data_6BDQ
#
_model_server_result.job_id            JBrTOH1We_1jsXmBFuIUJQ 
_model_server_result.datetime_utc      '2024-10-19 08:42:58' 
_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          6bdq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    6BDQ 
#
_exptl.entry_id    6BDQ 
_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-3'-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    1 
_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            6BDQ 
_cell.length_a            139.447 
_cell.length_b            38.668 
_cell.length_c            54.14 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6BDQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        18 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 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 1 1 
A,B,C,D 2 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' 2_755 -x+2,-y,z -1 0 0 0 -1 0 0 0 1 278.894 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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
covale ? covale1 A C GLN 234 A GLN 232 1_555 A N SME 235 A SME 233 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C SME 235 A SME 233 1_555 A N THR 236 A THR 234 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_chem_comp.formula           'C10 H15 N5 O10 P2' 
_chem_comp.formula_weight    427.201 
_chem_comp.id                A3P 
_chem_comp.mon_nstd_flag     n 
_chem_comp.name              "ADENOSINE-3'-5'-DIPHOSPHATE" 
_chem_comp.type              'rna linking' 
_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
P1 O1P A3P doub 1 n n 
P1 O2P A3P sing 2 n n 
P1 O3P A3P sing 3 n n 
P1 O3' A3P sing 4 n n 
O2P HOP2 A3P sing 5 n n 
O3P HOP3 A3P sing 6 n n 
P2 O4P A3P doub 7 n n 
P2 O5P A3P sing 8 n n 
P2 O6P A3P sing 9 n n 
P2 O5' A3P sing 10 n n 
O5P HOP5 A3P sing 11 n n 
O6P HOP6 A3P sing 12 n n 
O5' C5' A3P sing 13 n n 
C5' C4' A3P sing 14 n n 
C5' "H5'1" A3P sing 15 n n 
C5' "H5'2" A3P sing 16 n n 
C4' O4' A3P sing 17 n n 
C4' C3' A3P sing 18 n n 
C4' H4' A3P sing 19 n n 
O4' C1' A3P sing 20 n n 
C3' O3' A3P sing 21 n n 
C3' C2' A3P sing 22 n n 
C3' H3' A3P sing 23 n n 
C2' O2' A3P sing 24 n n 
C2' C1' A3P sing 25 n n 
C2' H2' A3P sing 26 n n 
O2' HO2' A3P sing 27 n n 
C1' N9 A3P sing 28 n n 
C1' H1' A3P sing 29 n n 
N9 C8 A3P sing 30 n y 
N9 C4 A3P sing 31 n y 
C8 N7 A3P doub 32 n y 
C8 H8 A3P sing 33 n n 
N7 C5 A3P sing 34 n y 
C5 C6 A3P sing 35 n y 
C5 C4 A3P doub 36 n y 
C6 N6 A3P sing 37 n n 
C6 N1 A3P doub 38 n y 
N6 HN61 A3P sing 39 n n 
N6 HN62 A3P sing 40 n n 
N1 C2 A3P sing 41 n y 
C2 N3 A3P doub 42 n y 
C2 H2 A3P sing 43 n n 
N3 C4 A3P sing 44 n y 
#
_atom_sites.entry_id                     6BDQ 
_atom_sites.fract_transf_matrix[1][1]    0.007171 
_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]    0.025861 
_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]    0.018471 
_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
B 2 A3P A 1 301 301 A3P A3P . 
C 3 DE7 A 1 302 302 DE7 74 . 
D 4 HOH A 1 401 99 HOH HOH . 
D 4 HOH A 2 402 62 HOH HOH . 
D 4 HOH A 3 403 85 HOH HOH . 
D 4 HOH A 4 404 71 HOH HOH . 
D 4 HOH A 5 405 73 HOH HOH . 
D 4 HOH A 6 406 91 HOH HOH . 
D 4 HOH A 7 407 8 HOH HOH . 
D 4 HOH A 8 408 39 HOH HOH . 
D 4 HOH A 9 409 69 HOH HOH . 
D 4 HOH A 10 410 105 HOH HOH . 
D 4 HOH A 11 411 36 HOH HOH . 
D 4 HOH A 12 412 79 HOH HOH . 
D 4 HOH A 13 413 24 HOH HOH . 
D 4 HOH A 14 414 57 HOH HOH . 
D 4 HOH A 15 415 75 HOH HOH . 
D 4 HOH A 16 416 84 HOH HOH . 
D 4 HOH A 17 417 54 HOH HOH . 
D 4 HOH A 18 418 9 HOH HOH . 
D 4 HOH A 19 419 93 HOH HOH . 
D 4 HOH A 20 420 16 HOH HOH . 
D 4 HOH A 21 421 70 HOH HOH . 
D 4 HOH A 22 422 14 HOH HOH . 
D 4 HOH A 23 423 3 HOH HOH . 
D 4 HOH A 24 424 68 HOH HOH . 
D 4 HOH A 25 425 35 HOH HOH . 
D 4 HOH A 26 426 28 HOH HOH . 
D 4 HOH A 27 427 5 HOH HOH . 
D 4 HOH A 28 428 19 HOH HOH . 
D 4 HOH A 29 429 122 HOH HOH . 
D 4 HOH A 30 430 89 HOH HOH . 
D 4 HOH A 31 431 1 HOH HOH . 
D 4 HOH A 32 432 49 HOH HOH . 
D 4 HOH A 33 433 10 HOH HOH . 
D 4 HOH A 34 434 27 HOH HOH . 
D 4 HOH A 35 435 17 HOH HOH . 
D 4 HOH A 36 436 65 HOH HOH . 
D 4 HOH A 37 437 82 HOH HOH . 
D 4 HOH A 38 438 26 HOH HOH . 
D 4 HOH A 39 439 44 HOH HOH . 
D 4 HOH A 40 440 101 HOH HOH . 
D 4 HOH A 41 441 7 HOH HOH . 
D 4 HOH A 42 442 22 HOH HOH . 
D 4 HOH A 43 443 4 HOH HOH . 
D 4 HOH A 44 444 77 HOH HOH . 
D 4 HOH A 45 445 66 HOH HOH . 
D 4 HOH A 46 446 53 HOH HOH . 
D 4 HOH A 47 447 43 HOH HOH . 
D 4 HOH A 48 448 33 HOH HOH . 
D 4 HOH A 49 449 13 HOH HOH . 
D 4 HOH A 50 450 64 HOH HOH . 
D 4 HOH A 51 451 60 HOH HOH . 
D 4 HOH A 52 452 76 HOH HOH . 
D 4 HOH A 53 453 90 HOH HOH . 
D 4 HOH A 54 454 6 HOH HOH . 
D 4 HOH A 55 455 67 HOH HOH . 
D 4 HOH A 56 456 98 HOH HOH . 
D 4 HOH A 57 457 88 HOH HOH . 
D 4 HOH A 58 458 29 HOH HOH . 
D 4 HOH A 59 459 55 HOH HOH . 
D 4 HOH A 60 460 18 HOH HOH . 
D 4 HOH A 61 461 81 HOH HOH . 
D 4 HOH A 62 462 20 HOH HOH . 
D 4 HOH A 63 463 63 HOH HOH . 
D 4 HOH A 64 464 34 HOH HOH . 
D 4 HOH A 65 465 38 HOH HOH . 
D 4 HOH A 66 466 47 HOH HOH . 
D 4 HOH A 67 467 32 HOH HOH . 
D 4 HOH A 68 468 56 HOH HOH . 
D 4 HOH A 69 469 59 HOH HOH . 
D 4 HOH A 70 470 100 HOH HOH . 
D 4 HOH A 71 471 45 HOH HOH . 
D 4 HOH A 72 472 124 HOH HOH . 
D 4 HOH A 73 473 95 HOH HOH . 
D 4 HOH A 74 474 119 HOH HOH . 
D 4 HOH A 75 475 31 HOH HOH . 
D 4 HOH A 76 476 37 HOH HOH . 
D 4 HOH A 77 477 118 HOH HOH . 
D 4 HOH A 78 478 46 HOH HOH . 
D 4 HOH A 79 479 72 HOH HOH . 
D 4 HOH A 80 480 21 HOH HOH . 
D 4 HOH A 81 481 12 HOH HOH . 
D 4 HOH A 82 482 108 HOH HOH . 
D 4 HOH A 83 483 40 HOH HOH . 
D 4 HOH A 84 484 94 HOH HOH . 
D 4 HOH A 85 485 15 HOH HOH . 
D 4 HOH A 86 486 106 HOH HOH . 
D 4 HOH A 87 487 30 HOH HOH . 
D 4 HOH A 88 488 102 HOH HOH . 
D 4 HOH A 89 489 50 HOH HOH . 
D 4 HOH A 90 490 120 HOH HOH . 
D 4 HOH A 91 491 121 HOH HOH . 
D 4 HOH A 92 492 23 HOH HOH . 
D 4 HOH A 93 493 41 HOH HOH . 
D 4 HOH A 94 494 107 HOH HOH . 
D 4 HOH A 95 495 83 HOH HOH . 
D 4 HOH A 96 496 103 HOH HOH . 
D 4 HOH A 97 497 52 HOH HOH . 
D 4 HOH A 98 498 48 HOH HOH . 
D 4 HOH A 99 499 116 HOH HOH . 
D 4 HOH A 100 500 51 HOH HOH . 
D 4 HOH A 101 501 42 HOH HOH . 
D 4 HOH A 102 502 58 HOH HOH . 
D 4 HOH A 103 503 112 HOH HOH . 
D 4 HOH A 104 504 111 HOH HOH . 
D 4 HOH A 105 505 92 HOH HOH . 
D 4 HOH A 106 506 78 HOH HOH . 
D 4 HOH A 107 507 125 HOH HOH . 
D 4 HOH A 108 508 61 HOH HOH . 
D 4 HOH A 109 509 2 HOH HOH . 
D 4 HOH A 110 510 127 HOH HOH . 
D 4 HOH A 111 511 115 HOH HOH . 
D 4 HOH A 112 512 123 HOH HOH . 
D 4 HOH A 113 513 96 HOH HOH . 
D 4 HOH A 114 514 114 HOH HOH . 
D 4 HOH A 115 515 110 HOH HOH . 
D 4 HOH A 116 516 117 HOH HOH . 
D 4 HOH A 117 517 25 HOH HOH . 
D 4 HOH A 118 518 87 HOH HOH . 
D 4 HOH A 119 519 86 HOH HOH . 
D 4 HOH A 120 520 109 HOH HOH . 
D 4 HOH A 121 521 113 HOH HOH . 
D 4 HOH A 122 522 104 HOH HOH . 
D 4 HOH A 123 523 126 HOH HOH . 
D 4 HOH A 124 524 80 HOH HOH . 
D 4 HOH A 125 525 74 HOH HOH . 
D 4 HOH A 126 526 11 HOH HOH . 
D 4 HOH A 127 527 97 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 P1 A3P . . . B 2 109.38 -4.454 13.904 1 19.08 ? P1 A3P 301 A 1 
HETATM 2 O O1P A3P . . . B 2 109.125 -5.274 12.675 1 18.56 ? O1P A3P 301 A 1 
HETATM 3 O O2P A3P . . . B 2 108.729 -3.092 13.848 1 20.73 ? O2P A3P 301 A 1 
HETATM 4 O O3P A3P . . . B 2 109.17 -5.153 15.215 1 20.75 ? O3P A3P 301 A 1 
HETATM 5 P P2 A3P . . . B 2 114.678 0.738 14.453 1 18.23 ? P2 A3P 301 A 1 
HETATM 6 O O4P A3P . . . B 2 115.726 0.936 13.395 1 19.2 ? O4P A3P 301 A 1 
HETATM 7 O O5P A3P . . . B 2 115.18 0.667 15.882 1 17.6 ? O5P A3P 301 A 1 
HETATM 8 O O6P A3P . . . B 2 113.435 1.564 14.31 1 19.16 ? O6P A3P 301 A 1 
HETATM 9 O O5' A3P . . . B 2 114.255 -0.785 14.098 1 17.99 ? O5' A3P 301 A 1 
HETATM 10 C C5' A3P . . . B 2 113.276 -1.474 14.883 1 16.1 ? C5' A3P 301 A 1 
HETATM 11 C C4' A3P . . . B 2 112.886 -2.787 14.192 1 18.65 ? C4' A3P 301 A 1 
HETATM 12 O O4' A3P . . . B 2 113.956 -3.725 14.326 1 18.98 ? O4' A3P 301 A 1 
HETATM 13 C C3' A3P . . . B 2 111.682 -3.461 14.841 1 18.25 ? C3' A3P 301 A 1 
HETATM 14 O O3' A3P . . . B 2 110.987 -4.224 13.84 1 18.19 ? O3' A3P 301 A 1 
HETATM 15 C C2' A3P . . . B 2 112.314 -4.383 15.862 1 18.64 ? C2' A3P 301 A 1 
HETATM 16 O O2' A3P . . . B 2 111.445 -5.455 16.247 1 20.93 ? O2' A3P 301 A 1 
HETATM 17 C C1' A3P . . . B 2 113.514 -4.864 15.069 1 19.27 ? C1' A3P 301 A 1 
HETATM 18 N N9 A3P . . . B 2 114.627 -5.296 15.927 1 21.32 ? N9 A3P 301 A 1 
HETATM 19 C C8 A3P . . . B 2 115.339 -4.541 16.792 1 20.58 ? C8 A3P 301 A 1 
HETATM 20 N N7 A3P . . . B 2 116.302 -5.286 17.41 1 18.49 ? N7 A3P 301 A 1 
HETATM 21 C C5 A3P . . . B 2 116.197 -6.537 16.908 1 22.79 ? C5 A3P 301 A 1 
HETATM 22 C C6 A3P . . . B 2 116.891 -7.821 17.122 1 23.23 ? C6 A3P 301 A 1 
HETATM 23 N N6 A3P . . . B 2 117.912 -7.894 18 1 23.7 ? N6 A3P 301 A 1 
HETATM 24 N N1 A3P . . . B 2 116.469 -8.896 16.421 1 21.45 ? N1 A3P 301 A 1 
HETATM 25 C C2 A3P . . . B 2 115.444 -8.807 15.542 1 26 ? C2 A3P 301 A 1 
HETATM 26 N N3 A3P . . . B 2 114.748 -7.681 15.287 1 18.49 ? N3 A3P 301 A 1 
HETATM 27 C C4 A3P . . . B 2 115.081 -6.539 15.945 1 23.06 ? C4 A3P 301 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           345 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#