data_5XB2
#
_model_server_result.job_id            n2GGzHci2pJ3z168SI7Wdg 
_model_server_result.datetime_utc      '2024-11-05 10:42:15' 
_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          5xb2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":201}' 
#
_entry.id    5XB2 
#
_exptl.entry_id    5XB2 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         88.9 
_cell.angle_beta          90.83 
_cell.angle_gamma         70.53 
_cell.entry_id            5XB2 
_cell.length_a            42.62 
_cell.length_b            52.99 
_cell.length_c            54.019 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XB2 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 I 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 A OG1 THR 14 B THR 14 1_555 E MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? 
metalc ? metalc2 D O1P TMP . B TMP 202 1_555 E MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.821 ? 
metalc ? metalc3 D O2P TMP . B TMP 202 1_555 E MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? 
#
_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                     5XB2 
_atom_sites.fract_transf_matrix[1][1]    0.023463 
_atom_sites.fract_transf_matrix[1][2]    -0.008295 
_atom_sites.fract_transf_matrix[1][3]    0.000551 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020016 
_atom_sites.fract_transf_matrix[2][3]    -0.00051 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.01852 
_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
C 2 ADP B 1 201 1 ADP ADP . 
D 3 TMP B 1 202 1 TMP TMP . 
E 4 MG B 1 203 3 MG MG . 
F 5 F B 1 204 1 F F . 
G 5 F B 1 205 4 F F . 
H 5 F B 1 206 5 F F . 
I 2 ADP A 1 201 2 ADP ADP . 
J 3 TMP A 1 202 2 TMP TMP . 
K 6 HOH B 1 301 91 HOH HOH . 
K 6 HOH B 2 302 133 HOH HOH . 
K 6 HOH B 3 303 39 HOH HOH . 
K 6 HOH B 4 304 16 HOH HOH . 
K 6 HOH B 5 305 49 HOH HOH . 
K 6 HOH B 6 306 132 HOH HOH . 
K 6 HOH B 7 307 45 HOH HOH . 
K 6 HOH B 8 308 145 HOH HOH . 
K 6 HOH B 9 309 61 HOH HOH . 
K 6 HOH B 10 310 62 HOH HOH . 
K 6 HOH B 11 311 68 HOH HOH . 
K 6 HOH B 12 312 54 HOH HOH . 
K 6 HOH B 13 313 135 HOH HOH . 
K 6 HOH B 14 314 15 HOH HOH . 
K 6 HOH B 15 315 88 HOH HOH . 
K 6 HOH B 16 316 46 HOH HOH . 
K 6 HOH B 17 317 48 HOH HOH . 
K 6 HOH B 18 318 52 HOH HOH . 
K 6 HOH B 19 319 33 HOH HOH . 
K 6 HOH B 20 320 37 HOH HOH . 
K 6 HOH B 21 321 44 HOH HOH . 
K 6 HOH B 22 322 105 HOH HOH . 
K 6 HOH B 23 323 75 HOH HOH . 
K 6 HOH B 24 324 136 HOH HOH . 
K 6 HOH B 25 325 41 HOH HOH . 
K 6 HOH B 26 326 60 HOH HOH . 
K 6 HOH B 27 327 31 HOH HOH . 
K 6 HOH B 28 328 32 HOH HOH . 
K 6 HOH B 29 329 66 HOH HOH . 
K 6 HOH B 30 330 36 HOH HOH . 
K 6 HOH B 31 331 92 HOH HOH . 
K 6 HOH B 32 332 38 HOH HOH . 
K 6 HOH B 33 333 35 HOH HOH . 
K 6 HOH B 34 334 51 HOH HOH . 
K 6 HOH B 35 335 87 HOH HOH . 
K 6 HOH B 36 336 138 HOH HOH . 
K 6 HOH B 37 337 40 HOH HOH . 
K 6 HOH B 38 338 139 HOH HOH . 
K 6 HOH B 39 339 30 HOH HOH . 
K 6 HOH B 40 340 67 HOH HOH . 
K 6 HOH B 41 341 77 HOH HOH . 
K 6 HOH B 42 342 89 HOH HOH . 
K 6 HOH B 43 343 95 HOH HOH . 
K 6 HOH B 44 344 71 HOH HOH . 
K 6 HOH B 45 345 74 HOH HOH . 
K 6 HOH B 46 346 81 HOH HOH . 
K 6 HOH B 47 347 82 HOH HOH . 
K 6 HOH B 48 348 43 HOH HOH . 
K 6 HOH B 49 349 59 HOH HOH . 
K 6 HOH B 50 350 93 HOH HOH . 
K 6 HOH B 51 351 79 HOH HOH . 
K 6 HOH B 52 352 72 HOH HOH . 
K 6 HOH B 53 353 78 HOH HOH . 
K 6 HOH B 54 354 134 HOH HOH . 
K 6 HOH B 55 355 96 HOH HOH . 
K 6 HOH B 56 356 104 HOH HOH . 
K 6 HOH B 57 357 57 HOH HOH . 
K 6 HOH B 58 358 119 HOH HOH . 
K 6 HOH B 59 359 53 HOH HOH . 
K 6 HOH B 60 360 63 HOH HOH . 
K 6 HOH B 61 361 103 HOH HOH . 
K 6 HOH B 62 362 14 HOH HOH . 
K 6 HOH B 63 363 55 HOH HOH . 
K 6 HOH B 64 364 64 HOH HOH . 
K 6 HOH B 65 365 58 HOH HOH . 
K 6 HOH B 66 366 101 HOH HOH . 
K 6 HOH B 67 367 29 HOH HOH . 
K 6 HOH B 68 368 90 HOH HOH . 
K 6 HOH B 69 369 69 HOH HOH . 
K 6 HOH B 70 370 94 HOH HOH . 
K 6 HOH B 71 371 50 HOH HOH . 
K 6 HOH B 72 372 73 HOH HOH . 
K 6 HOH B 73 373 21 HOH HOH . 
K 6 HOH B 74 374 42 HOH HOH . 
K 6 HOH B 75 375 76 HOH HOH . 
K 6 HOH B 76 376 102 HOH HOH . 
K 6 HOH B 77 377 17 HOH HOH . 
K 6 HOH B 78 378 70 HOH HOH . 
K 6 HOH B 79 379 56 HOH HOH . 
K 6 HOH B 80 380 80 HOH HOH . 
K 6 HOH B 81 381 137 HOH HOH . 
L 6 HOH A 1 301 117 HOH HOH . 
L 6 HOH A 2 302 99 HOH HOH . 
L 6 HOH A 3 303 11 HOH HOH . 
L 6 HOH A 4 304 98 HOH HOH . 
L 6 HOH A 5 305 115 HOH HOH . 
L 6 HOH A 6 306 8 HOH HOH . 
L 6 HOH A 7 307 24 HOH HOH . 
L 6 HOH A 8 308 20 HOH HOH . 
L 6 HOH A 9 309 106 HOH HOH . 
L 6 HOH A 10 310 141 HOH HOH . 
L 6 HOH A 11 311 118 HOH HOH . 
L 6 HOH A 12 312 114 HOH HOH . 
L 6 HOH A 13 313 143 HOH HOH . 
L 6 HOH A 14 314 121 HOH HOH . 
L 6 HOH A 15 315 127 HOH HOH . 
L 6 HOH A 16 316 107 HOH HOH . 
L 6 HOH A 17 317 10 HOH HOH . 
L 6 HOH A 18 318 4 HOH HOH . 
L 6 HOH A 19 319 13 HOH HOH . 
L 6 HOH A 20 320 83 HOH HOH . 
L 6 HOH A 21 321 9 HOH HOH . 
L 6 HOH A 22 322 126 HOH HOH . 
L 6 HOH A 23 323 125 HOH HOH . 
L 6 HOH A 24 324 12 HOH HOH . 
L 6 HOH A 25 325 97 HOH HOH . 
L 6 HOH A 26 326 129 HOH HOH . 
L 6 HOH A 27 327 28 HOH HOH . 
L 6 HOH A 28 328 1 HOH HOH . 
L 6 HOH A 29 329 27 HOH HOH . 
L 6 HOH A 30 330 86 HOH HOH . 
L 6 HOH A 31 331 122 HOH HOH . 
L 6 HOH A 32 332 130 HOH HOH . 
L 6 HOH A 33 333 131 HOH HOH . 
L 6 HOH A 34 334 5 HOH HOH . 
L 6 HOH A 35 335 2 HOH HOH . 
L 6 HOH A 36 336 3 HOH HOH . 
L 6 HOH A 37 337 123 HOH HOH . 
L 6 HOH A 38 338 25 HOH HOH . 
L 6 HOH A 39 339 23 HOH HOH . 
L 6 HOH A 40 340 120 HOH HOH . 
L 6 HOH A 41 341 128 HOH HOH . 
L 6 HOH A 42 342 113 HOH HOH . 
L 6 HOH A 43 343 112 HOH HOH . 
L 6 HOH A 44 344 110 HOH HOH . 
L 6 HOH A 45 345 142 HOH HOH . 
L 6 HOH A 46 346 111 HOH HOH . 
L 6 HOH A 47 347 144 HOH HOH . 
L 6 HOH A 48 348 18 HOH HOH . 
L 6 HOH A 49 349 116 HOH HOH . 
L 6 HOH A 50 350 85 HOH HOH . 
L 6 HOH A 51 351 84 HOH HOH . 
L 6 HOH A 52 352 47 HOH HOH . 
L 6 HOH A 53 353 140 HOH HOH . 
L 6 HOH A 54 354 19 HOH HOH . 
L 6 HOH A 55 355 109 HOH HOH . 
L 6 HOH A 56 356 100 HOH HOH . 
L 6 HOH A 57 357 26 HOH HOH . 
L 6 HOH A 58 358 7 HOH HOH . 
L 6 HOH A 59 359 124 HOH HOH . 
L 6 HOH A 60 360 22 HOH HOH . 
L 6 HOH A 61 361 108 HOH HOH . 
L 6 HOH A 62 362 6 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 . . . I 2 19.737 50.23 7.143 1 25.48 ? PB ADP 201 A 1 
HETATM 2 O O1B ADP . . . I 2 19.747 51.462 6.268 1 21.55 ? O1B ADP 201 A 1 
HETATM 3 O O2B ADP . . . I 2 18.47 49.399 7.019 1 26.27 ? O2B ADP 201 A 1 
HETATM 4 O O3B ADP . . . I 2 21.01 49.413 7.162 1 18.64 ? O3B ADP 201 A 1 
HETATM 5 P PA ADP . . . I 2 18.941 50.297 9.887 1 30.82 ? PA ADP 201 A 1 
HETATM 6 O O1A ADP . . . I 2 17.524 50.802 9.77 1 24.38 ? O1A ADP 201 A 1 
HETATM 7 O O2A ADP . . . I 2 19.239 48.838 10.092 1 18.97 ? O2A ADP 201 A 1 
HETATM 8 O O3A ADP . . . I 2 19.714 50.886 8.604 1 26.52 ? O3A ADP 201 A 1 
HETATM 9 O O5' ADP . . . I 2 19.736 51.137 11.019 1 33.47 ? O5' ADP 201 A 1 
HETATM 10 C C5' ADP . . . I 2 21.104 50.844 11.347 1 30.32 ? C5' ADP 201 A 1 
HETATM 11 C C4' ADP . . . I 2 21.359 51.084 12.835 1 24.68 ? C4' ADP 201 A 1 
HETATM 12 O O4' ADP . . . I 2 21.245 52.477 13.168 1 31.22 ? O4' ADP 201 A 1 
HETATM 13 C C3' ADP . . . I 2 20.347 50.337 13.687 1 33.49 ? C3' ADP 201 A 1 
HETATM 14 O O3' ADP . . . I 2 21.018 49.699 14.779 1 28.93 ? O3' ADP 201 A 1 
HETATM 15 C C2' ADP . . . I 2 19.424 51.421 14.217 1 28.34 ? C2' ADP 201 A 1 
HETATM 16 O O2' ADP . . . I 2 18.925 51.055 15.502 1 33.71 ? O2' ADP 201 A 1 
HETATM 17 C C1' ADP . . . I 2 20.296 52.67 14.218 1 25.11 ? C1' ADP 201 A 1 
HETATM 18 N N9 ADP . . . I 2 19.507 53.866 13.867 1 26.32 ? N9 ADP 201 A 1 
HETATM 19 C C8 ADP . . . I 2 18.399 53.876 13.102 1 29.39 ? C8 ADP 201 A 1 
HETATM 20 N N7 ADP . . . I 2 17.914 55.132 12.966 1 28.01 ? N7 ADP 201 A 1 
HETATM 21 C C5 ADP . . . I 2 18.724 55.951 13.666 1 29.24 ? C5 ADP 201 A 1 
HETATM 22 C C6 ADP . . . I 2 18.793 57.407 13.953 1 31.39 ? C6 ADP 201 A 1 
HETATM 23 N N6 ADP . . . I 2 17.865 58.259 13.446 1 27.32 ? N6 ADP 201 A 1 
HETATM 24 N N1 ADP . . . I 2 19.814 57.856 14.73 1 23.69 ? N1 ADP 201 A 1 
HETATM 25 C C2 ADP . . . I 2 20.74 57.022 15.238 1 23.52 ? C2 ADP 201 A 1 
HETATM 26 N N3 ADP . . . I 2 20.741 55.694 15.027 1 32.92 ? N3 ADP 201 A 1 
HETATM 27 C C4 ADP . . . I 2 19.776 55.109 14.258 1 34.43 ? C4 ADP 201 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#