data_6VFS
#
_model_server_result.job_id            sfKSpGTSfN8Rw01bsnmrJw 
_model_server_result.datetime_utc      '2025-08-31 11:19:25' 
_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          6vfs 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":501}' 
#
_entry.id    6VFS 
#
_exptl.entry_id    6VFS 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          6 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    21-meric 
_pdbx_struct_assembly.oligomeric_count      21 
_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 
_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
? 6 X N N 
? 6 Y 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 OG1 THR 126 E THR 126 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc2 A OD2 ASP 184 E ASP 184 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? 
metalc ? metalc3 V O3G ATP . E ATP 501 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.953 ? 
metalc ? metalc4 V O1B ATP . E ATP 501 1_555 W MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc5 D OG1 THR 126 C THR 126 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? 
metalc ? metalc6 D OD2 ASP 184 C ASP 184 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? 
metalc ? metalc7 Z O1G ATP . C ATP 501 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? 
metalc ? metalc8 Z O1B ATP . C ATP 501 1_555 AA MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc9 E OG1 THR 126 B THR 126 1_555 CA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? 
metalc ? metalc10 BA O3G ATP . B ATP 501 1_555 CA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc11 BA O1B ATP . B ATP 501 1_555 CA MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc12 F OG1 THR 126 D THR 126 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? 
metalc ? metalc13 DA O1G ATP . D ATP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? 
metalc ? metalc14 DA O3G ATP . D ATP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? 
metalc ? metalc15 DA O1B ATP . D ATP 501 1_555 EA MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
#
_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                     6VFS 
_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
V 4 ATP E 1 501 1 ATP ATP . 
W 5 MG E 1 502 1 MG MG . 
X 6 ADP A 1 501 1 ADP ADP . 
Y 6 ADP F 1 501 1 ADP ADP . 
Z 4 ATP C 1 501 1 ATP ATP . 
AA 5 MG C 1 502 3 MG MG . 
BA 4 ATP B 1 501 1 ATP ATP . 
CA 5 MG B 1 502 2 MG MG . 
DA 4 ATP D 1 501 1 ATP ATP . 
EA 5 MG D 1 502 4 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 . . . X 6 137.661 126.663 98.18 1 71.91 ? PB ADP 501 A 1 
HETATM 2 O O1B ADP . . . X 6 136.72 127.59 97.45 1 71.91 ? O1B ADP 501 A 1 
HETATM 3 O O2B ADP . . . X 6 137.139 126.156 99.503 1 71.91 ? O2B ADP 501 A 1 
HETATM 4 O O3B ADP . . . X 6 139.088 127.155 98.224 1 71.91 ? O3B ADP 501 A 1 
HETATM 5 P PA ADP . . . X 6 138.895 125.115 96.184 1 71.91 ? PA ADP 501 A 1 
HETATM 6 O O1A ADP . . . X 6 138.729 126.123 95.074 1 71.91 ? O1A ADP 501 A 1 
HETATM 7 O O2A ADP . . . X 6 140.193 125.056 96.953 1 71.91 ? O2A ADP 501 A 1 
HETATM 8 O O3A ADP . . . X 6 137.718 125.342 97.26 1 71.91 ? O3A ADP 501 A 1 
HETATM 9 O O5' ADP . . . X 6 138.526 123.642 95.636 1 71.91 ? O5' ADP 501 A 1 
HETATM 10 C C5' ADP . . . X 6 139.441 122.549 95.722 1 71.91 ? C5' ADP 501 A 1 
HETATM 11 C C4' ADP . . . X 6 138.712 121.31 96.236 1 71.91 ? C4' ADP 501 A 1 
HETATM 12 O O4' ADP . . . X 6 138.133 121.551 97.526 1 71.91 ? O4' ADP 501 A 1 
HETATM 13 C C3' ADP . . . X 6 137.568 120.846 95.337 1 71.91 ? C3' ADP 501 A 1 
HETATM 14 O O3' ADP . . . X 6 137.904 119.613 94.693 1 71.91 ? O3' ADP 501 A 1 
HETATM 15 C C2' ADP . . . X 6 136.382 120.65 96.267 1 71.91 ? C2' ADP 501 A 1 
HETATM 16 O O2' ADP . . . X 6 135.721 119.4 96.047 1 71.91 ? O2' ADP 501 A 1 
HETATM 17 C C1' ADP . . . X 6 136.994 120.695 97.658 1 71.91 ? C1' ADP 501 A 1 
HETATM 18 N N9 ADP . . . X 6 136.027 121.15 98.69 1 71.91 ? N9 ADP 501 A 1 
HETATM 19 C C8 ADP . . . X 6 136.22 122.129 99.598 1 71.91 ? C8 ADP 501 A 1 
HETATM 20 N N7 ADP . . . X 6 135.133 122.257 100.4 1 71.91 ? N7 ADP 501 A 1 
HETATM 21 C C5 ADP . . . X 6 134.232 121.339 100.012 1 71.91 ? C5 ADP 501 A 1 
HETATM 22 C C6 ADP . . . X 6 132.877 120.935 100.432 1 71.91 ? C6 ADP 501 A 1 
HETATM 23 N N6 ADP . . . X 6 132.26 121.558 101.452 1 71.91 ? N6 ADP 501 A 1 
HETATM 24 N N1 ADP . . . X 6 132.272 119.927 99.768 1 71.91 ? N1 ADP 501 A 1 
HETATM 25 C C2 ADP . . . X 6 132.869 119.291 98.745 1 71.91 ? C2 ADP 501 A 1 
HETATM 26 N N3 ADP . . . X 6 134.104 119.611 98.311 1 71.91 ? N3 ADP 501 A 1 
HETATM 27 C C4 ADP . . . X 6 134.825 120.603 98.892 1 71.91 ? C4 ADP 501 A 1 
HETATM 28 H "H5'1" ADP . . . X 6 140.257 122.797 96.403 1 71.91 ? "H5'1" ADP 501 A 1 
HETATM 29 H "H5'2" ADP . . . X 6 139.876 122.339 94.742 1 71.91 ? "H5'2" ADP 501 A 1 
HETATM 30 H H4' ADP . . . X 6 139.442 120.492 96.316 1 71.91 ? H4' ADP 501 A 1 
HETATM 31 H H3' ADP . . . X 6 137.34 121.62 94.591 1 71.91 ? H3' ADP 501 A 1 
HETATM 32 H HO3' ADP . . . X 6 137.19 119.35 94.096 1 71.91 ? HO3' ADP 501 A 1 
HETATM 33 H H2' ADP . . . X 6 135.678 121.485 96.143 1 71.91 ? H2' ADP 501 A 1 
HETATM 34 H HO2' ADP . . . X 6 135.251 119.423 95.202 1 71.91 ? HO2' ADP 501 A 1 
HETATM 35 H H1' ADP . . . X 6 137.336 119.685 97.919 1 71.91 ? H1' ADP 501 A 1 
HETATM 36 H H8 ADP . . . X 6 137.112 122.737 99.674 1 71.91 ? H8 ADP 501 A 1 
HETATM 37 H HN61 ADP . . . X 6 131.34 121.258 101.705 1 71.91 ? HN61 ADP 501 A 1 
HETATM 38 H HN62 ADP . . . X 6 132.713 122.309 101.95 1 71.91 ? HN62 ADP 501 A 1 
HETATM 39 H H2 ADP . . . X 6 132.333 118.489 98.252 1 71.91 ? H2 ADP 501 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    83 
_model_server_stats.query_time_ms           405 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           39 
#