data_6XTX
#
_model_server_result.job_id            Vxk1-6LW3ibDaxv46XCl9w 
_model_server_result.datetime_utc      '2024-10-25 20:30:39' 
_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          6xtx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":1001}' 
#
_entry.id    6XTX 
#
_exptl.entry_id    6XTX 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          14 
_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                     ? 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,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
? 14 N N N 
? 14 O 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 SG CYS 329 2 CYS 329 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc2 A SG CYS 332 2 CYS 332 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc3 A SG CYS 352 2 CYS 352 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? 
metalc ? metalc4 A SG CYS 355 2 CYS 355 1_555 M ZN ZN . 2 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? 
metalc ? metalc5 C SG CYS 326 4 CYS 306 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc6 C SG CYS 329 4 CYS 309 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? 
metalc ? metalc7 C SG CYS 348 4 CYS 328 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc8 C SG CYS 351 4 CYS 331 1_555 P ZN ZN . 4 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? 
metalc ? metalc9 C OG SER 537 4 SER 517 1_555 R MG MG . 4 MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc10 Q O2G AGS . 4 AGS 902 1_555 R MG MG . 4 MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc11 Q O2B AGS . 4 AGS 902 1_555 R MG MG . 4 MG 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc12 S O2G AGS . 4 AGS 904 1_555 V MG MG . 6 MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc13 S O2B AGS . 4 AGS 904 1_555 V MG MG . 6 MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc14 D SG CYS 172 5 CYS 172 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc15 D SG CYS 175 5 CYS 175 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc16 D SG CYS 197 5 CYS 197 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc17 D SG CYS 207 5 CYS 207 1_555 T ZN ZN . 5 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc18 E SG CYS 158 6 CYS 158 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc19 E SG CYS 161 6 CYS 161 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc20 E SG CYS 180 6 CYS 180 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? 
metalc ? metalc21 E SG CYS 185 6 CYS 185 1_555 U ZN ZN . 6 ZN 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc22 E OG SER 403 6 SER 403 1_555 V MG MG . 6 MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc23 F SG CYS 184 7 CYS 184 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc24 F SG CYS 187 7 CYS 187 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc25 F SG CYS 206 7 CYS 206 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc26 F SG CYS 211 7 CYS 211 1_555 W ZN ZN . 7 ZN 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc27 F OG SER 388 7 SER 388 1_555 Y MG MG . 7 MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc28 X O2G AGS . 7 AGS 1001 1_555 Y MG MG . 7 MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc29 X O2B AGS . 7 AGS 1001 1_555 Y MG MG . 7 MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
#
_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                     6XTX 
_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
M 13 ZN 2 1 1000 1000 ZN ZN . 
N 14 ADP 2 1 1001 1001 ADP ADP . 
O 14 ADP 3 1 1001 1001 ADP ADP . 
P 13 ZN 4 1 901 1000 ZN ZN . 
Q 15 AGS 4 1 902 1001 AGS AGS . 
R 16 MG 4 1 903 1002 MG MG . 
S 15 AGS 4 1 904 1001 AGS AGS . 
T 13 ZN 5 1 1000 1000 ZN ZN . 
U 13 ZN 6 1 901 1000 ZN ZN . 
V 16 MG 6 1 902 1002 MG MG . 
W 13 ZN 7 1 1000 1000 ZN ZN . 
X 15 AGS 7 1 1001 1001 AGS AGS . 
Y 16 MG 7 1 1002 1002 MG MG . 
#
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 . . . N 14 220.623 170.971 193.536 1 117.66 ? PB ADP 1001 2 1 
HETATM 2 O O1B ADP . . . N 14 221.209 171.47 192.24 1 117.66 ? O1B ADP 1001 2 1 
HETATM 3 O O2B ADP . . . N 14 219.133 171.158 193.677 1 117.66 ? O2B ADP 1001 2 1 
HETATM 4 O O3B ADP . . . N 14 221.401 171.365 194.762 1 117.66 ? O3B ADP 1001 2 1 
HETATM 5 P PA ADP . . . N 14 220.393 168.455 194.681 1 117.66 ? PA ADP 1001 2 1 
HETATM 6 O O1A ADP . . . N 14 218.926 168.655 194.94 1 117.66 ? O1A ADP 1001 2 1 
HETATM 7 O O2A ADP . . . N 14 221.368 168.681 195.8 1 117.66 ? O2A ADP 1001 2 1 
HETATM 8 O O3A ADP . . . N 14 220.823 169.38 193.446 1 117.66 ? O3A ADP 1001 2 1 
HETATM 9 O O5' ADP . . . N 14 220.603 166.968 194.119 1 117.66 ? O5' ADP 1001 2 1 
HETATM 10 C C5' ADP . . . N 14 220.445 165.895 195.035 1 117.66 ? C5' ADP 1001 2 1 
HETATM 11 C C4' ADP . . . N 14 220.489 164.541 194.343 1 117.66 ? C4' ADP 1001 2 1 
HETATM 12 O O4' ADP . . . N 14 221.833 164.12 194.089 1 117.66 ? O4' ADP 1001 2 1 
HETATM 13 C C3' ADP . . . N 14 219.869 163.498 195.252 1 117.66 ? C3' ADP 1001 2 1 
HETATM 14 O O3' ADP . . . N 14 218.607 163.069 194.74 1 117.66 ? O3' ADP 1001 2 1 
HETATM 15 C C2' ADP . . . N 14 220.835 162.337 195.276 1 117.66 ? C2' ADP 1001 2 1 
HETATM 16 O O2' ADP . . . N 14 220.232 161.202 194.652 1 117.66 ? O2' ADP 1001 2 1 
HETATM 17 C C1' ADP . . . N 14 222.059 162.761 194.487 1 117.66 ? C1' ADP 1001 2 1 
HETATM 18 N N9 ADP . . . N 14 223.271 162.723 195.347 1 117.66 ? N9 ADP 1001 2 1 
HETATM 19 C C8 ADP . . . N 14 224.292 163.587 195.226 1 117.66 ? C8 ADP 1001 2 1 
HETATM 20 N N7 ADP . . . N 14 225.272 163.338 196.126 1 117.66 ? N7 ADP 1001 2 1 
HETATM 21 C C5 ADP . . . N 14 224.882 162.282 196.851 1 117.66 ? C5 ADP 1001 2 1 
HETATM 22 C C6 ADP . . . N 14 225.46 161.51 197.968 1 117.66 ? C6 ADP 1001 2 1 
HETATM 23 N N6 ADP . . . N 14 226.667 161.833 198.485 1 117.66 ? N6 ADP 1001 2 1 
HETATM 24 N N1 ADP . . . N 14 224.75 160.476 198.453 1 117.66 ? N1 ADP 1001 2 1 
HETATM 25 C C2 ADP . . . N 14 223.553 160.155 197.943 1 117.66 ? C2 ADP 1001 2 1 
HETATM 26 N N3 ADP . . . N 14 222.97 160.812 196.928 1 117.66 ? N3 ADP 1001 2 1 
HETATM 27 C C4 ADP . . . N 14 223.569 161.87 196.336 1 117.66 ? C4 ADP 1001 2 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    68 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#