data_8E70
#
_model_server_result.job_id            oPt2aki_XeHwDQUSXFmKCQ 
_model_server_result.datetime_utc      '2024-11-14 19:44:24' 
_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          8e70 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"K","auth_seq_id":1000}' 
#
_entry.id    8E70 
#
_exptl.entry_id    8E70 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    heptameric 
_pdbx_struct_assembly.oligomeric_count      7 
_pdbx_struct_assembly.details               author_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,O,P,Q,R,S,T,U,V,W,X,Y 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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 H N N 
? 3 K N N 
? 3 N N N 
? 3 Q N N 
? 3 T N N 
? 3 W 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 B NZ LYS 184 e LYS 184 1_555 J BE BEF . e BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc2 H O2B ADP . e ADP 1000 1_555 I MG MG . e MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc3 H O1B ADP . e ADP 1000 1_555 J BE BEF . e BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? 
metalc ? metalc4 C NZ LYS 184 f LYS 184 1_555 M BE BEF . f BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc5 K O2B ADP . f ADP 1000 1_555 L MG MG . f MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc6 K O1B ADP . f ADP 1000 1_555 M BE BEF . f BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? 
metalc ? metalc7 D NZ LYS 184 c LYS 184 1_555 P BE BEF . c BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc8 N O3B ADP . c ADP 1000 1_555 O MG MG . c MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc9 N O2B ADP . c ADP 1000 1_555 P BE BEF . c BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.75 ? 
metalc ? metalc10 E NZ LYS 184 b LYS 184 1_555 S BE BEF . b BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc11 Q O1B ADP . b ADP 1000 1_555 R MG MG . b MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc12 Q O2B ADP . b ADP 1000 1_555 S BE BEF . b BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.753 ? 
metalc ? metalc13 F NZ LYS 184 a LYS 184 1_555 V BE BEF . a BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
metalc ? metalc14 T O1B ADP . a ADP 1000 1_555 U MG MG . a MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc15 T O2B ADP . a ADP 1000 1_555 V BE BEF . a BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? 
metalc ? metalc16 G NZ LYS 184 d LYS 184 1_555 Y BE BEF . d BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc17 W O3B ADP . d ADP 1000 1_555 X MG MG . d MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc18 W O2B ADP . d ADP 1000 1_555 Y BE BEF . d BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.754 ? 
#
_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                     8E70 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
H 3 ADP e 1 1000 1000 ADP ADP . 
I 4 MG e 1 1001 1001 MG MG . 
J 5 BEF e 1 1002 1002 BEF BEF . 
K 3 ADP f 1 1000 1000 ADP ADP . 
L 4 MG f 1 1001 1001 MG MG . 
M 5 BEF f 1 1002 1002 BEF BEF . 
N 3 ADP c 1 1000 1000 ADP ADP . 
O 4 MG c 1 1001 1001 MG MG . 
P 5 BEF c 1 1002 1002 BEF BEF . 
Q 3 ADP b 1 1000 1000 ADP ADP . 
R 4 MG b 1 1001 1001 MG MG . 
S 5 BEF b 1 1002 1002 BEF BEF . 
T 3 ADP a 1 1000 1000 ADP ADP . 
U 4 MG a 1 1001 1001 MG MG . 
V 5 BEF a 1 1002 1002 BEF BEF . 
W 3 ADP d 1 1000 1000 ADP ADP . 
X 4 MG d 1 1001 1001 MG MG . 
Y 5 BEF d 1 1002 1002 BEF BEF . 
#
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 . . . K 3 252.409 210.703 188.901 1 191.21 0 PB ADP 1000 f 1 
HETATM 2 O O1B ADP . . . K 3 252.538 209.428 188.093 1 168.31 0 O1B ADP 1000 f 1 
HETATM 3 O O2B ADP . . . K 3 253.676 211.518 188.969 1 188.54 0 O2B ADP 1000 f 1 
HETATM 4 O O3B ADP . . . K 3 251.712 210.557 190.231 1 178.66 0 O3B ADP 1000 f 1 
HETATM 5 P PA ADP . . . K 3 251.858 212.639 186.897 1 227.18 0 PA ADP 1000 f 1 
HETATM 6 O O1A ADP . . . K 3 252.787 211.885 185.972 1 210.73 0 O1A ADP 1000 f 1 
HETATM 7 O O2A ADP . . . K 3 252.258 213.942 187.563 1 197.86 0 O2A ADP 1000 f 1 
HETATM 8 O O3A ADP . . . K 3 251.386 211.618 188.055 1 230.81 0 O3A ADP 1000 f 1 
HETATM 9 O O5' ADP . . . K 3 250.492 212.871 186.077 1 205.27 0 O5' ADP 1000 f 1 
HETATM 10 C C5' ADP . . . K 3 250.13 211.948 185.054 1 163.81 0 C5' ADP 1000 f 1 
HETATM 11 C C4' ADP . . . K 3 249.132 212.615 184.125 1 172.89 0 C4' ADP 1000 f 1 
HETATM 12 O O4' ADP . . . K 3 248.129 213.304 184.871 1 195.6 0 O4' ADP 1000 f 1 
HETATM 13 C C3' ADP . . . K 3 249.813 213.68 183.291 1 175.82 0 C3' ADP 1000 f 1 
HETATM 14 O O3' ADP . . . K 3 250.273 213.115 182.061 1 174.08 0 O3' ADP 1000 f 1 
HETATM 15 C C2' ADP . . . K 3 248.742 214.727 183.074 1 187.58 0 C2' ADP 1000 f 1 
HETATM 16 O O2' ADP . . . K 3 248.084 214.514 181.824 1 206.19 0 O2' ADP 1000 f 1 
HETATM 17 C C1' ADP . . . K 3 247.761 214.523 184.213 1 181.57 0 C1' ADP 1000 f 1 
HETATM 18 N N9 ADP . . . K 3 247.94 215.667 185.135 1 157.02 0 N9 ADP 1000 f 1 
HETATM 19 C C8 ADP . . . K 3 248.617 215.648 186.297 1 157.02 0 C8 ADP 1000 f 1 
HETATM 20 N N7 ADP . . . K 3 248.599 216.869 186.882 1 163.92 0 N7 ADP 1000 f 1 
HETATM 21 C C5 ADP . . . K 3 247.898 217.7 186.082 1 162.64 0 C5 ADP 1000 f 1 
HETATM 22 C C6 ADP . . . K 3 247.492 219.126 186.098 1 162.32 0 C6 ADP 1000 f 1 
HETATM 23 N N6 ADP . . . K 3 247.831 219.954 187.113 1 157.02 0 N6 ADP 1000 f 1 
HETATM 24 N N1 ADP . . . K 3 246.76 219.578 185.054 1 174.51 0 N1 ADP 1000 f 1 
HETATM 25 C C2 ADP . . . K 3 246.406 218.78 184.028 1 170.22 0 C2 ADP 1000 f 1 
HETATM 26 N N3 ADP . . . K 3 246.741 217.482 183.949 1 157.31 0 N3 ADP 1000 f 1 
HETATM 27 C C4 ADP . . . K 3 247.469 216.896 184.928 1 157.02 0 C4 ADP 1000 f 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           220 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#