773 -3.996 -83.262 1 300 ? C2 ADP 702 C 1 
HETATM 26 N N3 ADP . . . J 3 -49.056 -4.885 -83.957 1 300 ? N3 ADP 702 C 1 
HETATM 27 C C4 ADP . . . J 3 -47.765 -4.86 -83.589 1 300 ? C4 ADP 702 C 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           311 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#