data_2O8C
#
_model_server_result.job_id            '_EKN5PNH-vdzigCx_QSMiA' 
_model_server_result.datetime_utc      '2025-02-17 01:38:52' 
_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          2o8c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":202}' 
#
_entry.id    2O8C 
#
_exptl.entry_id    2O8C 
_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            2O8C 
_cell.length_a            259.81 
_cell.length_b            259.81 
_cell.length_c            259.81 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2O8C 
_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 
_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
covale ? covale1 A O3' DC 7 E DC 7 1_555 A P 6OG 8 E 6OG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? 
covale ? covale2 A O3' 6OG 8 E 6OG 8 1_555 A P DC 9 E DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.59 ? 
metalc ? metalc1 C OG SER 676 A SER 676 1_555 E MG MG . A MG 935 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc2 E MG MG . A MG 935 1_555 F O1B ADP . A ADP 936 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? 
metalc ? metalc3 G MG MG . B MG 102 1_555 H O2B ADP . B ADP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.145 ? 
metalc ? metalc4 G MG MG . B MG 102 1_555 H O3B ADP . B ADP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? 
metalc ? metalc5 G MG MG . B MG 102 1_555 D OG SER 803 B SER 1141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
hydrog 'DG-DC PAIR' hydrog1 A N2 DG 1 E DG 1 1_555 B O2 DC 15 F DC 30 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N1 DA 3 E DA 3 1_555 B N3 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A N6 DA 3 E DA 3 1_555 B O4 DT 13 F DT 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DC-DG PAIR' hydrog4 A O2 DC 4 E DC 4 1_555 B N1 DG 12 F DG 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N3 DC 5 E DC 5 1_555 B N1 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N4 DC 5 E DC 5 1_555 B O6 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A O2 DC 5 E DC 5 1_555 B N2 DG 11 F DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N1 DG 6 E DG 6 1_555 B N3 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N2 DG 6 E DG 6 1_555 B O2 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A O6 DG 6 E DG 6 1_555 B N4 DC 10 F DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N3 DC 7 E DC 7 1_555 B N1 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N4 DC 7 E DC 7 1_555 B O6 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A O2 DC 7 E DC 7 1_555 B N2 DG 9 F DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog '6OG-DT MISPAIR' hydrog14 A N1 6OG 8 E 6OG 8 1_555 B O4 DT 8 F DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N3 DC 9 E DC 9 1_555 B N1 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N4 DC 9 E DC 9 1_555 B O6 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A O2 DC 9 E DC 9 1_555 B N2 DG 7 F DG 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A N1 DG 10 E DG 10 1_555 B N3 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A N2 DG 10 E DG 10 1_555 B O2 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A O6 DG 10 E DG 10 1_555 B N4 DC 6 F DC 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A N3 DC 11 E DC 11 1_555 B N1 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A N4 DC 11 E DC 11 1_555 B O6 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A O2 DC 11 E DC 11 1_555 B N2 DG 5 F DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DT-DA PAIR' hydrog24 A N3 DT 12 E DT 12 1_555 B N1 DA 4 F DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DA-DT PAIR' hydrog25 A N1 DA 13 E DA 13 1_555 B N3 DT 3 F DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog26 A N2 DG 14 E DG 14 1_555 B O2 DC 2 F DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'DG-DC PAIR' hydrog27 A N1 DG 15 E DG 15 1_555 B N3 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 43 n n 
PB O2B ADP sing 44 n n 
PB O3B ADP sing 45 n n 
PB O3A ADP sing 46 n n 
O2B HOB2 ADP sing 47 n n 
O3B HOB3 ADP sing 48 n n 
PA O1A ADP doub 49 n n 
PA O2A ADP sing 50 n n 
PA O3A ADP sing 51 n n 
PA O5' ADP sing 52 n n 
O2A HOA2 ADP sing 53 n n 
O5' C5' ADP sing 54 n n 
C5' C4' ADP sing 55 n n 
C5' "H5'1" ADP sing 56 n n 
C5' "H5'2" ADP sing 57 n n 
C4' O4' ADP sing 58 n n 
C4' C3' ADP sing 59 n n 
C4' H4' ADP sing 60 n n 
O4' C1' ADP sing 61 n n 
C3' O3' ADP sing 62 n n 
C3' C2' ADP sing 63 n n 
C3' H3' ADP sing 64 n n 
O3' HO3' ADP sing 65 n n 
C2' O2' ADP sing 66 n n 
C2' C1' ADP sing 67 n n 
C2' H2' ADP sing 68 n n 
O2' HO2' ADP sing 69 n n 
C1' N9 ADP sing 70 n n 
C1' H1' ADP sing 71 n n 
N9 C8 ADP sing 72 n y 
N9 C4 ADP sing 73 n y 
C8 N7 ADP doub 74 n y 
C8 H8 ADP sing 75 n n 
N7 C5 ADP sing 76 n y 
C5 C6 ADP sing 77 n y 
C5 C4 ADP doub 78 n y 
C6 N6 ADP sing 79 n n 
C6 N1 ADP doub 80 n y 
N6 HN61 ADP sing 81 n n 
N6 HN62 ADP sing 82 n n 
N1 C2 ADP sing 83 n y 
C2 N3 ADP doub 84 n y 
C2 H2 ADP sing 85 n n 
N3 C4 ADP sing 86 n y 
#
_atom_sites.entry_id                     2O8C 
_atom_sites.fract_transf_matrix[1][1]    0.003849 
_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]    0.003849 
_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]    0.003849 
_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 F 1 13 13 HOH HOH . 
J 7 HOH A 1 937 50 HOH HOH . 
K 7 HOH B 1 1 1 HOH HOH . 
K 7 HOH B 2 2 2 HOH HOH . 
K 7 HOH B 3 6 6 HOH HOH . 
K 7 HOH B 4 8 8 HOH HOH . 
K 7 HOH B 5 9 9 HOH HOH . 
K 7 HOH B 6 10 10 HOH HOH . 
K 7 HOH B 7 12 12 HOH HOH . 
K 7 HOH B 8 14 14 HOH HOH . 
K 7 HOH B 9 16 16 HOH HOH . 
K 7 HOH B 10 18 18 HOH HOH . 
K 7 HOH B 11 19 19 HOH HOH . 
K 7 HOH B 12 23 23 HOH HOH . 
K 7 HOH B 13 25 25 HOH HOH . 
K 7 HOH B 14 30 30 HOH HOH . 
K 7 HOH B 15 31 31 HOH HOH . 
K 7 HOH B 16 37 37 HOH HOH . 
K 7 HOH B 17 40 40 HOH HOH . 
K 7 HOH B 18 45 45 HOH HOH . 
K 7 HOH B 19 46 46 HOH HOH . 
K 7 HOH B 20 47 47 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 -56.311 -8.582 24.122 1 83.24 ? PB ADP 202 B 1 
HETATM 2 O O1B ADP . . . H 6 -56.137 -10 23.645 1 83.26 ? O1B ADP 202 B 1 
HETATM 3 O O2B ADP . . . H 6 -55.043 -7.937 24.628 1 83.31 ? O2B ADP 202 B 1 
HETATM 4 O O3B ADP . . . H 6 -57.522 -8.364 24.999 1 83.27 ? O3B ADP 202 B 1 
HETATM 5 P PA ADP . . . H 6 -57.407 -6.361 22.848 1 82.95 ? PA ADP 202 B 1 
HETATM 6 O O1A ADP . . . H 6 -58.89 -6.622 22.907 1 83.02 ? O1A ADP 202 B 1 
HETATM 7 O O2A ADP . . . H 6 -56.763 -5.548 23.946 1 83.19 ? O2A ADP 202 B 1 
HETATM 8 O O3A ADP . . . H 6 -56.65 -7.777 22.771 1 83.05 ? O3A ADP 202 B 1 
HETATM 9 O O5' ADP . . . H 6 -57.054 -5.692 21.427 1 82.72 ? O5' ADP 202 B 1 
HETATM 10 C C5' ADP . . . H 6 -55.74 -5.201 21.172 1 82.67 ? C5' ADP 202 B 1 
HETATM 11 C C4' ADP . . . H 6 -55.637 -4.697 19.739 1 82.77 ? C4' ADP 202 B 1 
HETATM 12 O O4' ADP . . . H 6 -56.319 -5.578 18.843 1 82.78 ? O4' ADP 202 B 1 
HETATM 13 C C3' ADP . . . H 6 -56.264 -3.321 19.568 1 82.85 ? C3' ADP 202 B 1 
HETATM 14 O O3' ADP . . . H 6 -55.238 -2.334 19.405 1 82.93 ? O3' ADP 202 B 1 
HETATM 15 C C2' ADP . . . H 6 -57.128 -3.414 18.323 1 82.82 ? C2' ADP 202 B 1 
HETATM 16 O O2' ADP . . . H 6 -56.719 -2.448 17.351 1 82.83 ? O2' ADP 202 B 1 
HETATM 17 C C1' ADP . . . H 6 -56.91 -4.82 17.783 1 82.75 ? C1' ADP 202 B 1 
HETATM 18 N N9 ADP . . . H 6 -58.181 -5.438 17.312 1 82.76 ? N9 ADP 202 B 1 
HETATM 19 C C8 ADP . . . H 6 -59.136 -6.002 18.079 1 82.72 ? C8 ADP 202 B 1 
HETATM 20 N N7 ADP . . . H 6 -60.162 -6.473 17.321 1 82.75 ? N7 ADP 202 B 1 
HETATM 21 C C5 ADP . . . H 6 -59.867 -6.212 16.032 1 82.73 ? C5 ADP 202 B 1 
HETATM 22 C C6 ADP . . . H 6 -60.507 -6.44 14.711 1 82.62 ? C6 ADP 202 B 1 
HETATM 23 N N6 ADP . . . H 6 -61.709 -7.053 14.607 1 82.67 ? N6 ADP 202 B 1 
HETATM 24 N N1 ADP . . . H 6 -59.858 -6.007 13.607 1 82.67 ? N1 ADP 202 B 1 
HETATM 25 C C2 ADP . . . H 6 -58.662 -5.392 13.684 1 82.73 ? C2 ADP 202 B 1 
HETATM 26 N N3 ADP . . . H 6 -58.022 -5.155 14.844 1 82.74 ? N3 ADP 202 B 1 
HETATM 27 C C4 ADP . . . H 6 -58.56 -5.532 16.033 1 82.79 ? C4 ADP 202 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    24 
_model_server_stats.query_time_ms           295 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#