data_8E5P
#
_model_server_result.job_id            SCx52QLQbaL7AULK8LGxvA 
_model_server_result.datetime_utc      '2024-10-20 03:47:13' 
_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          8e5p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"T","auth_seq_id":1000}' 
#
_entry.id    8E5P 
#
_exptl.entry_id    8E5P 
_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 O1B ADP . e ADP 1000 1_555 I MG MG . e MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc3 H O2B 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc5 K O1B ADP . f ADP 1000 1_555 L MG MG . f MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc6 K O2B 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 O2B ADP . c ADP 1000 1_555 O MG MG . c MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc9 N O1B ADP . c ADP 1000 1_555 P BE BEF . c BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? 
metalc ? metalc10 E NZ LYS 184 b LYS 184 1_555 S BE BEF . b BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc11 Q O3B ADP . b ADP 1000 1_555 R MG MG . b MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc12 Q O2B ADP . b ADP 1000 1_555 S BE BEF . b BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.752 ? 
metalc ? metalc13 F NZ LYS 184 a LYS 184 1_555 V BE BEF . a BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
metalc ? metalc14 T O3B ADP . a ADP 1000 1_555 U MG MG . a MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc15 T O2B ADP . a ADP 1000 1_555 V BE BEF . a BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? 
metalc ? metalc16 G NZ LYS 184 d LYS 184 1_555 Y BE BEF . d BEF 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc17 W O2B ADP . d ADP 1000 1_555 X MG MG . d MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc18 W O1B 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 40 n n 
PB O2B ADP sing 41 n n 
PB O3B ADP sing 42 n n 
PB O3A ADP sing 43 n n 
O2B HOB2 ADP sing 44 n n 
O3B HOB3 ADP sing 45 n n 
PA O1A ADP doub 46 n n 
PA O2A ADP sing 47 n n 
PA O3A ADP sing 48 n n 
PA O5' ADP sing 49 n n 
O2A HOA2 ADP sing 50 n n 
O5' C5' ADP sing 51 n n 
C5' C4' ADP sing 52 n n 
C5' "H5'1" ADP sing 53 n n 
C5' "H5'2" ADP sing 54 n n 
C4' O4' ADP sing 55 n n 
C4' C3' ADP sing 56 n n 
C4' H4' ADP sing 57 n n 
O4' C1' ADP sing 58 n n 
C3' O3' ADP sing 59 n n 
C3' C2' ADP sing 60 n n 
C3' H3' ADP sing 61 n n 
O3' HO3' ADP sing 62 n n 
C2' O2' ADP sing 63 n n 
C2' C1' ADP sing 64 n n 
C2' H2' ADP sing 65 n n 
O2' HO2' ADP sing 66 n n 
C1' N9 ADP sing 67 n n 
C1' H1' ADP sing 68 n n 
N9 C8 ADP sing 69 n y 
N9 C4 ADP sing 70 n y 
C8 N7 ADP doub 71 n y 
C8 H8 ADP sing 72 n n 
N7 C5 ADP sing 73 n y 
C5 C6 ADP sing 74 n y 
C5 C4 ADP doub 75 n y 
C6 N6 ADP sing 76 n n 
C6 N1 ADP doub 77 n y 
N6 HN61 ADP sing 78 n n 
N6 HN62 ADP sing 79 n n 
N1 C2 ADP sing 80 n y 
C2 N3 ADP doub 81 n y 
C2 H2 ADP sing 82 n n 
N3 C4 ADP sing 83 n y 
#
_atom_sites.entry_id                     8E5P 
_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 . . . T 3 172.349 185.808 223.969 1 191.21 0 PB ADP 1000 a 1 
HETATM 2 O O1B ADP . . . T 3 173.238 185.972 222.762 1 178.66 0 O1B ADP 1000 a 1 
HETATM 3 O O2B ADP . . . T 3 172.97 185.067 225.137 1 168.31 0 O2B ADP 1000 a 1 
HETATM 4 O O3B ADP . . . T 3 170.949 185.359 223.634 1 188.54 0 O3B ADP 1000 a 1 
HETATM 5 P PA ADP . . . T 3 170.854 187.845 225.27 1 227.18 0 PA ADP 1000 a 1 
HETATM 6 O O1A ADP . . . T 3 169.826 188.232 224.224 1 197.86 0 O1A ADP 1000 a 1 
HETATM 7 O O2A ADP . . . T 3 170.548 186.86 226.374 1 210.73 0 O2A ADP 1000 a 1 
HETATM 8 O O3A ADP . . . T 3 172.172 187.322 224.495 1 230.81 0 O3A ADP 1000 a 1 
HETATM 9 O O5' ADP . . . T 3 171.398 189.178 225.988 1 205.27 0 O5' ADP 1000 a 1 
HETATM 10 C C5' ADP . . . T 3 172.043 189.074 227.255 1 163.81 0 C5' ADP 1000 a 1 
HETATM 11 C C4' ADP . . . T 3 172.006 190.428 227.936 1 172.89 0 C4' ADP 1000 a 1 
HETATM 12 O O4' ADP . . . T 3 172.361 191.466 227.023 1 195.6 0 O4' ADP 1000 a 1 
HETATM 13 C C3' ADP . . . T 3 170.595 190.757 228.386 1 175.82 0 C3' ADP 1000 a 1 
HETATM 14 O O3' ADP . . . T 3 170.393 190.304 229.726 1 174.08 0 O3' ADP 1000 a 1 
HETATM 15 C C2' ADP . . . T 3 170.508 192.263 228.272 1 187.58 0 C2' ADP 1000 a 1 
HETATM 16 O O2' ADP . . . T 3 170.794 192.873 229.536 1 206.19 0 O2' ADP 1000 a 1 
HETATM 17 C C1' ADP . . . T 3 171.581 192.642 227.266 1 181.57 0 C1' ADP 1000 a 1 
HETATM 18 N N9 ADP . . . T 3 170.876 193.045 226.03 1 157.02 0 N9 ADP 1000 a 1 
HETATM 19 C C8 ADP . . . T 3 170.722 192.291 224.924 1 157.02 0 C8 ADP 1000 a 1 
HETATM 20 N N7 ADP . . . T 3 170.012 192.961 223.986 1 163.92 0 N7 ADP 1000 a 1 
HETATM 21 C C5 ADP . . . T 3 169.693 194.169 224.493 1 162.64 0 C5 ADP 1000 a 1 
HETATM 22 C C6 ADP . . . T 3 168.954 195.371 224.034 1 162.32 0 C6 ADP 1000 a 1 
HETATM 23 N N6 ADP . . . T 3 168.388 195.435 222.804 1 157.02 0 N6 ADP 1000 a 1 
HETATM 24 N N1 ADP . . . T 3 168.862 196.414 224.891 1 174.51 0 N1 ADP 1000 a 1 
HETATM 25 C C2 ADP . . . T 3 169.415 196.382 226.118 1 170.22 0 C2 ADP 1000 a 1 
HETATM 26 N N3 ADP . . . T 3 170.095 195.326 226.597 1 157.31 0 N3 ADP 1000 a 1 
HETATM 27 C C4 ADP . . . T 3 170.265 194.216 225.845 1 157.02 0 C4 ADP 1000 a 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           262 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#