data_4TYP
#
_model_server_result.job_id            0HTlKaboIIQHckLnxpftOQ 
_model_server_result.datetime_utc      '2024-11-30 10:44:52' 
_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          4typ 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":301}' 
#
_entry.id    4TYP 
#
_exptl.entry_id    4TYP 
_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          98.28 
_cell.angle_gamma         90 
_cell.entry_id            4TYP 
_cell.length_a            43.641 
_cell.length_b            123.338 
_cell.length_c            86.693 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4TYP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,K 1 1 
B,F,G,L 2 1 
C,H,I,M 3 1 
D,J 4 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
? 2 E N N 
? 2 G N N 
? 2 I N N 
? 2 J 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 B SG CYS 130 B CYS 130 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? 
metalc ? metalc2 B SG CYS 133 B CYS 133 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? 
metalc ? metalc3 B SG CYS 150 B CYS 150 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? 
metalc ? metalc4 B OD2 ASP 153 B ASP 153 1_555 F ZN ZN . B ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? 
metalc ? metalc5 C SG CYS 130 A CYS 130 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? 
metalc ? metalc6 C SG CYS 133 A CYS 133 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? 
metalc ? metalc7 C OD1 ASP 153 A ASP 153 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.691 ? 
metalc ? metalc8 C OD2 ASP 153 A ASP 153 1_555 H ZN ZN . A ZN 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
#
_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                     4TYP 
_atom_sites.fract_transf_matrix[1][1]    0.022914 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003336 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008108 
_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]    0.011657 
_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 C 1 301 220 AP5 AP5 . 
F 3 ZN B 1 301 218 ZN ZN . 
G 2 AP5 B 1 302 224 AP5 AP5 . 
H 3 ZN A 1 301 218 ZN ZN . 
I 2 AP5 A 1 302 220 AP5 AP5 . 
J 2 AP5 D 1 301 220 AP5 AP5 . 
K 4 HOH C 1 401 6 HOH HOH . 
K 4 HOH C 2 402 3 HOH HOH . 
K 4 HOH C 3 403 37 HOH HOH . 
K 4 HOH C 4 404 12 HOH HOH . 
K 4 HOH C 5 405 33 HOH HOH . 
K 4 HOH C 6 406 36 HOH HOH . 
K 4 HOH C 7 407 72 HOH HOH . 
L 4 HOH B 1 401 11 HOH HOH . 
L 4 HOH B 2 402 24 HOH HOH . 
L 4 HOH B 3 403 77 HOH HOH . 
L 4 HOH B 4 404 102 HOH HOH . 
M 4 HOH A 1 401 9 HOH HOH . 
M 4 HOH A 2 402 1 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 . . . J 2 11.055 -7.485 140.051 1 83.7 ? PA AP5 301 D 1 
HETATM 2 O O1A AP5 . . . J 2 9.584 -7.665 140.328 1 84.79 ? O1A AP5 301 D 1 
HETATM 3 O O2A AP5 . . . J 2 11.482 -6.533 138.978 1 85.74 ? O2A AP5 301 D 1 
HETATM 4 O O3A AP5 . . . J 2 11.945 -7.159 141.351 1 81.42 ? O3A AP5 301 D 1 
HETATM 5 P PB AP5 . . . J 2 11.492 -6.338 142.65 1 77.23 ? PB AP5 301 D 1 
HETATM 6 O O1B AP5 . . . J 2 11.169 -7.392 143.68 1 77.16 ? O1B AP5 301 D 1 
HETATM 7 O O2B AP5 . . . J 2 10.47 -5.288 142.284 1 76.42 ? O2B AP5 301 D 1 
HETATM 8 O O3B AP5 . . . J 2 12.88 -5.655 143.103 1 77.98 ? O3B AP5 301 D 1 
HETATM 9 P PG AP5 . . . J 2 13.256 -4.142 142.75 1 77.26 ? PG AP5 301 D 1 
HETATM 10 O O1G AP5 . . . J 2 14.737 -3.991 142.742 1 76.54 ? O1G AP5 301 D 1 
HETATM 11 O O2G AP5 . . . J 2 12.476 -3.749 141.535 1 79.5 ? O2G AP5 301 D 1 
HETATM 12 O O3G AP5 . . . J 2 12.645 -3.286 143.963 1 82.92 ? O3G AP5 301 D 1 
HETATM 13 P PD AP5 . . . J 2 13.485 -2.773 145.224 1 82.39 ? PD AP5 301 D 1 
HETATM 14 O O1D AP5 . . . J 2 12.6 -2.794 146.441 1 83.63 ? O1D AP5 301 D 1 
HETATM 15 O O2D AP5 . . . J 2 14.835 -3.412 145.271 1 81.25 ? O2D AP5 301 D 1 
HETATM 16 O O3D AP5 . . . J 2 13.719 -1.245 144.863 1 87.25 ? O3D AP5 301 D 1 
HETATM 17 P PE AP5 . . . J 2 12.585 -0.232 144.35 1 89.82 ? PE AP5 301 D 1 
HETATM 18 O O1E AP5 . . . J 2 12.583 -0.247 142.848 1 89.34 ? O1E AP5 301 D 1 
HETATM 19 O O2E AP5 . . . J 2 11.305 -0.393 145.129 1 92.72 ? O2E AP5 301 D 1 
HETATM 20 O O5F AP5 . . . J 2 11.634 -8.921 139.704 1 87.54 ? O5F AP5 301 D 1 
HETATM 21 C C5F AP5 . . . J 2 13.02 -9.026 139.492 1 94.07 ? C5F AP5 301 D 1 
HETATM 22 C C4F AP5 . . . J 2 13.209 -10.269 138.674 1 97.46 ? C4F AP5 301 D 1 
HETATM 23 O O4F AP5 . . . J 2 12.785 -11.379 139.455 1 100.96 ? O4F AP5 301 D 1 
HETATM 24 C C3F AP5 . . . J 2 12.347 -10.213 137.429 1 99.68 ? C3F AP5 301 D 1 
HETATM 25 O O3F AP5 . . . J 2 13.198 -10.293 136.29 1 98.28 ? O3F AP5 301 D 1 
HETATM 26 C C2F AP5 . . . J 2 11.394 -11.388 137.556 1 101.98 ? C2F AP5 301 D 1 
HETATM 27 O O2F AP5 . . . J 2 11.231 -12.07 136.315 1 98.11 ? O2F AP5 301 D 1 
HETATM 28 C C1F AP5 . . . J 2 12.049 -12.252 138.613 1 104.48 ? C1F AP5 301 D 1 
HETATM 29 N N9A AP5 . . . J 2 11.076 -12.968 139.441 1 111.89 ? N9A AP5 301 D 1 
HETATM 30 C C8A AP5 . . . J 2 10.3 -12.475 140.421 1 119.65 ? C8A AP5 301 D 1 
HETATM 31 N N7A AP5 . . . J 2 9.536 -13.455 140.969 1 121.66 ? N7A AP5 301 D 1 
HETATM 32 C C5A AP5 . . . J 2 9.848 -14.59 140.323 1 119.79 ? C5A AP5 301 D 1 
HETATM 33 C C6A AP5 . . . J 2 9.438 -16.003 140.373 1 119.87 ? C6A AP5 301 D 1 
HETATM 34 N N6A AP5 . . . J 2 8.509 -16.421 141.256 1 121.13 ? N6A AP5 301 D 1 
HETATM 35 N N1A AP5 . . . J 2 10.026 -16.856 139.508 1 119.41 ? N1A AP5 301 D 1 
HETATM 36 C C2A AP5 . . . J 2 10.955 -16.467 138.618 1 116.92 ? C2A AP5 301 D 1 
HETATM 37 N N3A AP5 . . . J 2 11.369 -15.195 138.517 1 115.62 ? N3A AP5 301 D 1 
HETATM 38 C C4A AP5 . . . J 2 10.863 -14.251 139.324 1 115.66 ? C4A AP5 301 D 1 
HETATM 39 O O5J AP5 . . . J 2 13.301 1.132 144.79 1 92.54 ? O5J AP5 301 D 1 
HETATM 40 C C5J AP5 . . . J 2 14.663 1.321 144.423 1 93.73 ? C5J AP5 301 D 1 
HETATM 41 C C4J AP5 . . . J 2 15.366 2.133 145.489 1 94.52 ? C4J AP5 301 D 1 
HETATM 42 O O4J AP5 . . . J 2 14.523 3.2 145.913 1 96.72 ? O4J AP5 301 D 1 
HETATM 43 C C3J AP5 . . . J 2 15.685 1.307 146.716 1 94.86 ? C3J AP5 301 D 1 
HETATM 44 O O3J AP5 . . . J 2 16.985 0.71 146.629 1 93.52 ? O3J AP5 301 D 1 
HETATM 45 C C2J AP5 . . . J 2 15.567 2.312 147.828 1 94.95 ? C2J AP5 301 D 1 
HETATM 46 O O2J AP5 . . . J 2 16.834 2.893 148.068 1 96.4 ? O2J AP5 301 D 1 
HETATM 47 C C1J AP5 . . . J 2 14.648 3.398 147.315 1 96.32 ? C1J AP5 301 D 1 
HETATM 48 N N9B AP5 . . . J 2 13.343 3.245 147.979 1 98.2 ? N9B AP5 301 D 1 
HETATM 49 C C8B AP5 . . . J 2 12.173 2.923 147.405 1 100.17 ? C8B AP5 301 D 1 
HETATM 50 N N7B AP5 . . . J 2 11.186 2.859 148.328 1 99.31 ? N7B AP5 301 D 1 
HETATM 51 C C5B AP5 . . . J 2 11.735 3.156 149.515 1 97.57 ? C5B AP5 301 D 1 
HETATM 52 C C6B AP5 . . . J 2 11.276 3.273 150.909 1 94.31 ? C6B AP5 301 D 1 
HETATM 53 N N6B AP5 . . . J 2 9.993 3.061 151.243 1 95.39 ? N6B AP5 301 D 1 
HETATM 54 N N1B AP5 . . . J 2 12.186 3.591 151.849 1 93.38 ? N1B AP5 301 D 1 
HETATM 55 C C2B AP5 . . . J 2 13.48 3.805 151.56 1 93.84 ? C2B AP5 301 D 1 
HETATM 56 N N3B AP5 . . . J 2 13.968 3.713 150.313 1 95.62 ? N3B AP5 301 D 1 
HETATM 57 C C4B AP5 . . . J 2 13.161 3.398 149.277 1 97.59 ? C4B AP5 301 D 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           57 
#