data_9E8I
#
_model_server_result.job_id            O5mdLEJPlDNM5lI492RfEw 
_model_server_result.datetime_utc      '2024-12-28 01:59:51' 
_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          9e8i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"FA","auth_seq_id":501}' 
#
_entry.id    9E8I 
#
_exptl.entry_id    9E8I 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          30 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    27-meric 
_pdbx_struct_assembly.oligomeric_count      27 
_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,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      30 
_struct_asym.id                             FA 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
disulf ? disulf1 G SG CYS 115 G CYS 115 1_555 G SG CYS 154 G CYS 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
metalc ? metalc1 A OG1 THR 223 A THR 223 1_555 CA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc2 BA O3G ATP . A ATP 501 1_555 CA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc3 BA O2B ATP . A ATP 501 1_555 CA MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? 
metalc ? metalc4 B OG1 THR 233 B THR 233 1_555 EA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? 
metalc ? metalc5 DA O1G ATP . B ATP 501 1_555 EA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
metalc ? metalc6 DA O1B ATP . B ATP 501 1_555 EA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? 
metalc ? metalc7 D OG1 THR 213 D THR 213 1_555 IA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc8 HA O3G ATP . D ATP 501 1_555 IA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.571 ? 
metalc ? metalc9 HA O2B ATP . D ATP 501 1_555 IA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? 
metalc ? metalc10 E OG1 THR 181 E THR 181 1_555 KA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? 
metalc ? metalc11 JA O2G ATP . E ATP 501 1_555 KA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc12 JA O2B ATP . E ATP 501 1_555 KA MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc13 LA O3G ATP . F ATP 501 1_555 MA MG MG . F MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc14 V OE2 GLU 52 c GLU 52 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc15 V NE2 HIS 113 c HIS 113 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc16 V NE2 HIS 115 c HIS 115 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc17 V OD1 ASP 126 c ASP 126 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc18 V OD2 ASP 126 c ASP 126 1_555 NA ZN ZN . c ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? 
#
_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                     9E8I 
_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
BA 28 ATP A 1 501 501 ATP ATP . 
CA 29 MG A 1 502 502 MG MG . 
DA 28 ATP B 1 501 501 ATP ATP . 
EA 29 MG B 1 502 502 MG MG . 
FA 30 ADP C 1 501 501 ADP ADP . 
GA 29 MG C 1 502 502 MG MG . 
HA 28 ATP D 1 501 501 ATP ATP . 
IA 29 MG D 1 502 502 MG MG . 
JA 28 ATP E 1 501 501 ATP ATP . 
KA 29 MG E 1 502 502 MG MG . 
LA 28 ATP F 1 501 501 ATP ATP . 
MA 29 MG F 1 502 502 MG MG . 
NA 31 ZN c 1 501 401 ZN ZN . 
#
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 . . . FA 30 163.59 177.029 194.767 1 44.47 ? PB ADP 501 C 1 
HETATM 2 O O1B ADP . . . FA 30 162.925 176.896 196.111 1 49.79 ? O1B ADP 501 C 1 
HETATM 3 O O2B ADP . . . FA 30 163.779 175.727 194.031 1 46.31 ? O2B ADP 501 C 1 
HETATM 4 O O3B ADP . . . FA 30 164.804 177.921 194.761 1 48.32 ? O3B ADP 501 C 1 
HETATM 5 P PA ADP . . . FA 30 162.441 179.425 193.88 1 51.48 ? PA ADP 501 C 1 
HETATM 6 O O1A ADP . . . FA 30 162.383 179.897 195.311 1 48.28 ? O1A ADP 501 C 1 
HETATM 7 O O2A ADP . . . FA 30 163.534 179.915 192.964 1 55.19 ? O2A ADP 501 C 1 
HETATM 8 O O3A ADP . . . FA 30 162.506 177.82 193.881 1 47.71 ? O3A ADP 501 C 1 
HETATM 9 O O5' ADP . . . FA 30 161.018 179.716 193.187 1 51.09 ? O5' ADP 501 C 1 
HETATM 10 C C5' ADP . . . FA 30 160.929 180.578 192.055 1 49.7 ? C5' ADP 501 C 1 
HETATM 11 C C4' ADP . . . FA 30 159.584 181.293 192.041 1 45.61 ? C4' ADP 501 C 1 
HETATM 12 O O4' ADP . . . FA 30 158.526 180.397 192.386 1 43.71 ? O4' ADP 501 C 1 
HETATM 13 C C3' ADP . . . FA 30 159.56 182.421 193.053 1 44.86 ? C3' ADP 501 C 1 
HETATM 14 O O3' ADP . . . FA 30 159.612 183.683 192.382 1 49.32 ? O3' ADP 501 C 1 
HETATM 15 C C2' ADP . . . FA 30 158.25 182.279 193.796 1 44.89 ? C2' ADP 501 C 1 
HETATM 16 O O2' ADP . . . FA 30 157.425 183.418 193.535 1 49.3 ? O2' ADP 501 C 1 
HETATM 17 C C1' ADP . . . FA 30 157.588 181.023 193.261 1 41.94 ? C1' ADP 501 C 1 
HETATM 18 N N9 ADP . . . FA 30 157.319 180.107 194.392 1 40.11 ? N9 ADP 501 C 1 
HETATM 19 C C8 ADP . . . FA 30 157.924 178.923 194.576 1 42.39 ? C8 ADP 501 C 1 
HETATM 20 N N7 ADP . . . FA 30 157.477 178.313 195.698 1 44.13 ? N7 ADP 501 C 1 
HETATM 21 C C5 ADP . . . FA 30 156.562 179.12 196.254 1 39.25 ? C5 ADP 501 C 1 
HETATM 22 C C6 ADP . . . FA 30 155.705 179.072 197.454 1 40.13 ? C6 ADP 501 C 1 
HETATM 23 N N6 ADP . . . FA 30 155.745 178.013 198.295 1 42.32 ? N6 ADP 501 C 1 
HETATM 24 N N1 ADP . . . FA 30 154.884 180.119 197.678 1 43 ? N1 ADP 501 C 1 
HETATM 25 C C2 ADP . . . FA 30 154.841 181.173 196.845 1 42.61 ? C2 ADP 501 C 1 
HETATM 26 N N3 ADP . . . FA 30 155.591 181.281 195.737 1 42.12 ? N3 ADP 501 C 1 
HETATM 27 C C4 ADP . . . FA 30 156.457 180.301 195.39 1 39.42 ? C4 ADP 501 C 1 
#
_model_server_stats.io_time_ms              34 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    102 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           27 
#