data_6C1D
#
_model_server_result.job_id            iEW_nF86-DJIz56taghzBQ 
_model_server_result.datetime_utc      '2025-07-25 12:51:31' 
_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          6c1d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":401}' 
#
_entry.id    6C1D 
#
_exptl.entry_id    6C1D 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          5 
_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 
_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
? 5 I N N 
? 5 K N N 
? 5 M N N 
? 5 O N N 
? 5 Q N N 
? 5 T 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
covale ? covale1 H C ALA 1 F ALA 1 1_555 H N 2TL 2 F 2TL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? 
covale ? covale2 H N ALA 1 F ALA 1 1_555 H C EEP 7 F EEP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? 
covale ? covale3 H C 2TL 2 F 2TL 2 1_555 H N DCY 3 F DCY 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.302 ? 
covale ? covale4 H C DCY 3 F DCY 3 1_555 H N HYP 4 F HYP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? 
covale ? covale5 H SG DCY 3 F DCY 3 1_555 H CD1 TRP 6 F TRP 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? 
covale ? covale6 H C HYP 4 F HYP 4 1_555 H N ALA 5 F ALA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.278 ? 
covale ? covale7 H C TRP 6 F TRP 6 1_555 H N EEP 7 F EEP 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.285 ? 
metalc ? metalc1 I O3B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.799 ? 
metalc ? metalc2 I O1A ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? 
metalc ? metalc3 K O1B ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.931 ? 
metalc ? metalc4 K O1A ADP . B ADP 401 1_555 L MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.952 ? 
metalc ? metalc5 M O1B ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? 
metalc ? metalc6 M O1A ADP . C ADP 401 1_555 N MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? 
metalc ? metalc7 O O3B ADP . D ADP 401 1_555 P MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? 
metalc ? metalc8 O O1A ADP . D ADP 401 1_555 P MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? 
metalc ? metalc9 Q O3B ADP . E ADP 401 1_555 R MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? 
metalc ? metalc10 Q O1A ADP . E ADP 401 1_555 R MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.768 ? 
metalc ? metalc11 F OG1 THR 110 P THR 115 1_555 S MG MG . P MG 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? 
metalc ? metalc12 S MG MG . P MG 801 1_555 T O3B ADP . P ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? 
metalc ? metalc13 S MG MG . P MG 801 1_555 T O2B ADP . P ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.576 ? 
#
_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 17 n n 
PB O2B ADP sing 18 n n 
PB O3B ADP sing 19 n n 
PB O3A ADP sing 20 n n 
O2B HOB2 ADP sing 21 n n 
O3B HOB3 ADP sing 22 n n 
PA O1A ADP doub 23 n n 
PA O2A ADP sing 24 n n 
PA O3A ADP sing 25 n n 
PA O5' ADP sing 26 n n 
O2A HOA2 ADP sing 27 n n 
O5' C5' ADP sing 28 n n 
C5' C4' ADP sing 29 n n 
C5' "H5'1" ADP sing 30 n n 
C5' "H5'2" ADP sing 31 n n 
C4' O4' ADP sing 32 n n 
C4' C3' ADP sing 33 n n 
C4' H4' ADP sing 34 n n 
O4' C1' ADP sing 35 n n 
C3' O3' ADP sing 36 n n 
C3' C2' ADP sing 37 n n 
C3' H3' ADP sing 38 n n 
O3' HO3' ADP sing 39 n n 
C2' O2' ADP sing 40 n n 
C2' C1' ADP sing 41 n n 
C2' H2' ADP sing 42 n n 
O2' HO2' ADP sing 43 n n 
C1' N9 ADP sing 44 n n 
C1' H1' ADP sing 45 n n 
N9 C8 ADP sing 46 n y 
N9 C4 ADP sing 47 n y 
C8 N7 ADP doub 48 n y 
C8 H8 ADP sing 49 n n 
N7 C5 ADP sing 50 n y 
C5 C6 ADP sing 51 n y 
C5 C4 ADP doub 52 n y 
C6 N6 ADP sing 53 n n 
C6 N1 ADP doub 54 n y 
N6 HN61 ADP sing 55 n n 
N6 HN62 ADP sing 56 n n 
N1 C2 ADP sing 57 n y 
C2 N3 ADP doub 58 n y 
C2 H2 ADP sing 59 n n 
N3 C4 ADP sing 60 n y 
#
_atom_sites.entry_id                     6C1D 
_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
I 5 ADP A 1 401 401 ADP ADP . 
J 6 MG A 1 402 402 MG MG . 
K 5 ADP B 1 401 401 ADP ADP . 
L 6 MG B 1 402 402 MG MG . 
M 5 ADP C 1 401 401 ADP ADP . 
N 6 MG C 1 402 402 MG MG . 
O 5 ADP D 1 401 401 ADP ADP . 
P 6 MG D 1 402 402 MG MG . 
Q 5 ADP E 1 401 401 ADP ADP . 
R 6 MG E 1 402 402 MG MG . 
S 6 MG P 1 801 790 MG MG . 
T 5 ADP P 1 802 791 ADP ADP . 
#
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 . . . M 5 274.11 250.723 252.461 1 0 ? PB ADP 401 C 1 
HETATM 2 O O1B ADP . . . M 5 275.071 249.967 251.59 1 0 ? O1B ADP 401 C 1 
HETATM 3 O O2B ADP . . . M 5 274.684 251.349 253.692 1 0 ? O2B ADP 401 C 1 
HETATM 4 O O3B ADP . . . M 5 273.146 251.611 251.736 1 0 ? O3B ADP 401 C 1 
HETATM 5 P PA ADP . . . M 5 273.116 248.096 252.433 1 0 ? PA ADP 401 C 1 
HETATM 6 O O1A ADP . . . M 5 272.899 248.139 250.948 1 0 ? O1A ADP 401 C 1 
HETATM 7 O O2A ADP . . . M 5 274.229 247.28 253.01 1 0 ? O2A ADP 401 C 1 
HETATM 8 O O3A ADP . . . M 5 273.156 249.583 253.021 1 0 ? O3A ADP 401 C 1 
HETATM 9 O O5' ADP . . . M 5 271.774 247.679 253.171 1 0 ? O5' ADP 401 C 1 
HETATM 10 C C5' ADP . . . M 5 271.617 248.152 254.497 1 0 ? C5' ADP 401 C 1 
HETATM 11 C C4' ADP . . . M 5 270.142 248.187 254.818 1 0 ? C4' ADP 401 C 1 
HETATM 12 O O4' ADP . . . M 5 269.635 246.885 254.583 1 0 ? O4' ADP 401 C 1 
HETATM 13 C C3' ADP . . . M 5 269.877 248.505 256.263 1 0 ? C3' ADP 401 C 1 
HETATM 14 O O3' ADP . . . M 5 268.781 249.398 256.327 1 0 ? O3' ADP 401 C 1 
HETATM 15 C C2' ADP . . . M 5 269.391 247.224 256.865 1 0 ? C2' ADP 401 C 1 
HETATM 16 O O2' ADP . . . M 5 268.328 247.537 257.753 1 0 ? O2' ADP 401 C 1 
HETATM 17 C C1' ADP . . . M 5 268.885 246.435 255.691 1 0 ? C1' ADP 401 C 1 
HETATM 18 N N9 ADP . . . M 5 269.184 245.011 255.889 1 0 ? N9 ADP 401 C 1 
HETATM 19 C C8 ADP . . . M 5 270.403 244.492 256.074 1 0 ? C8 ADP 401 C 1 
HETATM 20 N N7 ADP . . . M 5 270.333 243.153 256.225 1 0 ? N7 ADP 401 C 1 
HETATM 21 C C5 ADP . . . M 5 269.045 242.811 256.137 1 0 ? C5 ADP 401 C 1 
HETATM 22 C C6 ADP . . . M 5 268.279 241.564 256.205 1 0 ? C6 ADP 401 C 1 
HETATM 23 N N6 ADP . . . M 5 268.896 240.38 256.407 1 0 ? N6 ADP 401 C 1 
HETATM 24 N N1 ADP . . . M 5 266.946 241.647 256.06 1 0 ? N1 ADP 401 C 1 
HETATM 25 C C2 ADP . . . M 5 266.317 242.812 255.856 1 0 ? C2 ADP 401 C 1 
HETATM 26 N N3 ADP . . . M 5 266.951 243.981 255.781 1 0 ? N3 ADP 401 C 1 
HETATM 27 C C4 ADP . . . M 5 268.289 244.038 255.913 1 0 ? C4 ADP 401 C 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    19 
_model_server_stats.query_time_ms           231 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#