data_3H86
#
_model_server_result.job_id            CqUTXz2Bgjcqmler_k9S-g 
_model_server_result.datetime_utc      '2024-11-15 05:39:48' 
_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          3h86 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":193}' 
#
_entry.id    3H86 
#
_exptl.entry_id    3H86 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              916.367 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "BIS(ADENOSINE)-5'-PENTAPHOSPHATE" 
_entity.pdbx_number_of_molecules    4 
_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         120 
_cell.entry_id            3H86 
_cell.length_a            102.84 
_cell.length_b            102.84 
_cell.length_c            228.72 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3H86 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
PISA dodecameric 12 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,E,F,G,I,J,K 1 1 
D,H,L 2 1,2,3 
D,H,L 3 4,5,6 
A,B,C,E,F,G,I,J,K 3 1,7,8 
#
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' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 x+2/3,y+1/3,z+1/3 1 0 0 0 1 0 0 0 1 51.42 29.687351 76.24 
5 'crystal symmetry operation' 5_555 -y+2/3,x-y+1/3,z+1/3 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 51.42 29.687351 76.24 
6 'crystal symmetry operation' 6_555 -x+y+2/3,-x+1/3,z+1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.42 29.687351 76.24 
7 'crystal symmetry operation' 2_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 102.84 0 0 
8 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 51.42 89.062053 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C20 H29 N10 O22 P5' 
_chem_comp.formula_weight    916.367 
_chem_comp.id                AP5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "BIS(ADENOSINE)-5'-PENTAPHOSPHATE" 
_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
PA O1A AP5 doub 13 n n 
PA O2A AP5 sing 14 n n 
PA O3A AP5 sing 15 n n 
PA O5F AP5 sing 16 n n 
O2A HOA2 AP5 sing 17 n n 
O3A PB AP5 sing 18 n n 
PB O1B AP5 doub 19 n n 
PB O2B AP5 sing 20 n n 
PB O3B AP5 sing 21 n n 
O2B HOB2 AP5 sing 22 n n 
O3B PG AP5 sing 23 n n 
PG O1G AP5 doub 24 n n 
PG O2G AP5 sing 25 n n 
PG O3G AP5 sing 26 n n 
O2G HOG2 AP5 sing 27 n n 
O3G PD AP5 sing 28 n n 
PD O1D AP5 doub 29 n n 
PD O2D AP5 sing 30 n n 
PD O3D AP5 sing 31 n n 
O2D HOD2 AP5 sing 32 n n 
O3D PE AP5 sing 33 n n 
PE O1E AP5 doub 34 n n 
PE O2E AP5 sing 35 n n 
PE O5J AP5 sing 36 n n 
O2E HOE2 AP5 sing 37 n n 
O5F C5F AP5 sing 38 n n 
C5F C4F AP5 sing 39 n n 
C5F H51A AP5 sing 40 n n 
C5F H52A AP5 sing 41 n n 
C4F O4F AP5 sing 42 n n 
C4F C3F AP5 sing 43 n n 
C4F H4F AP5 sing 44 n n 
O4F C1F AP5 sing 45 n n 
C3F O3F AP5 sing 46 n n 
C3F C2F AP5 sing 47 n n 
C3F H3F AP5 sing 48 n n 
O3F HO3A AP5 sing 49 n n 
C2F O2F AP5 sing 50 n n 
C2F C1F AP5 sing 51 n n 
C2F H2F AP5 sing 52 n n 
O2F HO2A AP5 sing 53 n n 
C1F N9A AP5 sing 54 n n 
C1F H1F AP5 sing 55 n n 
N9A C8A AP5 sing 56 n y 
N9A C4A AP5 sing 57 n y 
C8A N7A AP5 doub 58 n y 
C8A H8A AP5 sing 59 n n 
N7A C5A AP5 sing 60 n y 
C5A C6A AP5 sing 61 n y 
C5A C4A AP5 doub 62 n y 
C6A N6A AP5 sing 63 n n 
C6A N1A AP5 doub 64 n y 
N6A H61A AP5 sing 65 n n 
N6A H62A AP5 sing 66 n n 
N1A C2A AP5 sing 67 n y 
C2A N3A AP5 doub 68 n y 
C2A H2A AP5 sing 69 n n 
N3A C4A AP5 sing 70 n y 
O5J C5J AP5 sing 71 n n 
C5J C4J AP5 sing 72 n n 
C5J H51B AP5 sing 73 n n 
C5J H52B AP5 sing 74 n n 
C4J O4J AP5 sing 75 n n 
C4J C3J AP5 sing 76 n n 
C4J H4J AP5 sing 77 n n 
O4J C1J AP5 sing 78 n n 
C3J O3J AP5 sing 79 n n 
C3J C2J AP5 sing 80 n n 
C3J H3J AP5 sing 81 n n 
O3J HO3B AP5 sing 82 n n 
C2J O2J AP5 sing 83 n n 
C2J C1J AP5 sing 84 n n 
C2J H2J AP5 sing 85 n n 
O2J HO2B AP5 sing 86 n n 
C1J N9B AP5 sing 87 n n 
C1J H1J AP5 sing 88 n n 
N9B C8B AP5 sing 89 n y 
N9B C4B AP5 sing 90 n y 
C8B N7B AP5 doub 91 n y 
C8B H8B AP5 sing 92 n n 
N7B C5B AP5 sing 93 n y 
C5B C6B AP5 sing 94 n y 
C5B C4B AP5 doub 95 n y 
C6B N6B AP5 sing 96 n n 
C6B N1B AP5 doub 97 n y 
N6B H61B AP5 sing 98 n n 
N6B H62B AP5 sing 99 n n 
N1B C2B AP5 sing 100 n y 
C2B N3B AP5 doub 101 n y 
C2B H2B AP5 sing 102 n n 
N3B C4B AP5 sing 103 n y 
#
_atom_sites.entry_id                     3H86 
_atom_sites.fract_transf_matrix[1][1]    0.009724 
_atom_sites.fract_transf_matrix[1][2]    0.005614 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011228 
_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]    0.004372 
_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 2 AP5 B 1 193 1 AP5 AP5 . 
F 2 AP5 A 1 193 1 AP5 AP5 . 
G 2 AP5 C 1 193 1 AP5 AP5 . 
H 2 AP5 G 1 193 1 AP5 AP5 . 
I 3 HOH B 1 194 6 HOH HOH . 
I 3 HOH B 2 195 8 HOH HOH . 
I 3 HOH B 3 196 16 HOH HOH . 
I 3 HOH B 4 197 18 HOH HOH . 
I 3 HOH B 5 198 19 HOH HOH . 
I 3 HOH B 6 199 32 HOH HOH . 
I 3 HOH B 7 200 33 HOH HOH . 
I 3 HOH B 8 201 34 HOH HOH . 
J 3 HOH A 1 194 1 HOH HOH . 
J 3 HOH A 2 195 2 HOH HOH . 
J 3 HOH A 3 196 3 HOH HOH . 
J 3 HOH A 4 197 4 HOH HOH . 
J 3 HOH A 5 198 26 HOH HOH . 
J 3 HOH A 6 199 28 HOH HOH . 
J 3 HOH A 7 200 29 HOH HOH . 
J 3 HOH A 8 201 35 HOH HOH . 
J 3 HOH A 9 202 36 HOH HOH . 
J 3 HOH A 10 203 39 HOH HOH . 
J 3 HOH A 11 204 42 HOH HOH . 
J 3 HOH A 12 205 43 HOH HOH . 
K 3 HOH C 1 194 5 HOH HOH . 
K 3 HOH C 2 195 11 HOH HOH . 
K 3 HOH C 3 196 12 HOH HOH . 
K 3 HOH C 4 197 14 HOH HOH . 
K 3 HOH C 5 198 15 HOH HOH . 
K 3 HOH C 6 199 20 HOH HOH . 
K 3 HOH C 7 200 22 HOH HOH . 
K 3 HOH C 8 201 25 HOH HOH . 
K 3 HOH C 9 202 27 HOH HOH . 
K 3 HOH C 10 203 30 HOH HOH . 
K 3 HOH C 11 204 31 HOH HOH . 
K 3 HOH C 12 205 37 HOH HOH . 
K 3 HOH C 13 206 38 HOH HOH . 
K 3 HOH C 14 207 40 HOH HOH . 
K 3 HOH C 15 208 41 HOH HOH . 
L 3 HOH G 1 194 7 HOH HOH . 
L 3 HOH G 2 195 9 HOH HOH . 
L 3 HOH G 3 196 10 HOH HOH . 
L 3 HOH G 4 197 13 HOH HOH . 
L 3 HOH G 5 198 17 HOH HOH . 
L 3 HOH G 6 199 21 HOH HOH . 
L 3 HOH G 7 200 23 HOH HOH . 
L 3 HOH G 8 201 24 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 PA AP5 . . . H 2 12.043 -19.643 -33.28 1 49.4 ? PA AP5 193 G 1 
HETATM 2 O O1A AP5 . . . H 2 13.349 -20.246 -33.612 1 48.27 ? O1A AP5 193 G 1 
HETATM 3 O O2A AP5 . . . H 2 12.036 -18.377 -32.465 1 56.42 ? O2A AP5 193 G 1 
HETATM 4 O O3A AP5 . . . H 2 11.241 -19.173 -34.57 1 54.42 ? O3A AP5 193 G 1 
HETATM 5 P PB AP5 . . . H 2 11.45 -19.746 -36.033 1 48.98 ? PB AP5 193 G 1 
HETATM 6 O O1B AP5 . . . H 2 10.053 -19.868 -36.479 1 43.33 ? O1B AP5 193 G 1 
HETATM 7 O O2B AP5 . . . H 2 12.157 -21.083 -35.964 1 55.95 ? O2B AP5 193 G 1 
HETATM 8 O O3B AP5 . . . H 2 12.493 -18.708 -36.735 1 48.82 ? O3B AP5 193 G 1 
HETATM 9 P PG AP5 . . . H 2 13.463 -19.215 -37.94 1 47.65 ? PG AP5 193 G 1 
HETATM 10 O O1G AP5 . . . H 2 12.583 -20.25 -38.624 1 51.21 ? O1G AP5 193 G 1 
HETATM 11 O O2G AP5 . . . H 2 14.74 -19.929 -37.642 1 50.52 ? O2G AP5 193 G 1 
HETATM 12 O O3G AP5 . . . H 2 13.718 -17.947 -38.891 1 46.97 ? O3G AP5 193 G 1 
HETATM 13 P PD AP5 . . . H 2 15.068 -17.084 -39.026 1 46.62 ? PD AP5 193 G 1 
HETATM 14 O O1D AP5 . . . H 2 15.233 -16.234 -37.803 1 46.78 ? O1D AP5 193 G 1 
HETATM 15 O O2D AP5 . . . H 2 14.974 -16.137 -40.181 1 44.09 ? O2D AP5 193 G 1 
HETATM 16 O O3D AP5 . . . H 2 16.096 -18.269 -39.128 1 41.81 ? O3D AP5 193 G 1 
HETATM 17 P PE AP5 . . . H 2 17.356 -18.313 -40.052 1 41.39 ? PE AP5 193 G 1 
HETATM 18 O O1E AP5 . . . H 2 18.181 -19.531 -39.777 1 42.51 ? O1E AP5 193 G 1 
HETATM 19 O O2E AP5 . . . H 2 18.18 -17.101 -39.726 1 40.08 ? O2E AP5 193 G 1 
HETATM 20 O O5F AP5 . . . H 2 11.02 -20.678 -32.616 1 50.44 ? O5F AP5 193 G 1 
HETATM 21 C C5F AP5 . . . H 2 9.706 -20.52 -33.075 1 48.14 ? C5F AP5 193 G 1 
HETATM 22 C C4F AP5 . . . H 2 8.747 -21.073 -32.08 1 45.68 ? C4F AP5 193 G 1 
HETATM 23 O O4F AP5 . . . H 2 9.072 -20.454 -30.878 1 44.21 ? O4F AP5 193 G 1 
HETATM 24 C C3F AP5 . . . H 2 7.352 -20.655 -32.506 1 47.11 ? C3F AP5 193 G 1 
HETATM 25 O O3F AP5 . . . H 2 6.555 -21.799 -32.777 1 48.69 ? O3F AP5 193 G 1 
HETATM 26 C C2F AP5 . . . H 2 6.864 -19.84 -31.319 1 45.3 ? C2F AP5 193 G 1 
HETATM 27 O O2F AP5 . . . H 2 5.793 -20.469 -30.675 1 48.89 ? O2F AP5 193 G 1 
HETATM 28 C C1F AP5 . . . H 2 7.97 -19.809 -30.298 1 42.69 ? C1F AP5 193 G 1 
HETATM 29 N N9A AP5 . . . H 2 8.264 -18.413 -29.869 1 36.1 ? N9A AP5 193 G 1 
HETATM 30 C C8A AP5 . . . H 2 9.383 -17.694 -30.091 1 35.16 ? C8A AP5 193 G 1 
HETATM 31 N N7A AP5 . . . H 2 9.278 -16.464 -29.509 1 36.25 ? N7A AP5 193 G 1 
HETATM 32 C C5A AP5 . . . H 2 8.074 -16.427 -28.911 1 33.65 ? C5A AP5 193 G 1 
HETATM 33 C C6A AP5 . . . H 2 7.463 -15.439 -28.195 1 33.01 ? C6A AP5 193 G 1 
HETATM 34 N N6A AP5 . . . H 2 8.109 -14.268 -28.008 1 31.56 ? N6A AP5 193 G 1 
HETATM 35 N N1A AP5 . . . H 2 6.194 -15.656 -27.73 1 33.24 ? N1A AP5 193 G 1 
HETATM 36 C C2A AP5 . . . H 2 5.548 -16.834 -27.944 1 34.71 ? C2A AP5 193 G 1 
HETATM 37 N N3A AP5 . . . H 2 6.204 -17.849 -28.61 1 34.64 ? N3A AP5 193 G 1 
HETATM 38 C C4A AP5 . . . H 2 7.435 -17.628 -29.116 1 33.54 ? C4A AP5 193 G 1 
HETATM 39 O O5J AP5 . . . H 2 16.683 -18.512 -41.557 1 43.17 ? O5J AP5 193 G 1 
HETATM 40 C C5J AP5 . . . H 2 17.276 -19.068 -42.761 1 50.31 ? C5J AP5 193 G 1 
HETATM 41 C C4J AP5 . . . H 2 18.055 -17.874 -43.302 1 56.04 ? C4J AP5 193 G 1 
HETATM 42 O O4J AP5 . . . H 2 18.782 -17.885 -44.512 1 54.22 ? O4J AP5 193 G 1 
HETATM 43 C C3J AP5 . . . H 2 17.212 -16.63 -43.511 1 58.48 ? C3J AP5 193 G 1 
HETATM 44 O O3J AP5 . . . H 2 16.591 -16.285 -42.278 1 58.33 ? O3J AP5 193 G 1 
HETATM 45 C C2J AP5 . . . H 2 18.238 -15.666 -44.227 1 56.45 ? C2J AP5 193 G 1 
HETATM 46 O O2J AP5 . . . H 2 18.926 -14.573 -43.618 1 58.04 ? O2J AP5 193 G 1 
HETATM 47 C C1J AP5 . . . H 2 19.345 -16.584 -44.54 1 50.06 ? C1J AP5 193 G 1 
HETATM 48 N N9B AP5 . . . H 2 19.536 -16.079 -45.837 1 50.21 ? N9B AP5 193 G 1 
HETATM 49 C C8B AP5 . . . H 2 19.549 -16.84 -46.998 1 51.93 ? C8B AP5 193 G 1 
HETATM 50 N N7B AP5 . . . H 2 19.78 -15.986 -48.026 1 48.17 ? N7B AP5 193 G 1 
HETATM 51 C C5B AP5 . . . H 2 19.903 -14.751 -47.548 1 44.09 ? C5B AP5 193 G 1 
HETATM 52 C C6B AP5 . . . H 2 20.162 -13.607 -48.223 1 49.66 ? C6B AP5 193 G 1 
HETATM 53 N N6B AP5 . . . H 2 20.833 -13.779 -49.402 1 56.2 ? N6B AP5 193 G 1 
HETATM 54 N N1B AP5 . . . H 2 20.248 -12.414 -47.498 1 46.47 ? N1B AP5 193 G 1 
HETATM 55 C C2B AP5 . . . H 2 20.111 -12.465 -46.143 1 45.41 ? C2B AP5 193 G 1 
HETATM 56 N N3B AP5 . . . H 2 19.874 -13.668 -45.443 1 40.53 ? N3B AP5 193 G 1 
HETATM 57 C C4B AP5 . . . H 2 19.751 -14.774 -46.172 1 46.27 ? C4B AP5 193 G 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           242 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           57 
#