data_8VZK
#
_model_server_result.job_id            r4lTP4hH7ach1SQPBxT9Kw 
_model_server_result.datetime_utc      '2024-11-18 07:36:59' 
_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          8vzk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    8VZK 
#
_exptl.entry_id    8VZK 
_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         120 
_cell.entry_id            8VZK 
_cell.length_a            111.327 
_cell.length_b            111.327 
_cell.length_c            193.164 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VZK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    'P 31 2"' 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -64.388 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D 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 OD1 ASP 446 A ASP 448 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc2 A OD1 ASN 473 A ASN 475 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc3 A O GLY 475 A GLY 477 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? 
metalc ? metalc4 C O2A TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc5 C O1B TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc6 C O2B TPP . A TPP 601 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc7 B OD1 ASP 446 B ASP 448 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc8 B OD1 ASN 473 B ASN 475 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc9 I O2A TPP . B TPP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
metalc ? metalc10 I O1B TPP . B TPP 601 1_555 K MG MG . B MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
#
_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                     8VZK 
_atom_sites.fract_transf_matrix[1][1]    0.008983 
_atom_sites.fract_transf_matrix[1][2]    0.005186 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010372 
_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]    0.005177 
_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
C 2 TPP A 1 601 601 TPP TPP . 
D 3 ADP A 1 602 602 ADP ADP . 
E 4 MG A 1 603 605 MG MG . 
F 5 EDO A 1 604 611 EDO EDO . 
G 5 EDO A 1 605 612 EDO EDO . 
H 6 PEG A 1 606 613 PEG PEG . 
I 2 TPP B 1 601 601 TPP TPP . 
J 3 ADP B 1 602 602 ADP ADP . 
K 4 MG B 1 603 605 MG MG . 
L 5 EDO B 1 604 611 EDO EDO . 
M 7 HOH A 1 701 4 HOH HOH . 
N 7 HOH B 1 701 3 HOH HOH . 
N 7 HOH B 2 702 2 HOH HOH . 
N 7 HOH B 3 703 1 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 . . . D 3 63.85 -23.221 -19.016 1 59.81 ? PB ADP 602 A 1 
HETATM 2 O O1B ADP . . . D 3 63.026 -24.339 -18.423 1 56 ? O1B ADP 602 A 1 
HETATM 3 O O2B ADP . . . D 3 63.383 -21.838 -18.632 1 64.43 ? O2B ADP 602 A 1 
HETATM 4 O O3B ADP . . . D 3 65.344 -23.416 -18.944 1 59.93 ? O3B ADP 602 A 1 
HETATM 5 P PA ADP . . . D 3 62.498 -22.355 -21.318 1 58.06 ? PA ADP 602 A 1 
HETATM 6 O O1A ADP . . . D 3 61.294 -22.175 -20.429 1 64.96 ? O1A ADP 602 A 1 
HETATM 7 O O2A ADP . . . D 3 63.221 -21.129 -21.822 1 62.65 ? O2A ADP 602 A 1 
HETATM 8 O O3A ADP . . . D 3 63.558 -23.321 -20.593 1 66.63 ? O3A ADP 602 A 1 
HETATM 9 O O5' ADP . . . D 3 62.04 -23.267 -22.559 1 60.14 ? O5' ADP 602 A 1 
HETATM 10 C C5' ADP . . . D 3 60.659 -23.366 -22.886 1 60.16 ? C5' ADP 602 A 1 
HETATM 11 C C4' ADP . . . D 3 60.51 -24.075 -24.223 1 58.46 ? C4' ADP 602 A 1 
HETATM 12 O O4' ADP . . . D 3 59.777 -25.294 -24.07 1 55.29 ? O4' ADP 602 A 1 
HETATM 13 C C3' ADP . . . D 3 59.745 -23.204 -25.206 1 61.53 ? C3' ADP 602 A 1 
HETATM 14 O O3' ADP . . . D 3 60.612 -22.747 -26.249 1 61.44 ? O3' ADP 602 A 1 
HETATM 15 C C2' ADP . . . D 3 58.664 -24.098 -25.778 1 58.12 ? C2' ADP 602 A 1 
HETATM 16 O O2' ADP . . . D 3 58.735 -24.106 -27.207 1 59.23 ? O2' ADP 602 A 1 
HETATM 17 C C1' ADP . . . D 3 58.936 -25.483 -25.208 1 54.25 ? C1' ADP 602 A 1 
HETATM 18 N N9 ADP . . . D 3 57.648 -26.129 -24.852 1 52.77 ? N9 ADP 602 A 1 
HETATM 19 C C8 ADP . . . D 3 56.692 -25.598 -24.068 1 58.21 ? C8 ADP 602 A 1 
HETATM 20 N N7 ADP . . . D 3 55.63 -26.436 -23.955 1 59.08 ? N7 ADP 602 A 1 
HETATM 21 C C5 ADP . . . D 3 55.9 -27.531 -24.689 1 54.32 ? C5 ADP 602 A 1 
HETATM 22 C C6 ADP . . . D 3 55.206 -28.802 -25.004 1 58.99 ? C6 ADP 602 A 1 
HETATM 23 N N6 ADP . . . D 3 53.978 -29.07 -24.498 1 60.14 ? N6 ADP 602 A 1 
HETATM 24 N N1 ADP . . . D 3 55.839 -29.68 -25.814 1 60.56 ? N1 ADP 602 A 1 
HETATM 25 C C2 ADP . . . D 3 57.058 -29.42 -26.323 1 57.45 ? C2 ADP 602 A 1 
HETATM 26 N N3 ADP . . . D 3 57.744 -28.289 -26.078 1 58.38 ? N3 ADP 602 A 1 
HETATM 27 C C4 ADP . . . D 3 57.229 -27.322 -25.281 1 56.37 ? C4 ADP 602 A 1 
#
_model_server_stats.io_time_ms              167 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           235 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#