data_5DM3
#
_model_server_result.job_id            Ts8S8rZtzDUat9jlTOdzpQ 
_model_server_result.datetime_utc      '2024-12-21 14:34:39' 
_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          5dm3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":501}' 
#
_entry.id    5DM3 
#
_exptl.entry_id    5DM3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    6 
_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            5DM3 
_cell.length_a            132.983 
_cell.length_b            221.339 
_cell.length_c            199.353 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DM3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
PISA monomeric 1 author_and_software_defined_assembly 5 
PISA monomeric 1 author_and_software_defined_assembly 6 
PISA dodecameric 12 software_defined_assembly 7 
PISA dimeric 2 software_defined_assembly 8 
PISA dimeric 2 software_defined_assembly 9 
PISA dimeric 2 software_defined_assembly 10 
PISA dimeric 2 software_defined_assembly 11 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,G,M 1 1 
B,H,N 2 1 
C,I,O 3 1 
D,J,P 4 1 
E,K,Q 5 1 
F,L,R 6 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R 7 1,2 
A,G,M 8 1 
E,K,Q 8 2 
B,H,N 9 1,2 
C,I,O 10 1 
F,L,R 10 2 
D,J,P 11 1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 3_555 -x,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 0 99.6765 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
#
_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                     5DM3 
_atom_sites.fract_transf_matrix[1][1]    0.00752 
_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]    0.004518 
_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]    0.005016 
_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
G 2 ADP A 1 501 3 ADP ADP . 
H 2 ADP B 1 501 5 ADP ADP . 
I 2 ADP C 1 501 6 ADP ADP . 
J 2 ADP D 1 501 1 ADP ADP . 
K 2 ADP E 1 501 2 ADP ADP . 
L 2 ADP F 1 501 4 ADP ADP . 
M 3 HOH A 1 601 92 HOH HOH . 
M 3 HOH A 2 602 8 HOH HOH . 
M 3 HOH A 3 603 33 HOH HOH . 
M 3 HOH A 4 604 105 HOH HOH . 
M 3 HOH A 5 605 18 HOH HOH . 
M 3 HOH A 6 606 125 HOH HOH . 
M 3 HOH A 7 607 91 HOH HOH . 
M 3 HOH A 8 608 106 HOH HOH . 
M 3 HOH A 9 609 49 HOH HOH . 
N 3 HOH B 1 601 11 HOH HOH . 
N 3 HOH B 2 602 2 HOH HOH . 
N 3 HOH B 3 603 30 HOH HOH . 
N 3 HOH B 4 604 13 HOH HOH . 
N 3 HOH B 5 605 51 HOH HOH . 
N 3 HOH B 6 606 84 HOH HOH . 
N 3 HOH B 7 607 9 HOH HOH . 
N 3 HOH B 8 608 107 HOH HOH . 
N 3 HOH B 9 609 45 HOH HOH . 
N 3 HOH B 10 610 81 HOH HOH . 
N 3 HOH B 11 611 70 HOH HOH . 
O 3 HOH C 1 601 29 HOH HOH . 
O 3 HOH C 2 602 31 HOH HOH . 
O 3 HOH C 3 603 88 HOH HOH . 
O 3 HOH C 4 604 44 HOH HOH . 
O 3 HOH C 5 605 24 HOH HOH . 
O 3 HOH C 6 606 89 HOH HOH . 
O 3 HOH C 7 607 34 HOH HOH . 
O 3 HOH C 8 608 124 HOH HOH . 
O 3 HOH C 9 609 40 HOH HOH . 
O 3 HOH C 10 610 20 HOH HOH . 
O 3 HOH C 11 611 117 HOH HOH . 
P 3 HOH D 1 601 7 HOH HOH . 
P 3 HOH D 2 602 64 HOH HOH . 
P 3 HOH D 3 603 35 HOH HOH . 
P 3 HOH D 4 604 58 HOH HOH . 
P 3 HOH D 5 605 36 HOH HOH . 
P 3 HOH D 6 606 111 HOH HOH . 
P 3 HOH D 7 607 57 HOH HOH . 
P 3 HOH D 8 608 42 HOH HOH . 
P 3 HOH D 9 609 61 HOH HOH . 
P 3 HOH D 10 610 68 HOH HOH . 
P 3 HOH D 11 611 74 HOH HOH . 
P 3 HOH D 12 612 22 HOH HOH . 
P 3 HOH D 13 613 126 HOH HOH . 
Q 3 HOH E 1 601 90 HOH HOH . 
Q 3 HOH E 2 602 69 HOH HOH . 
Q 3 HOH E 3 603 27 HOH HOH . 
Q 3 HOH E 4 604 21 HOH HOH . 
Q 3 HOH E 5 605 79 HOH HOH . 
Q 3 HOH E 6 606 28 HOH HOH . 
Q 3 HOH E 7 607 66 HOH HOH . 
R 3 HOH F 1 601 48 HOH HOH . 
R 3 HOH F 2 602 75 HOH HOH . 
R 3 HOH F 3 603 80 HOH HOH . 
R 3 HOH F 4 604 112 HOH HOH . 
R 3 HOH F 5 605 32 HOH HOH . 
R 3 HOH F 6 606 119 HOH HOH . 
R 3 HOH F 7 607 55 HOH HOH . 
R 3 HOH F 8 608 63 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 . . . J 2 -26.378 -78.715 23.252 1 168.13 ? PB ADP 501 D 1 
HETATM 2 O O1B ADP . . . J 2 -25.666 -79.865 22.577 1 168.41 ? O1B ADP 501 D 1 
HETATM 3 O O2B ADP . . . J 2 -25.645 -77.396 23.186 1 166.76 ? O2B ADP 501 D 1 
HETATM 4 O O3B ADP . . . J 2 -27.848 -78.639 22.904 1 167.86 ? O3B ADP 501 D 1 
HETATM 5 P PA ADP . . . J 2 -25.1 -79.567 25.67 1 183.75 ? PA ADP 501 D 1 
HETATM 6 O O1A ADP . . . J 2 -25.472 -80.819 26.428 1 184.47 ? O1A ADP 501 D 1 
HETATM 7 O O2A ADP . . . J 2 -24.555 -78.383 26.433 1 182.85 ? O2A ADP 501 D 1 
HETATM 8 O O3A ADP . . . J 2 -26.39 -79.097 24.819 1 162.06 ? O3A ADP 501 D 1 
HETATM 9 O O5' ADP . . . J 2 -23.983 -79.953 24.58 1 90.76 ? O5' ADP 501 D 1 
HETATM 10 C C5' ADP . . . J 2 -22.968 -78.997 24.294 1 89.58 ? C5' ADP 501 D 1 
HETATM 11 C C4' ADP . . . J 2 -21.783 -79.644 23.593 1 84.06 ? C4' ADP 501 D 1 
HETATM 12 O O4' ADP . . . J 2 -22.036 -81.02 23.279 1 79.04 ? O4' ADP 501 D 1 
HETATM 13 C C3' ADP . . . J 2 -21.505 -78.915 22.285 1 80.31 ? C3' ADP 501 D 1 
HETATM 14 O O3' ADP . . . J 2 -20.151 -78.437 22.276 1 73.85 ? O3' ADP 501 D 1 
HETATM 15 C C2' ADP . . . J 2 -21.763 -79.965 21.218 1 76.88 ? C2' ADP 501 D 1 
HETATM 16 O O2' ADP . . . J 2 -20.926 -79.836 20.064 1 83.18 ? O2' ADP 501 D 1 
HETATM 17 C C1' ADP . . . J 2 -21.5 -81.249 21.977 1 73.49 ? C1' ADP 501 D 1 
HETATM 18 N N9 ADP . . . J 2 -22.057 -82.434 21.274 1 69.23 ? N9 ADP 501 D 1 
HETATM 19 C C8 ADP . . . J 2 -23.27 -82.536 20.701 1 62.24 ? C8 ADP 501 D 1 
HETATM 20 N N7 ADP . . . J 2 -23.425 -83.761 20.14 1 60.04 ? N7 ADP 501 D 1 
HETATM 21 C C5 ADP . . . J 2 -22.291 -84.461 20.333 1 59.9 ? C5 ADP 501 D 1 
HETATM 22 C C6 ADP . . . J 2 -21.785 -85.814 19.995 1 61.86 ? C6 ADP 501 D 1 
HETATM 23 N N6 ADP . . . J 2 -22.545 -86.7 19.311 1 68.04 ? N6 ADP 501 D 1 
HETATM 24 N N1 ADP . . . J 2 -20.54 -86.143 20.396 1 57.38 ? N1 ADP 501 D 1 
HETATM 25 C C2 ADP . . . J 2 -19.766 -85.274 21.074 1 55.94 ? C2 ADP 501 D 1 
HETATM 26 N N3 ADP . . . J 2 -20.156 -84.043 21.413 1 54.69 ? N3 ADP 501 D 1 
HETATM 27 C C4 ADP . . . J 2 -21.386 -83.58 21.077 1 62.01 ? C4 ADP 501 D 1 
#
_model_server_stats.io_time_ms              85 
_model_server_stats.parse_time_ms           30 
_model_server_stats.create_model_time_ms    58 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           27 
#