data_3V8M
#
_model_server_result.job_id            aMsjM-lhM-85F4WdPo61-g 
_model_server_result.datetime_utc      '2024-11-08 18:54:50' 
_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          3v8m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":301}' 
#
_entry.id    3V8M 
#
_exptl.entry_id    3V8M 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              371.15 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-azido-8-bromo-5'-deoxyadenosine" 
_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            3V8M 
_cell.length_a            62.528 
_cell.length_b            75.654 
_cell.length_c            118.241 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3V8M 
_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 
_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 62.528 0 0 
3 'crystal symmetry operation' 3_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 62.528 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           'C10 H11 Br N8 O3' 
_chem_comp.formula_weight    371.15 
_chem_comp.id                Z8B 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-azido-8-bromo-5'-deoxyadenosine" 
_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
N53 N52 Z8B doub 396 n n 
N52 N51 Z8B doub 397 n n 
N51 C5' Z8B sing 398 n n 
N6 C6 Z8B sing 399 n n 
N7 C5 Z8B sing 400 n y 
N7 C8 Z8B doub 401 n y 
C6 C5 Z8B doub 402 n y 
C6 N1 Z8B sing 403 n y 
C5 C4 Z8B sing 404 n y 
BR8 C8 Z8B sing 405 n n 
C8 N9 Z8B sing 406 n y 
N1 C2 Z8B doub 407 n y 
O5' C4' Z8B sing 408 n n 
O5' C1' Z8B sing 409 n n 
C5' C4' Z8B sing 410 n n 
C4 N9 Z8B sing 411 n y 
C4 N3 Z8B doub 412 n y 
N9 C1' Z8B sing 413 n n 
C2 N3 Z8B sing 414 n y 
C4' C3' Z8B sing 415 n n 
C1' C2' Z8B sing 416 n n 
C2' C3' Z8B sing 417 n n 
C2' O2' Z8B sing 418 n n 
C3' O3' Z8B sing 419 n n 
C2 H2 Z8B sing 420 n n 
N6 H1N6 Z8B sing 421 n n 
N6 H2N6 Z8B sing 422 n n 
C1' H1' Z8B sing 423 n n 
C2' H2' Z8B sing 424 n n 
O2' HO2' Z8B sing 425 n n 
C3' H3' Z8B sing 426 n n 
O3' HO3' Z8B sing 427 n n 
C4' H4' Z8B sing 428 n n 
C5' H15' Z8B sing 429 n n 
C5' H25' Z8B sing 430 n n 
#
_atom_sites.entry_id                     3V8M 
_atom_sites.fract_transf_matrix[1][1]    0.015993 
_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]    0.013218 
_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]    0.008457 
_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 Z8B A 1 301 1 Z8B Z8B . 
C 2 Z8B A 1 302 2 Z8B Z8B . 
D 3 CIT A 1 303 1 CIT CIT . 
E 4 HOH A 1 401 1 HOH HOH . 
E 4 HOH A 2 402 2 HOH HOH . 
E 4 HOH A 3 403 3 HOH HOH . 
E 4 HOH A 4 404 4 HOH HOH . 
E 4 HOH A 5 405 5 HOH HOH . 
E 4 HOH A 6 406 6 HOH HOH . 
E 4 HOH A 7 407 7 HOH HOH . 
E 4 HOH A 8 408 8 HOH HOH . 
E 4 HOH A 9 409 9 HOH HOH . 
E 4 HOH A 10 410 10 HOH HOH . 
E 4 HOH A 11 411 12 HOH HOH . 
E 4 HOH A 12 412 13 HOH HOH . 
E 4 HOH A 13 413 14 HOH HOH . 
E 4 HOH A 14 414 16 HOH HOH . 
E 4 HOH A 15 415 18 HOH HOH . 
E 4 HOH A 16 416 20 HOH HOH . 
E 4 HOH A 17 417 23 HOH HOH . 
E 4 HOH A 18 418 25 HOH HOH . 
E 4 HOH A 19 419 26 HOH HOH . 
E 4 HOH A 20 420 27 HOH HOH . 
E 4 HOH A 21 421 28 HOH HOH . 
E 4 HOH A 22 422 30 HOH HOH . 
E 4 HOH A 23 423 33 HOH HOH . 
E 4 HOH A 24 424 34 HOH HOH . 
E 4 HOH A 25 425 36 HOH HOH . 
E 4 HOH A 26 426 37 HOH HOH . 
E 4 HOH A 27 427 38 HOH HOH . 
E 4 HOH A 28 428 40 HOH HOH . 
E 4 HOH A 29 429 42 HOH HOH . 
E 4 HOH A 30 430 44 HOH HOH . 
E 4 HOH A 31 431 45 HOH HOH . 
E 4 HOH A 32 432 49 HOH HOH . 
E 4 HOH A 33 433 52 HOH HOH . 
E 4 HOH A 34 434 53 HOH HOH . 
E 4 HOH A 35 435 57 HOH HOH . 
E 4 HOH A 36 436 62 HOH HOH . 
E 4 HOH A 37 437 64 HOH HOH . 
E 4 HOH A 38 438 65 HOH HOH . 
E 4 HOH A 39 439 67 HOH HOH . 
E 4 HOH A 40 440 68 HOH HOH . 
E 4 HOH A 41 441 69 HOH HOH . 
E 4 HOH A 42 442 70 HOH HOH . 
E 4 HOH A 43 443 71 HOH HOH . 
E 4 HOH A 44 444 72 HOH HOH . 
E 4 HOH A 45 445 73 HOH HOH . 
E 4 HOH A 46 446 74 HOH HOH . 
E 4 HOH A 47 447 75 HOH HOH . 
E 4 HOH A 48 448 76 HOH HOH . 
E 4 HOH A 49 449 77 HOH HOH . 
E 4 HOH A 50 450 78 HOH HOH . 
E 4 HOH A 51 451 79 HOH HOH . 
E 4 HOH A 52 452 80 HOH HOH . 
E 4 HOH A 53 453 81 HOH HOH . 
E 4 HOH A 54 454 82 HOH HOH . 
E 4 HOH A 55 455 83 HOH HOH . 
E 4 HOH A 56 456 84 HOH HOH . 
E 4 HOH A 57 457 85 HOH HOH . 
E 4 HOH A 58 458 86 HOH HOH . 
E 4 HOH A 59 459 87 HOH HOH . 
E 4 HOH A 60 460 88 HOH HOH . 
E 4 HOH A 61 461 89 HOH HOH . 
E 4 HOH A 62 462 90 HOH HOH . 
E 4 HOH A 63 463 92 HOH HOH . 
E 4 HOH A 64 464 93 HOH HOH . 
E 4 HOH A 65 465 95 HOH HOH . 
E 4 HOH A 66 466 96 HOH HOH . 
E 4 HOH A 67 467 97 HOH HOH . 
E 4 HOH A 68 468 98 HOH HOH . 
E 4 HOH A 69 469 99 HOH HOH . 
E 4 HOH A 70 470 100 HOH HOH . 
E 4 HOH A 71 471 101 HOH HOH . 
E 4 HOH A 72 472 102 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 N N1 Z8B . . . B 2 22.468 12.817 11.934 0.7 34.36 ? N1 Z8B 301 A 1 
HETATM 2 C C2 Z8B . . . B 2 22.637 11.681 12.573 0.7 36.32 ? C2 Z8B 301 A 1 
HETATM 3 N N3 Z8B . . . B 2 21.631 10.992 13.041 0.7 37.22 ? N3 Z8B 301 A 1 
HETATM 4 C C4 Z8B . . . B 2 20.388 11.456 12.869 0.7 39.52 ? C4 Z8B 301 A 1 
HETATM 5 C C5 Z8B . . . B 2 20.177 12.645 12.217 0.7 35.17 ? C5 Z8B 301 A 1 
HETATM 6 C C6 Z8B . . . B 2 21.262 13.325 11.743 0.7 31.53 ? C6 Z8B 301 A 1 
HETATM 7 N N6 Z8B . . . B 2 21.122 14.452 11.106 0.7 27.82 ? N6 Z8B 301 A 1 
HETATM 8 N N7 Z8B . . . B 2 18.885 12.863 12.197 0.7 35.03 ? N7 Z8B 301 A 1 
HETATM 9 C C8 Z8B . . . B 2 18.301 11.852 12.795 0.7 37.9 ? C8 Z8B 301 A 1 
HETATM 10 BR BR8 Z8B . . . B 2 16.434 11.784 12.985 0.5 67.46 ? BR8 Z8B 301 A 1 
HETATM 11 N N9 Z8B . . . B 2 19.206 10.988 13.232 0.7 42.88 ? N9 Z8B 301 A 1 
HETATM 12 C C1' Z8B . . . B 2 19.098 9.712 13.949 0.7 50.71 ? C1' Z8B 301 A 1 
HETATM 13 C C2' Z8B . . . B 2 17.997 9.471 14.961 0.7 55.59 ? C2' Z8B 301 A 1 
HETATM 14 O O2' Z8B . . . B 2 18.657 9.055 16.144 0.7 60.96 ? O2' Z8B 301 A 1 
HETATM 15 C C3' Z8B . . . B 2 17.204 8.299 14.408 0.7 55.08 ? C3' Z8B 301 A 1 
HETATM 16 O O3' Z8B . . . B 2 17.03 7.304 15.418 0.7 55.4 ? O3' Z8B 301 A 1 
HETATM 17 C C4' Z8B . . . B 2 18.075 7.744 13.298 0.7 55.78 ? C4' Z8B 301 A 1 
HETATM 18 C C5' Z8B . . . B 2 17.227 7.656 12.052 0.7 56 ? C5' Z8B 301 A 1 
HETATM 19 O O5' Z8B . . . B 2 18.948 8.77 12.901 0.7 54.38 ? O5' Z8B 301 A 1 
HETATM 20 N N51 Z8B . . . B 2 16.751 6.296 11.858 0.6 57.47 ? N51 Z8B 301 A 1 
HETATM 21 N N52 Z8B . . . B 2 15.531 6.146 11.573 0.6 59.6 ? N52 Z8B 301 A 1 
HETATM 22 N N53 Z8B . . . B 2 14.288 5.993 11.28 0.6 60.49 ? N53 Z8B 301 A 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           22 
#