data_5ND4
#
_model_server_result.job_id            xu3TYYf5DEuDjB25g9LwrA 
_model_server_result.datetime_utc      '2025-07-04 21:02:20' 
_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          5nd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":601}' 
#
_entry.id    5ND4 
#
_exptl.entry_id    5ND4 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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 
_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                      4 
_struct_asym.id                             D 
_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
metalc ? metalc1 A OG SER 357 C SER 377 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc2 D O2B ADP . C ADP 601 1_555 E MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc3 G O2G GTP . A GTP 500 1_555 H MG MG . A MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? 
#
_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                     5ND4 
_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
D 4 ADP C 1 601 511 ADP ADP . 
E 5 MG C 1 602 512 MG MG . 
F 6 ALF C 1 603 513 ALF ALF . 
G 7 GTP A 1 500 500 GTP GTP . 
H 5 MG A 1 501 501 MG MG . 
I 8 GDP B 1 600 600 GDP GDP . 
J 9 TA1 B 1 601 601 TA1 TA1 . 
#
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 . . . D 4 188.554 209.417 311.961 1 26.82 ? PB ADP 601 C 1 
HETATM 2 O O1B ADP . . . D 4 188.652 208.003 311.508 1 26.82 ? O1B ADP 601 C 1 
HETATM 3 O O2B ADP . . . D 4 188.285 209.425 313.466 1 26.82 ? O2B ADP 601 C 1 
HETATM 4 O O3B ADP . . . D 4 189.933 210.041 311.64 1 26.82 ? O3B ADP 601 C 1 
HETATM 5 P PA ADP . . . D 4 185.774 210.242 311.441 1 26.82 ? PA ADP 601 C 1 
HETATM 6 O O1A ADP . . . D 4 185.509 211.575 312.031 1 26.82 ? O1A ADP 601 C 1 
HETATM 7 O O2A ADP . . . D 4 185.299 209.206 312.406 1 26.82 ? O2A ADP 601 C 1 
HETATM 8 O O3A ADP . . . D 4 187.343 210.099 311.176 1 26.82 ? O3A ADP 601 C 1 
HETATM 9 O O5' ADP . . . D 4 184.962 210.078 310.11 1 26.82 ? O5' ADP 601 C 1 
HETATM 10 C C5' ADP . . . D 4 185.121 211.005 309.033 1 26.82 ? C5' ADP 601 C 1 
HETATM 11 C C4' ADP . . . D 4 183.799 211.156 308.317 1 26.82 ? C4' ADP 601 C 1 
HETATM 12 O O4' ADP . . . D 4 183.374 209.889 307.773 1 26.82 ? O4' ADP 601 C 1 
HETATM 13 C C3' ADP . . . D 4 182.628 211.702 309.131 1 26.82 ? C3' ADP 601 C 1 
HETATM 14 O O3' ADP . . . D 4 181.979 212.721 308.366 1 26.82 ? O3' ADP 601 C 1 
HETATM 15 C C2' ADP . . . D 4 181.788 210.45 309.428 1 26.82 ? C2' ADP 601 C 1 
HETATM 16 O O2' ADP . . . D 4 180.423 210.726 309.715 1 26.82 ? O2' ADP 601 C 1 
HETATM 17 C C1' ADP . . . D 4 182.049 209.61 308.157 1 26.82 ? C1' ADP 601 C 1 
HETATM 18 N N9 ADP . . . D 4 181.966 208.164 308.35 1 26.82 ? N9 ADP 601 C 1 
HETATM 19 C C8 ADP . . . D 4 182.866 207.386 309.021 1 26.82 ? C8 ADP 601 C 1 
HETATM 20 N N7 ADP . . . D 4 182.537 206.115 309.094 1 26.82 ? N7 ADP 601 C 1 
HETATM 21 C C5 ADP . . . D 4 181.332 206.054 308.425 1 26.82 ? C5 ADP 601 C 1 
HETATM 22 C C6 ADP . . . D 4 180.494 204.971 308.089 1 26.82 ? C6 ADP 601 C 1 
HETATM 23 N N6 ADP . . . D 4 180.686 203.722 308.52 1 26.82 ? N6 ADP 601 C 1 
HETATM 24 N N1 ADP . . . D 4 179.384 205.244 307.364 1 26.82 ? N1 ADP 601 C 1 
HETATM 25 C C2 ADP . . . D 4 179.154 206.507 306.988 1 26.82 ? C2 ADP 601 C 1 
HETATM 26 N N3 ADP . . . D 4 179.892 207.602 307.209 1 26.82 ? N3 ADP 601 C 1 
HETATM 27 C C4 ADP . . . D 4 180.96 207.306 307.961 1 26.82 ? C4 ADP 601 C 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#