data_6RE8
#
_model_server_result.job_id            TE1W2VqWtK5mZY9mSpmaCQ 
_model_server_result.datetime_utc      '2024-11-02 19:39:59' 
_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          6re8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"MA","auth_seq_id":601}' 
#
_entry.id    6RE8 
#
_exptl.entry_id    6RE8 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          22 
_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            6RE8 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6RE8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    31-meric 
_pdbx_struct_assembly.oligomeric_count      31 
_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,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA 
_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
? 22 MA N N 
? 22 OA 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 U NE2 HIS 248 M HIS 248 1_555 FA ZN ZN . M ZN 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc2 Z OG1 THR 232 T THR 232 1_555 HA MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc3 GA O1G ATP . T ATP 1001 1_555 HA MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc4 GA O2B ATP . T ATP 1001 1_555 HA MG MG . T MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? 
metalc ? metalc5 AA OG1 THR 232 U THR 232 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? 
metalc ? metalc6 IA O1G ATP . U ATP 1001 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc7 IA O3G ATP . U ATP 1001 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc8 IA O1B ATP . U ATP 1001 1_555 JA MG MG . U MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
metalc ? metalc9 BA OG1 THR 232 V THR 232 1_555 LA MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc10 KA O2B ATP . V ATP 1001 1_555 LA MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
metalc ? metalc11 KA O3B ATP . V ATP 1001 1_555 LA MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc12 KA O3A ATP . V ATP 1001 1_555 LA MG MG . V MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.795 ? 
metalc ? metalc13 DA OG1 THR 190 Y THR 190 1_555 NA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc14 DA OE1 GLU 215 Y GLU 215 1_555 NA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? 
metalc ? metalc15 MA O3B ADP . Y ADP 601 1_555 NA MG MG . Y MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc16 EA OG1 THR 190 Z THR 190 1_555 PA MG MG . Z MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? 
metalc ? metalc17 EA OE1 GLU 215 Z GLU 215 1_555 PA MG MG . Z MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc18 EA OE1 GLU 219 Z GLU 219 1_555 PA MG MG . Z MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc19 OA O3B ADP . Z ADP 601 1_555 PA MG MG . Z MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? 
#
_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                     6RE8 
_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
FA 19 ZN M 1 600 600 ZN ZN . 
GA 20 ATP T 1 1001 1001 ATP ATP . 
HA 21 MG T 1 1002 1002 MG MG . 
IA 20 ATP U 1 1001 1001 ATP ATP . 
JA 21 MG U 1 1002 1002 MG MG . 
KA 20 ATP V 1 1001 1001 ATP ATP . 
LA 21 MG V 1 1002 1002 MG MG . 
MA 22 ADP Y 1 601 1028 ADP ADP . 
NA 21 MG Y 1 602 1029 MG MG . 
OA 22 ADP Z 1 601 1028 ADP ADP . 
PA 21 MG Z 1 602 1029 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 . . . MA 22 139.127 275.619 269.905 1 16.97 ? PB ADP 601 Y 1 
HETATM 2 O O1B ADP . . . MA 22 138.221 274.617 269.242 1 16.97 ? O1B ADP 601 Y 1 
HETATM 3 O O2B ADP . . . MA 22 140.379 275.015 270.481 1 16.97 ? O2B ADP 601 Y 1 
HETATM 4 O O3B ADP . . . MA 22 138.406 276.576 270.817 1 16.97 ? O3B ADP 601 Y 1 
HETATM 5 P PA ADP . . . MA 22 140.545 277.852 268.999 1 16.97 ? PA ADP 601 Y 1 
HETATM 6 O O1A ADP . . . MA 22 139.856 279.049 268.405 1 16.97 ? O1A ADP 601 Y 1 
HETATM 7 O O2A ADP . . . MA 22 140.956 277.855 270.446 1 16.97 ? O2A ADP 601 Y 1 
HETATM 8 O O3A ADP . . . MA 22 139.688 276.526 268.701 1 16.97 ? O3A ADP 601 Y 1 
HETATM 9 O O5' ADP . . . MA 22 141.887 277.597 268.163 1 16.97 ? O5' ADP 601 Y 1 
HETATM 10 C C5' ADP . . . MA 22 143.09 278.092 268.732 1 16.97 ? C5' ADP 601 Y 1 
HETATM 11 C C4' ADP . . . MA 22 144.255 278.047 267.76 1 16.97 ? C4' ADP 601 Y 1 
HETATM 12 O O4' ADP . . . MA 22 143.817 278.054 266.405 1 16.97 ? O4' ADP 601 Y 1 
HETATM 13 C C3' ADP . . . MA 22 145.086 279.294 267.958 1 16.97 ? C3' ADP 601 Y 1 
HETATM 14 O O3' ADP . . . MA 22 146.28 278.995 268.679 1 16.97 ? O3' ADP 601 Y 1 
HETATM 15 C C2' ADP . . . MA 22 145.422 279.771 266.569 1 16.97 ? C2' ADP 601 Y 1 
HETATM 16 O O2' ADP . . . MA 22 146.824 279.645 266.346 1 16.97 ? O2' ADP 601 Y 1 
HETATM 17 C C1' ADP . . . MA 22 144.669 278.876 265.611 1 16.97 ? C1' ADP 601 Y 1 
HETATM 18 N N9 ADP . . . MA 22 143.858 279.765 264.755 1 16.97 ? N9 ADP 601 Y 1 
HETATM 19 C C8 ADP . . . MA 22 142.524 279.876 264.797 1 16.97 ? C8 ADP 601 Y 1 
HETATM 20 N N7 ADP . . . MA 22 142.072 280.779 263.894 1 16.97 ? N7 ADP 601 Y 1 
HETATM 21 C C5 ADP . . . MA 22 143.143 281.269 263.26 1 16.97 ? C5 ADP 601 Y 1 
HETATM 22 C C6 ADP . . . MA 22 143.376 282.255 262.19 1 16.97 ? C6 ADP 601 Y 1 
HETATM 23 N N6 ADP . . . MA 22 142.346 282.911 261.613 1 16.97 ? N6 ADP 601 Y 1 
HETATM 24 N N1 ADP . . . MA 22 144.648 282.48 261.805 1 16.97 ? N1 ADP 601 Y 1 
HETATM 25 C C2 ADP . . . MA 22 145.68 281.83 262.369 1 16.97 ? C2 ADP 601 Y 1 
HETATM 26 N N3 ADP . . . MA 22 145.539 280.918 263.345 1 16.97 ? N3 ADP 601 Y 1 
HETATM 27 C C4 ADP . . . MA 22 144.317 280.597 263.825 1 16.97 ? C4 ADP 601 Y 1 
#
_model_server_stats.io_time_ms              25 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    85 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#