data_2O8D
#
_model_server_result.job_id            bZwXMIP6wg97LIpH2c3Y3Q 
_model_server_result.datetime_utc      '2024-11-25 16:39:19' 
_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          2o8d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":202}' 
#
_entry.id    2O8D 
#
_exptl.entry_id    2O8D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            2O8D 
_cell.length_a            260.379 
_cell.length_b            260.379 
_cell.length_c            260.379 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2O8D 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        212 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 3 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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    x,y,z 
_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 F N N 
? 6 H 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 C OG SER 676 A SER 676 1_555 E MG MG . A MG 935 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc2 E MG MG . A MG 935 1_555 F O1B ADP . A ADP 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc3 G MG MG . B MG 102 1_555 H O3B ADP . B ADP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? 
metalc ? metalc4 G MG MG . B MG 102 1_555 D OG SER 803 B SER 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
hydrog 'DG-DC PAIR' hydrog1 A N1 DG 1 E DG 1 1_555 B N3 DC 15 F DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N1 DA 2 E DA 2 1_555 B N3 DT 14 F DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N6 DA 2 E DA 2 1_555 B O4 DT 14 F DT 29 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DA 3 E DA 3 1_555 B N3 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N6 DA 3 E DA 3 1_555 B O4 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N3 DC 4 E DC 4 1_555 B N1 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N4 DC 4 E DC 4 1_555 B O6 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A O2 DC 4 E DC 4 1_555 B N2 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N3 DC 5 E DC 5 1_555 B N1 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N4 DC 5 E DC 5 1_555 B O6 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A O2 DC 5 E DC 5 1_555 B N2 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N1 DG 6 E DG 6 1_555 B N3 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N2 DG 6 E DG 6 1_555 B O2 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A O6 DG 6 E DG 6 1_555 B N4 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N3 DC 7 E DC 7 1_555 B N1 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N4 DC 7 E DC 7 1_555 B O6 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A O2 DC 7 E DC 7 1_555 B N2 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DU MISPAIR' hydrog18 A N1 DG 8 E DG 8 1_555 B O4 DU 8 F DU 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A N3 DC 9 E DC 9 1_555 B N1 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A N4 DC 9 E DC 9 1_555 B O6 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A O2 DC 9 E DC 9 1_555 B N2 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A N1 DG 10 E DG 10 1_555 B N3 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A N2 DG 10 E DG 10 1_555 B O2 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 A O6 DG 10 E DG 10 1_555 B N4 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog25 A N3 DC 11 E DC 11 1_555 B N1 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog26 A N4 DC 11 E DC 11 1_555 B O6 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog27 A O2 DC 11 E DC 11 1_555 B N2 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog28 A N3 DT 12 E DT 12 1_555 B N1 DA 4 F DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog29 A O4 DT 12 E DT 12 1_555 B N6 DA 4 F DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog30 A N1 DA 13 E DA 13 1_555 B N3 DT 3 F DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog31 A N6 DA 13 E DA 13 1_555 B O4 DT 3 F DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog32 A N1 DG 14 E DG 14 1_555 B N3 DC 2 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog33 A N1 DG 15 E DG 15 1_555 B O2 DC 1 F DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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                     2O8D 
_atom_sites.fract_transf_matrix[1][1]    0.003841 
_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]    0.003841 
_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]    0.003841 
_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
E 5 MG A 1 935 101 MG MG . 
F 6 ADP A 1 936 201 ADP ADP . 
G 5 MG B 1 102 102 MG MG . 
H 6 ADP B 1 202 202 ADP ADP . 
I 7 HOH E 1 16 15 HOH HOH . 
J 7 HOH F 1 4 4 HOH HOH . 
J 7 HOH F 2 13 13 HOH HOH . 
J 7 HOH F 3 51 51 HOH HOH . 
K 7 HOH A 1 937 36 HOH HOH . 
K 7 HOH A 2 938 50 HOH HOH . 
L 7 HOH B 1 1 1 HOH HOH . 
L 7 HOH B 2 2 2 HOH HOH . 
L 7 HOH B 3 3 3 HOH HOH . 
L 7 HOH B 4 6 6 HOH HOH . 
L 7 HOH B 5 7 7 HOH HOH . 
L 7 HOH B 6 8 8 HOH HOH . 
L 7 HOH B 7 9 9 HOH HOH . 
L 7 HOH B 8 10 10 HOH HOH . 
L 7 HOH B 9 11 11 HOH HOH . 
L 7 HOH B 10 12 12 HOH HOH . 
L 7 HOH B 11 14 14 HOH HOH . 
L 7 HOH B 12 16 16 HOH HOH . 
L 7 HOH B 13 17 17 HOH HOH . 
L 7 HOH B 14 18 18 HOH HOH . 
L 7 HOH B 15 19 19 HOH HOH . 
L 7 HOH B 16 21 21 HOH HOH . 
L 7 HOH B 17 22 22 HOH HOH . 
L 7 HOH B 18 23 23 HOH HOH . 
L 7 HOH B 19 24 24 HOH HOH . 
L 7 HOH B 20 25 25 HOH HOH . 
L 7 HOH B 21 26 26 HOH HOH . 
L 7 HOH B 22 27 27 HOH HOH . 
L 7 HOH B 23 29 29 HOH HOH . 
L 7 HOH B 24 30 30 HOH HOH . 
L 7 HOH B 25 31 31 HOH HOH . 
L 7 HOH B 26 32 32 HOH HOH . 
L 7 HOH B 27 34 34 HOH HOH . 
L 7 HOH B 28 35 35 HOH HOH . 
L 7 HOH B 29 37 37 HOH HOH . 
L 7 HOH B 30 39 39 HOH HOH . 
L 7 HOH B 31 40 40 HOH HOH . 
L 7 HOH B 32 41 41 HOH HOH . 
L 7 HOH B 33 42 42 HOH HOH . 
L 7 HOH B 34 43 43 HOH HOH . 
L 7 HOH B 35 44 44 HOH HOH . 
L 7 HOH B 36 45 45 HOH HOH . 
L 7 HOH B 37 46 46 HOH HOH . 
L 7 HOH B 38 47 47 HOH HOH . 
L 7 HOH B 39 48 48 HOH HOH . 
L 7 HOH B 40 49 49 HOH HOH . 
#
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 . . . H 6 -56.575 -8.349 24.171 1 101.16 ? PB ADP 202 B 1 
HETATM 2 O O1B ADP . . . H 6 -57.031 -9.689 23.662 1 101.14 ? O1B ADP 202 B 1 
HETATM 3 O O2B ADP . . . H 6 -55.114 -8.26 24.536 1 101.01 ? O2B ADP 202 B 1 
HETATM 4 O O3B ADP . . . H 6 -57.494 -7.707 25.181 1 101.16 ? O3B ADP 202 B 1 
HETATM 5 P PA ADP . . . H 6 -57.594 -6.133 22.737 1 101.73 ? PA ADP 202 B 1 
HETATM 6 O O1A ADP . . . H 6 -59.054 -6.512 22.836 1 101.47 ? O1A ADP 202 B 1 
HETATM 7 O O2A ADP . . . H 6 -57.027 -5.132 23.717 1 101.88 ? O2A ADP 202 B 1 
HETATM 8 O O3A ADP . . . H 6 -56.695 -7.465 22.833 1 101.55 ? O3A ADP 202 B 1 
HETATM 9 O O5' ADP . . . H 6 -57.256 -5.646 21.235 1 101.02 ? O5' ADP 202 B 1 
HETATM 10 C C5' ADP . . . H 6 -55.903 -5.385 20.867 1 100.68 ? C5' ADP 202 B 1 
HETATM 11 C C4' ADP . . . H 6 -55.795 -4.784 19.468 1 100.77 ? C4' ADP 202 B 1 
HETATM 12 O O4' ADP . . . H 6 -56.345 -5.666 18.485 1 100.5 ? O4' ADP 202 B 1 
HETATM 13 C C3' ADP . . . H 6 -56.525 -3.453 19.331 1 100.79 ? C3' ADP 202 B 1 
HETATM 14 O O3' ADP . . . H 6 -55.602 -2.361 19.434 1 101.1 ? O3' ADP 202 B 1 
HETATM 15 C C2' ADP . . . H 6 -57.181 -3.493 17.962 1 100.36 ? C2' ADP 202 B 1 
HETATM 16 O O2' ADP . . . H 6 -56.508 -2.619 17.052 1 99.99 ? O2' ADP 202 B 1 
HETATM 17 C C1' ADP . . . H 6 -57.044 -4.929 17.478 1 99.86 ? C1' ADP 202 B 1 
HETATM 18 N N9 ADP . . . H 6 -58.378 -5.542 17.243 1 99.73 ? N9 ADP 202 B 1 
HETATM 19 C C8 ADP . . . H 6 -59.238 -5.983 18.186 1 99.54 ? C8 ADP 202 B 1 
HETATM 20 N N7 ADP . . . H 6 -60.367 -6.492 17.628 1 99.43 ? N7 ADP 202 B 1 
HETATM 21 C C5 ADP . . . H 6 -60.235 -6.381 16.29 1 99.75 ? C5 ADP 202 B 1 
HETATM 22 C C6 ADP . . . H 6 -61.047 -6.721 15.092 1 99.61 ? C6 ADP 202 B 1 
HETATM 23 N N6 ADP . . . H 6 -62.265 -7.297 15.217 1 99.63 ? N6 ADP 202 B 1 
HETATM 24 N N1 ADP . . . H 6 -60.537 -6.435 13.871 1 99.53 ? N1 ADP 202 B 1 
HETATM 25 C C2 ADP . . . H 6 -59.328 -5.861 13.722 1 99.54 ? C2 ADP 202 B 1 
HETATM 26 N N3 ADP . . . H 6 -58.536 -5.527 14.758 1 99.63 ? N3 ADP 202 B 1 
HETATM 27 C C4 ADP . . . H 6 -58.924 -5.754 16.042 1 99.8 ? C4 ADP 202 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           255 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#