data_3V80
#
_model_server_result.job_id            L-6BEea0eLjKKUT9PaZ5mQ 
_model_server_result.datetime_utc      '2024-11-28 06:08:04' 
_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          3v80 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":302}' 
#
_entry.id    3V80 
#
_exptl.entry_id    3V80 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              305.289 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-O-prop-2-yn-1-yladenosine" 
_entity.pdbx_number_of_molecules    2 
_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            3V80 
_cell.length_a            62.961 
_cell.length_b            75.172 
_cell.length_c            118.531 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3V80 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 62.961 0 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 62.961 0 0 
4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C N N 
#
_chem_comp.formula           'C13 H15 N5 O4' 
_chem_comp.formula_weight    305.289 
_chem_comp.id                AOC 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-O-prop-2-yn-1-yladenosine" 
_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
N6 C6 AOC sing 13 n n 
N7 C5 AOC sing 14 n y 
N7 C8 AOC doub 15 n y 
C6 C5 AOC doub 16 n y 
C6 N1 AOC sing 17 n y 
C5 C4 AOC sing 18 n y 
C8 N9 AOC sing 19 n y 
N1 C2 AOC doub 20 n y 
O2' C2' AOC sing 21 n n 
C2' C3' AOC sing 22 n n 
C2' C1' AOC sing 23 n n 
C4 N9 AOC sing 24 n y 
C4 N3 AOC doub 25 n y 
N9 C1' AOC sing 26 n n 
C2 N3 AOC sing 27 n y 
O3' C3' AOC sing 28 n n 
C3' C4' AOC sing 29 n n 
C1' O4' AOC sing 30 n n 
O4' C4' AOC sing 31 n n 
C4' C5' AOC sing 32 n n 
C5' O5' AOC sing 33 n n 
O5' CAH AOC sing 34 n n 
CAH CAE AOC sing 35 n n 
CAE CAA AOC trip 36 n n 
CAA HAA AOC sing 37 n n 
CAH HAH1 AOC sing 38 n n 
CAH HAH2 AOC sing 39 n n 
C5' H5' AOC sing 40 n n 
C5' "H5''" AOC sing 41 n n 
C4' H4' AOC sing 42 n n 
C3' H3' AOC sing 43 n n 
O3' HO3' AOC sing 44 n n 
C2' H2' AOC sing 45 n n 
O2' HO2' AOC sing 46 n n 
C1' H1' AOC sing 47 n n 
C8 H8 AOC sing 48 n n 
C2 H2 AOC sing 49 n n 
N6 H61 AOC sing 50 n n 
N6 H62 AOC sing 51 n n 
#
_atom_sites.entry_id                     3V80 
_atom_sites.fract_transf_matrix[1][1]    0.015883 
_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]    0.013303 
_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]    0.008437 
_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 AOC A 1 301 1 AOC AOC . 
C 2 AOC A 1 302 2 AOC AOC . 
D 3 CIT A 1 303 1 CIT CIT . 
E 4 GOL A 1 304 3 GOL GOL . 
F 5 HOH A 1 401 1 HOH HOH . 
F 5 HOH A 2 402 2 HOH HOH . 
F 5 HOH A 3 403 3 HOH HOH . 
F 5 HOH A 4 404 4 HOH HOH . 
F 5 HOH A 5 405 5 HOH HOH . 
F 5 HOH A 6 406 6 HOH HOH . 
F 5 HOH A 7 407 7 HOH HOH . 
F 5 HOH A 8 408 8 HOH HOH . 
F 5 HOH A 9 409 9 HOH HOH . 
F 5 HOH A 10 410 10 HOH HOH . 
F 5 HOH A 11 411 11 HOH HOH . 
F 5 HOH A 12 412 12 HOH HOH . 
F 5 HOH A 13 413 13 HOH HOH . 
F 5 HOH A 14 414 14 HOH HOH . 
F 5 HOH A 15 415 15 HOH HOH . 
F 5 HOH A 16 416 16 HOH HOH . 
F 5 HOH A 17 417 18 HOH HOH . 
F 5 HOH A 18 418 19 HOH HOH . 
F 5 HOH A 19 419 20 HOH HOH . 
F 5 HOH A 20 420 21 HOH HOH . 
F 5 HOH A 21 421 22 HOH HOH . 
F 5 HOH A 22 422 23 HOH HOH . 
F 5 HOH A 23 423 25 HOH HOH . 
F 5 HOH A 24 424 26 HOH HOH . 
F 5 HOH A 25 425 27 HOH HOH . 
F 5 HOH A 26 426 28 HOH HOH . 
F 5 HOH A 27 427 29 HOH HOH . 
F 5 HOH A 28 428 31 HOH HOH . 
F 5 HOH A 29 429 32 HOH HOH . 
F 5 HOH A 30 430 33 HOH HOH . 
F 5 HOH A 31 431 34 HOH HOH . 
F 5 HOH A 32 432 36 HOH HOH . 
F 5 HOH A 33 433 37 HOH HOH . 
F 5 HOH A 34 434 38 HOH HOH . 
F 5 HOH A 35 435 40 HOH HOH . 
F 5 HOH A 36 436 41 HOH HOH . 
F 5 HOH A 37 437 42 HOH HOH . 
F 5 HOH A 38 438 43 HOH HOH . 
F 5 HOH A 39 439 46 HOH HOH . 
F 5 HOH A 40 440 47 HOH HOH . 
F 5 HOH A 41 441 48 HOH HOH . 
F 5 HOH A 42 442 49 HOH HOH . 
F 5 HOH A 43 443 50 HOH HOH . 
F 5 HOH A 44 444 51 HOH HOH . 
F 5 HOH A 45 445 52 HOH HOH . 
F 5 HOH A 46 446 53 HOH HOH . 
F 5 HOH A 47 447 54 HOH HOH . 
F 5 HOH A 48 448 55 HOH HOH . 
F 5 HOH A 49 449 56 HOH HOH . 
F 5 HOH A 50 450 59 HOH HOH . 
F 5 HOH A 51 451 60 HOH HOH . 
F 5 HOH A 52 452 61 HOH HOH . 
F 5 HOH A 53 453 63 HOH HOH . 
F 5 HOH A 54 454 64 HOH HOH . 
F 5 HOH A 55 455 65 HOH HOH . 
F 5 HOH A 56 456 66 HOH HOH . 
F 5 HOH A 57 457 67 HOH HOH . 
F 5 HOH A 58 458 68 HOH HOH . 
F 5 HOH A 59 459 70 HOH HOH . 
F 5 HOH A 60 460 71 HOH HOH . 
F 5 HOH A 61 461 72 HOH HOH . 
F 5 HOH A 62 462 73 HOH HOH . 
F 5 HOH A 63 463 75 HOH HOH . 
F 5 HOH A 64 464 76 HOH HOH . 
F 5 HOH A 65 465 77 HOH HOH . 
F 5 HOH A 66 466 80 HOH HOH . 
F 5 HOH A 67 467 81 HOH HOH . 
F 5 HOH A 68 468 86 HOH HOH . 
F 5 HOH A 69 469 87 HOH HOH . 
F 5 HOH A 70 470 89 HOH HOH . 
F 5 HOH A 71 471 92 HOH HOH . 
F 5 HOH A 72 472 94 HOH HOH . 
F 5 HOH A 73 473 98 HOH HOH . 
F 5 HOH A 74 474 100 HOH HOH . 
F 5 HOH A 75 475 101 HOH HOH . 
F 5 HOH A 76 476 102 HOH HOH . 
F 5 HOH A 77 477 103 HOH HOH . 
F 5 HOH A 78 478 105 HOH HOH . 
F 5 HOH A 79 479 107 HOH HOH . 
F 5 HOH A 80 480 109 HOH HOH . 
F 5 HOH A 81 481 111 HOH HOH . 
F 5 HOH A 82 482 112 HOH HOH . 
F 5 HOH A 83 483 114 HOH HOH . 
F 5 HOH A 84 484 115 HOH HOH . 
F 5 HOH A 85 485 116 HOH HOH . 
F 5 HOH A 86 486 120 HOH HOH . 
F 5 HOH A 87 487 123 HOH HOH . 
F 5 HOH A 88 488 127 HOH HOH . 
F 5 HOH A 89 489 130 HOH HOH . 
F 5 HOH A 90 490 132 HOH HOH . 
F 5 HOH A 91 491 133 HOH HOH . 
F 5 HOH A 92 492 134 HOH HOH . 
F 5 HOH A 93 493 136 HOH HOH . 
F 5 HOH A 94 494 137 HOH HOH . 
F 5 HOH A 95 495 138 HOH HOH . 
F 5 HOH A 96 496 140 HOH HOH . 
F 5 HOH A 97 497 142 HOH HOH . 
F 5 HOH A 98 498 143 HOH HOH . 
F 5 HOH A 99 499 145 HOH HOH . 
F 5 HOH A 100 500 147 HOH HOH . 
F 5 HOH A 101 501 148 HOH HOH . 
F 5 HOH A 102 502 149 HOH HOH . 
F 5 HOH A 103 503 150 HOH HOH . 
F 5 HOH A 104 504 152 HOH HOH . 
F 5 HOH A 105 505 153 HOH HOH . 
F 5 HOH A 106 506 154 HOH HOH . 
F 5 HOH A 107 507 155 HOH HOH . 
F 5 HOH A 108 508 156 HOH HOH . 
F 5 HOH A 109 509 157 HOH HOH . 
F 5 HOH A 110 510 158 HOH HOH . 
F 5 HOH A 111 511 159 HOH HOH . 
F 5 HOH A 112 512 160 HOH HOH . 
F 5 HOH A 113 513 161 HOH HOH . 
F 5 HOH A 114 514 162 HOH HOH . 
F 5 HOH A 115 515 163 HOH HOH . 
F 5 HOH A 116 516 164 HOH HOH . 
F 5 HOH A 117 517 165 HOH HOH . 
F 5 HOH A 118 518 166 HOH HOH . 
F 5 HOH A 119 519 167 HOH HOH . 
F 5 HOH A 120 520 168 HOH HOH . 
F 5 HOH A 121 521 169 HOH HOH . 
F 5 HOH A 122 522 170 HOH HOH . 
F 5 HOH A 123 523 171 HOH HOH . 
F 5 HOH A 124 524 172 HOH HOH . 
F 5 HOH A 125 525 173 HOH HOH . 
F 5 HOH A 126 526 174 HOH HOH . 
F 5 HOH A 127 527 175 HOH HOH . 
F 5 HOH A 128 528 176 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 C CAA AOC . . . C 2 15.136 4.292 10.553 0.6 52.21 ? CAA AOC 302 A 1 
HETATM 2 C CAE AOC . . . C 2 15.354 4.768 11.593 0.7 49.87 ? CAE AOC 302 A 1 
HETATM 3 C CAH AOC . . . C 2 15.651 5.4 12.86 0.8 50.07 ? CAH AOC 302 A 1 
HETATM 4 O O5' AOC . . . C 2 17.015 5.581 12.87 1 50.79 ? O5' AOC 302 A 1 
HETATM 5 C C5' AOC . . . C 2 17.333 6.891 12.61 1 48.63 ? C5' AOC 302 A 1 
HETATM 6 C C4' AOC . . . C 2 18.592 7.029 13.404 1 52.61 ? C4' AOC 302 A 1 
HETATM 7 O O4' AOC . . . C 2 19.378 8.085 12.924 1 52.52 ? O4' AOC 302 A 1 
HETATM 8 C C3' AOC . . . C 2 18.22 7.416 14.825 1 55.38 ? C3' AOC 302 A 1 
HETATM 9 O O3' AOC . . . C 2 19.296 7.053 15.692 1 54.8 ? O3' AOC 302 A 1 
HETATM 10 C C2' AOC . . . C 2 18.157 8.907 14.691 1 50.04 ? C2' AOC 302 A 1 
HETATM 11 O O2' AOC . . . C 2 18.411 9.464 15.939 1 53.98 ? O2' AOC 302 A 1 
HETATM 12 C C1' AOC . . . C 2 19.395 9.13 13.872 1 47.52 ? C1' AOC 302 A 1 
HETATM 13 N N9 AOC . . . C 2 19.444 10.425 13.17 1 43.89 ? N9 AOC 302 A 1 
HETATM 14 C C8 AOC . . . C 2 18.443 11.177 12.757 1 35.05 ? C8 AOC 302 A 1 
HETATM 15 N N7 AOC . . . C 2 18.93 12.239 12.182 1 36.2 ? N7 AOC 302 A 1 
HETATM 16 C C5 AOC . . . C 2 20.237 12.159 12.218 1 43.23 ? C5 AOC 302 A 1 
HETATM 17 C C4 AOC . . . C 2 20.559 11.001 12.86 1 48.18 ? C4 AOC 302 A 1 
HETATM 18 N N3 AOC . . . C 2 21.818 10.665 13.055 1 34.67 ? N3 AOC 302 A 1 
HETATM 19 C C2 AOC . . . C 2 22.762 11.442 12.621 1 35.44 ? C2 AOC 302 A 1 
HETATM 20 N N1 AOC . . . C 2 22.506 12.562 12 1 34.09 ? N1 AOC 302 A 1 
HETATM 21 C C6 AOC . . . C 2 21.271 12.954 11.787 1 43.99 ? C6 AOC 302 A 1 
HETATM 22 N N6 AOC . . . C 2 21.068 14.083 11.177 1 33.75 ? N6 AOC 302 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           321 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#