data_4KOD
#
_model_server_result.job_id            NfPmn3_4p9X5RQmJvWN_wA 
_model_server_result.datetime_utc      '2024-12-02 21:00:08' 
_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          4kod 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":800}' 
#
_entry.id    4KOD 
#
_exptl.entry_id    4KOD 
_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    12 
_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            4KOD 
_cell.length_a            146.52 
_cell.length_b            170.737 
_cell.length_c            256.601 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KOD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 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 hexameric 6 author_and_software_defined_assembly 1 
PISA hexameric 6 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,M,N,O,P,Q,R,Y,Z,AA,BA,CA,DA 1 1 
G,H,I,J,K,L,S,T,U,V,W,X,EA,FA,GA,HA,IA,JA 2 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 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
? 2 S N N 
? 2 T N N 
? 2 U N N 
? 2 V N N 
? 2 W N N 
? 2 X 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                     4KOD 
_atom_sites.fract_transf_matrix[1][1]    0.006825 
_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]    0.005857 
_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]    0.003897 
_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
M 2 ADP A 1 800 800 ADP ADP . 
N 2 ADP B 1 800 800 ADP ADP . 
O 2 ADP C 1 800 800 ADP ADP . 
P 2 ADP D 1 800 800 ADP ADP . 
Q 2 ADP E 1 800 800 ADP ADP . 
R 2 ADP F 1 800 800 ADP ADP . 
S 2 ADP G 1 800 800 ADP ADP . 
T 2 ADP H 1 800 800 ADP ADP . 
U 2 ADP I 1 800 800 ADP ADP . 
V 2 ADP J 1 800 800 ADP ADP . 
W 2 ADP K 1 800 800 ADP ADP . 
X 2 ADP L 1 800 800 ADP ADP . 
Y 3 HOH A 1 901 38 HOH HOH . 
Y 3 HOH A 2 902 99 HOH HOH . 
Y 3 HOH A 3 903 119 HOH HOH . 
Y 3 HOH A 4 904 121 HOH HOH . 
Y 3 HOH A 5 905 125 HOH HOH . 
Y 3 HOH A 6 906 128 HOH HOH . 
Y 3 HOH A 7 907 129 HOH HOH . 
Y 3 HOH A 8 908 134 HOH HOH . 
Y 3 HOH A 9 909 196 HOH HOH . 
Y 3 HOH A 10 910 225 HOH HOH . 
Y 3 HOH A 11 911 230 HOH HOH . 
Y 3 HOH A 12 912 233 HOH HOH . 
Y 3 HOH A 13 913 235 HOH HOH . 
Y 3 HOH A 14 914 371 HOH HOH . 
Z 3 HOH B 1 901 29 HOH HOH . 
Z 3 HOH B 2 902 107 HOH HOH . 
Z 3 HOH B 3 903 118 HOH HOH . 
Z 3 HOH B 4 904 144 HOH HOH . 
Z 3 HOH B 5 905 227 HOH HOH . 
Z 3 HOH B 6 906 236 HOH HOH . 
Z 3 HOH B 7 907 248 HOH HOH . 
Z 3 HOH B 8 908 252 HOH HOH . 
Z 3 HOH B 9 909 373 HOH HOH . 
AA 3 HOH C 1 901 58 HOH HOH . 
AA 3 HOH C 2 902 109 HOH HOH . 
AA 3 HOH C 3 903 117 HOH HOH . 
AA 3 HOH C 4 904 145 HOH HOH . 
AA 3 HOH C 5 905 146 HOH HOH . 
AA 3 HOH C 6 906 148 HOH HOH . 
AA 3 HOH C 7 907 150 HOH HOH . 
AA 3 HOH C 8 908 181 HOH HOH . 
AA 3 HOH C 9 909 201 HOH HOH . 
AA 3 HOH C 10 910 237 HOH HOH . 
AA 3 HOH C 11 911 238 HOH HOH . 
AA 3 HOH C 12 912 259 HOH HOH . 
AA 3 HOH C 13 913 262 HOH HOH . 
AA 3 HOH C 14 914 376 HOH HOH . 
BA 3 HOH D 1 901 31 HOH HOH . 
BA 3 HOH D 2 902 41 HOH HOH . 
BA 3 HOH D 3 903 65 HOH HOH . 
BA 3 HOH D 4 904 153 HOH HOH . 
BA 3 HOH D 5 905 155 HOH HOH . 
BA 3 HOH D 6 906 203 HOH HOH . 
BA 3 HOH D 7 907 205 HOH HOH . 
BA 3 HOH D 8 908 206 HOH HOH . 
BA 3 HOH D 9 909 264 HOH HOH . 
BA 3 HOH D 10 910 265 HOH HOH . 
BA 3 HOH D 11 911 266 HOH HOH . 
BA 3 HOH D 12 912 268 HOH HOH . 
BA 3 HOH D 13 913 269 HOH HOH . 
BA 3 HOH D 14 914 271 HOH HOH . 
BA 3 HOH D 15 915 272 HOH HOH . 
BA 3 HOH D 16 916 273 HOH HOH . 
BA 3 HOH D 17 917 288 HOH HOH . 
CA 3 HOH E 1 901 7 HOH HOH . 
CA 3 HOH E 2 902 68 HOH HOH . 
CA 3 HOH E 3 903 100 HOH HOH . 
CA 3 HOH E 4 904 137 HOH HOH . 
CA 3 HOH E 5 905 156 HOH HOH . 
CA 3 HOH E 6 906 157 HOH HOH . 
CA 3 HOH E 7 907 158 HOH HOH . 
CA 3 HOH E 8 908 160 HOH HOH . 
CA 3 HOH E 9 909 170 HOH HOH . 
CA 3 HOH E 10 910 199 HOH HOH . 
CA 3 HOH E 11 911 210 HOH HOH . 
CA 3 HOH E 12 912 278 HOH HOH . 
CA 3 HOH E 13 913 281 HOH HOH . 
CA 3 HOH E 14 914 283 HOH HOH . 
CA 3 HOH E 15 915 286 HOH HOH . 
CA 3 HOH E 16 916 287 HOH HOH . 
CA 3 HOH E 17 917 377 HOH HOH . 
DA 3 HOH F 1 901 4 HOH HOH . 
DA 3 HOH F 2 902 5 HOH HOH . 
DA 3 HOH F 3 903 8 HOH HOH . 
DA 3 HOH F 4 904 9 HOH HOH . 
DA 3 HOH F 5 905 10 HOH HOH . 
DA 3 HOH F 6 906 19 HOH HOH . 
DA 3 HOH F 7 907 20 HOH HOH . 
DA 3 HOH F 8 908 71 HOH HOH . 
DA 3 HOH F 9 909 212 HOH HOH . 
DA 3 HOH F 10 910 213 HOH HOH . 
DA 3 HOH F 11 911 289 HOH HOH . 
DA 3 HOH F 12 912 290 HOH HOH . 
DA 3 HOH F 13 913 296 HOH HOH . 
DA 3 HOH F 14 914 297 HOH HOH . 
DA 3 HOH F 15 915 298 HOH HOH . 
EA 3 HOH G 1 901 11 HOH HOH . 
EA 3 HOH G 2 902 18 HOH HOH . 
EA 3 HOH G 3 903 22 HOH HOH . 
EA 3 HOH G 4 904 33 HOH HOH . 
EA 3 HOH G 5 905 43 HOH HOH . 
EA 3 HOH G 6 906 173 HOH HOH . 
EA 3 HOH G 7 907 209 HOH HOH . 
EA 3 HOH G 8 908 224 HOH HOH . 
EA 3 HOH G 9 909 240 HOH HOH . 
EA 3 HOH G 10 910 305 HOH HOH . 
EA 3 HOH G 11 911 306 HOH HOH . 
FA 3 HOH H 1 901 13 HOH HOH . 
FA 3 HOH H 2 902 46 HOH HOH . 
FA 3 HOH H 3 903 55 HOH HOH . 
FA 3 HOH H 4 904 66 HOH HOH . 
FA 3 HOH H 5 905 78 HOH HOH . 
FA 3 HOH H 6 906 79 HOH HOH . 
FA 3 HOH H 7 907 80 HOH HOH . 
FA 3 HOH H 8 908 83 HOH HOH . 
FA 3 HOH H 9 909 116 HOH HOH . 
FA 3 HOH H 10 910 172 HOH HOH . 
FA 3 HOH H 11 911 309 HOH HOH . 
FA 3 HOH H 12 912 313 HOH HOH . 
FA 3 HOH H 13 913 314 HOH HOH . 
FA 3 HOH H 14 914 316 HOH HOH . 
FA 3 HOH H 15 915 318 HOH HOH . 
FA 3 HOH H 16 916 319 HOH HOH . 
GA 3 HOH I 1 901 90 HOH HOH . 
GA 3 HOH I 2 902 98 HOH HOH . 
GA 3 HOH I 3 903 104 HOH HOH . 
GA 3 HOH I 4 904 112 HOH HOH . 
GA 3 HOH I 5 905 217 HOH HOH . 
GA 3 HOH I 6 906 226 HOH HOH . 
GA 3 HOH I 7 907 241 HOH HOH . 
GA 3 HOH I 8 908 321 HOH HOH . 
GA 3 HOH I 9 909 323 HOH HOH . 
GA 3 HOH I 10 910 324 HOH HOH . 
GA 3 HOH I 11 911 326 HOH HOH . 
HA 3 HOH J 1 901 82 HOH HOH . 
HA 3 HOH J 2 902 87 HOH HOH . 
HA 3 HOH J 3 903 105 HOH HOH . 
HA 3 HOH J 4 904 108 HOH HOH . 
HA 3 HOH J 5 905 163 HOH HOH . 
HA 3 HOH J 6 906 188 HOH HOH . 
HA 3 HOH J 7 907 218 HOH HOH . 
HA 3 HOH J 8 908 219 HOH HOH . 
HA 3 HOH J 9 909 243 HOH HOH . 
HA 3 HOH J 10 910 308 HOH HOH . 
HA 3 HOH J 11 911 310 HOH HOH . 
HA 3 HOH J 12 912 334 HOH HOH . 
HA 3 HOH J 13 913 336 HOH HOH . 
HA 3 HOH J 14 914 338 HOH HOH . 
HA 3 HOH J 15 915 339 HOH HOH . 
HA 3 HOH J 16 916 342 HOH HOH . 
HA 3 HOH J 17 917 350 HOH HOH . 
IA 3 HOH K 1 901 89 HOH HOH . 
IA 3 HOH K 2 902 93 HOH HOH . 
IA 3 HOH K 3 903 113 HOH HOH . 
IA 3 HOH K 4 904 115 HOH HOH . 
IA 3 HOH K 5 905 190 HOH HOH . 
IA 3 HOH K 6 906 193 HOH HOH . 
IA 3 HOH K 7 907 222 HOH HOH . 
IA 3 HOH K 8 908 352 HOH HOH . 
IA 3 HOH K 9 909 355 HOH HOH . 
IA 3 HOH K 10 910 357 HOH HOH . 
IA 3 HOH K 11 911 358 HOH HOH . 
JA 3 HOH L 1 901 17 HOH HOH . 
JA 3 HOH L 2 902 70 HOH HOH . 
JA 3 HOH L 3 903 94 HOH HOH . 
JA 3 HOH L 4 904 95 HOH HOH . 
JA 3 HOH L 5 905 165 HOH HOH . 
JA 3 HOH L 6 906 195 HOH HOH . 
JA 3 HOH L 7 907 362 HOH HOH . 
JA 3 HOH L 8 908 363 HOH HOH . 
JA 3 HOH L 9 909 364 HOH HOH . 
JA 3 HOH L 10 910 365 HOH HOH . 
JA 3 HOH L 11 911 366 HOH HOH . 
JA 3 HOH L 12 912 367 HOH HOH . 
JA 3 HOH L 13 913 368 HOH HOH . 
JA 3 HOH L 14 914 370 HOH HOH . 
JA 3 HOH L 15 915 379 HOH HOH . 
JA 3 HOH L 16 916 380 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 . . . O 2 29.913 16.791 89.531 1 91.7 ? PB ADP 800 C 1 
HETATM 2 O O1B ADP . . . O 2 30.514 18.184 89.624 1 93.93 ? O1B ADP 800 C 1 
HETATM 3 O O2B ADP . . . O 2 30.724 15.646 90.087 1 92.86 ? O2B ADP 800 C 1 
HETATM 4 O O3B ADP . . . O 2 29.381 16.523 88.148 1 90.96 ? O3B ADP 800 C 1 
HETATM 5 P PA ADP . . . O 2 27.645 18.123 90.607 1 89.01 ? PA ADP 800 C 1 
HETATM 6 O O1A ADP . . . O 2 27.803 18.654 92.001 1 91.16 ? O1A ADP 800 C 1 
HETATM 7 O O2A ADP . . . O 2 27.805 19.067 89.43 1 89.16 ? O2A ADP 800 C 1 
HETATM 8 O O3A ADP . . . O 2 28.588 16.804 90.464 1 89.47 ? O3A ADP 800 C 1 
HETATM 9 O O5' ADP . . . O 2 26.19 17.458 90.526 1 87.44 ? O5' ADP 800 C 1 
HETATM 10 C C5' ADP . . . O 2 25.929 16.248 91.225 1 87.05 ? C5' ADP 800 C 1 
HETATM 11 C C4' ADP . . . O 2 24.445 16.211 91.565 1 87.58 ? C4' ADP 800 C 1 
HETATM 12 O O4' ADP . . . O 2 24.047 14.941 92.088 1 87.93 ? O4' ADP 800 C 1 
HETATM 13 C C3' ADP . . . O 2 24.152 17.262 92.628 1 89.34 ? C3' ADP 800 C 1 
HETATM 14 O O3' ADP . . . O 2 22.963 17.978 92.335 1 90.83 ? O3' ADP 800 C 1 
HETATM 15 C C2' ADP . . . O 2 24 16.487 93.911 1 90.51 ? C2' ADP 800 C 1 
HETATM 16 O O2' ADP . . . O 2 22.777 16.835 94.568 1 92.33 ? O2' ADP 800 C 1 
HETATM 17 C C1' ADP . . . O 2 23.99 15.018 93.509 1 89.81 ? C1' ADP 800 C 1 
HETATM 18 N N9 ADP . . . O 2 25.153 14.288 94.054 1 91.51 ? N9 ADP 800 C 1 
HETATM 19 C C8 ADP . . . O 2 26.178 13.807 93.334 1 91.76 ? C8 ADP 800 C 1 
HETATM 20 N N7 ADP . . . O 2 27.074 13.18 94.125 1 94.6 ? N7 ADP 800 C 1 
HETATM 21 C C5 ADP . . . O 2 26.616 13.246 95.379 1 96.86 ? C5 ADP 800 C 1 
HETATM 22 C C6 ADP . . . O 2 27.083 12.772 96.702 1 101.74 ? C6 ADP 800 C 1 
HETATM 23 N N6 ADP . . . O 2 28.243 12.088 96.825 1 105.24 ? N6 ADP 800 C 1 
HETATM 24 N N1 ADP . . . O 2 26.31 13.04 97.772 1 103.54 ? N1 ADP 800 C 1 
HETATM 25 C C2 ADP . . . O 2 25.152 13.723 97.654 1 101.43 ? C2 ADP 800 C 1 
HETATM 26 N N3 ADP . . . O 2 24.674 14.186 96.484 1 97.63 ? N3 ADP 800 C 1 
HETATM 27 C C4 ADP . . . O 2 25.349 13.981 95.329 1 94.79 ? C4 ADP 800 C 1 
#
_model_server_stats.io_time_ms              82 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    51 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#