data_3DZ5
#
_model_server_result.job_id            M7lMKU6RcboRvi8kW2PLpg 
_model_server_result.datetime_utc      '2024-10-18 16:22:10' 
_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          3dz5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":368}' 
#
_entry.id    3DZ5 
#
_exptl.entry_id    3DZ5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              353.377 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine" 
_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          104.17 
_cell.angle_gamma         90 
_cell.entry_id            3DZ5 
_cell.length_a            96.778 
_cell.length_b            44.458 
_cell.length_c            70.554 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DZ5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 B C PYR 1 A PYR 68 1_555 B N SER 2 A SER 69 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? 
covale ? covale2 B CA PYR 1 A PYR 68 1_555 D N1 M8M . A M8M 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.493 ? 
#
_chem_comp.formula           'C14 H23 N7 O4' 
_chem_comp.formula_weight    353.377 
_chem_comp.id                M8M 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "5'-{[2-(aminooxy)ethyl](methyl)amino}-5'-deoxy-8-methyladenosine" 
_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
N1 O2 M8M sing 218 n n 
O2 C4 M8M sing 219 n n 
C4 C5 M8M sing 220 n n 
C5 N2 M8M sing 221 n n 
N2 C6 M8M sing 222 n n 
N2 C5' M8M sing 223 n n 
C5' C4' M8M sing 224 n n 
C4' O4' M8M sing 225 n n 
C4' C3' M8M sing 226 n n 
O4' C1' M8M sing 227 n n 
C1' N5 M8M sing 228 n n 
C1' C2' M8M sing 229 n n 
N5 C11 M8M sing 230 n y 
N5 C7 M8M sing 231 n y 
C11 N4 M8M doub 232 n y 
C11 C12 M8M sing 233 n y 
N4 C10 M8M sing 234 n y 
C10 N3 M8M doub 235 n y 
N3 C9 M8M sing 236 n y 
C9 N7 M8M sing 237 n n 
C9 C12 M8M doub 238 n y 
C12 N6 M8M sing 239 n y 
N6 C7 M8M doub 240 n y 
C7 C8 M8M sing 241 n n 
C2' O2' M8M sing 242 n n 
C2' C3' M8M sing 243 n n 
C3' O3' M8M sing 244 n n 
N1 HN1 M8M sing 245 n n 
N1 HN1A M8M sing 246 n n 
C4 H4 M8M sing 247 n n 
C4 H4A M8M sing 248 n n 
C5 H5 M8M sing 249 n n 
C5 H5A M8M sing 250 n n 
C6 H6 M8M sing 251 n n 
C6 H6A M8M sing 252 n n 
C6 H6B M8M sing 253 n n 
C5' H5' M8M sing 254 n n 
C5' "H5'A" M8M sing 255 n n 
C4' H4' M8M sing 256 n n 
C1' H1' M8M sing 257 n n 
C10 H10 M8M sing 258 n n 
N7 HN7 M8M sing 259 n n 
N7 HN7A M8M sing 260 n n 
C2' H2' M8M sing 261 n n 
O2' HO2' M8M sing 262 n n 
C3' H3' M8M sing 263 n n 
O3' HO3' M8M sing 264 n n 
C8 H8 M8M sing 265 n n 
C8 H8A M8M sing 266 n n 
C8 H8B M8M sing 267 n n 
#
_atom_sites.entry_id                     3DZ5 
_atom_sites.fract_transf_matrix[1][1]    0.010333 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002609 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.022493 
_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]    0.014618 
_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 3 PUT B 1 350 350 PUT PUT . 
D 4 M8M A 1 368 368 M8M M8M . 
E 5 HOH B 1 351 4 HOH HOH . 
E 5 HOH B 2 352 13 HOH HOH . 
E 5 HOH B 3 353 14 HOH HOH . 
E 5 HOH B 4 354 15 HOH HOH . 
E 5 HOH B 5 355 19 HOH HOH . 
E 5 HOH B 6 356 27 HOH HOH . 
E 5 HOH B 7 357 32 HOH HOH . 
E 5 HOH B 8 358 34 HOH HOH . 
E 5 HOH B 9 359 39 HOH HOH . 
E 5 HOH B 10 360 52 HOH HOH . 
E 5 HOH B 11 361 61 HOH HOH . 
E 5 HOH B 12 362 62 HOH HOH . 
E 5 HOH B 13 363 69 HOH HOH . 
F 5 HOH A 1 369 1 HOH HOH . 
F 5 HOH A 2 370 2 HOH HOH . 
F 5 HOH A 3 371 3 HOH HOH . 
F 5 HOH A 4 372 5 HOH HOH . 
F 5 HOH A 5 373 6 HOH HOH . 
F 5 HOH A 6 374 7 HOH HOH . 
F 5 HOH A 7 375 8 HOH HOH . 
F 5 HOH A 8 376 9 HOH HOH . 
F 5 HOH A 9 377 10 HOH HOH . 
F 5 HOH A 10 378 11 HOH HOH . 
F 5 HOH A 11 379 12 HOH HOH . 
F 5 HOH A 12 380 16 HOH HOH . 
F 5 HOH A 13 381 17 HOH HOH . 
F 5 HOH A 14 382 18 HOH HOH . 
F 5 HOH A 15 383 20 HOH HOH . 
F 5 HOH A 16 384 21 HOH HOH . 
F 5 HOH A 17 385 22 HOH HOH . 
F 5 HOH A 18 386 23 HOH HOH . 
F 5 HOH A 19 387 24 HOH HOH . 
F 5 HOH A 20 388 25 HOH HOH . 
F 5 HOH A 21 389 26 HOH HOH . 
F 5 HOH A 22 390 28 HOH HOH . 
F 5 HOH A 23 391 29 HOH HOH . 
F 5 HOH A 24 392 30 HOH HOH . 
F 5 HOH A 25 393 31 HOH HOH . 
F 5 HOH A 26 394 33 HOH HOH . 
F 5 HOH A 27 395 35 HOH HOH . 
F 5 HOH A 28 396 36 HOH HOH . 
F 5 HOH A 29 397 37 HOH HOH . 
F 5 HOH A 30 398 38 HOH HOH . 
F 5 HOH A 31 399 40 HOH HOH . 
F 5 HOH A 32 400 41 HOH HOH . 
F 5 HOH A 33 401 42 HOH HOH . 
F 5 HOH A 34 402 43 HOH HOH . 
F 5 HOH A 35 403 44 HOH HOH . 
F 5 HOH A 36 404 45 HOH HOH . 
F 5 HOH A 37 405 46 HOH HOH . 
F 5 HOH A 38 406 47 HOH HOH . 
F 5 HOH A 39 407 48 HOH HOH . 
F 5 HOH A 40 408 49 HOH HOH . 
F 5 HOH A 41 409 50 HOH HOH . 
F 5 HOH A 42 410 51 HOH HOH . 
F 5 HOH A 43 411 53 HOH HOH . 
F 5 HOH A 44 412 54 HOH HOH . 
F 5 HOH A 45 413 55 HOH HOH . 
F 5 HOH A 46 414 56 HOH HOH . 
F 5 HOH A 47 415 57 HOH HOH . 
F 5 HOH A 48 416 58 HOH HOH . 
F 5 HOH A 49 417 59 HOH HOH . 
F 5 HOH A 50 418 60 HOH HOH . 
F 5 HOH A 51 419 63 HOH HOH . 
F 5 HOH A 52 420 64 HOH HOH . 
F 5 HOH A 53 421 65 HOH HOH . 
F 5 HOH A 54 422 66 HOH HOH . 
F 5 HOH A 55 423 67 HOH HOH . 
F 5 HOH A 56 424 68 HOH HOH . 
F 5 HOH A 57 425 70 HOH HOH . 
F 5 HOH A 58 426 71 HOH HOH . 
F 5 HOH A 59 427 72 HOH HOH . 
F 5 HOH A 60 428 73 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 M8M . . . D 4 -21.012 -10.251 9.476 1 50.89 ? N1 M8M 368 A 1 
HETATM 2 O O2 M8M . . . D 4 -19.731 -9.753 9.81 1 48.96 ? O2 M8M 368 A 1 
HETATM 3 C C4 M8M . . . D 4 -18.988 -9.341 8.554 1 46.29 ? C4 M8M 368 A 1 
HETATM 4 C C5 M8M . . . D 4 -17.618 -8.795 8.823 1 42.84 ? C5 M8M 368 A 1 
HETATM 5 N N2 M8M . . . D 4 -16.824 -8.707 7.553 1 40.67 ? N2 M8M 368 A 1 
HETATM 6 C C6 M8M . . . D 4 -16.252 -10.048 7.284 1 40.4 ? C6 M8M 368 A 1 
HETATM 7 C C5' M8M . . . D 4 -15.711 -7.71 7.687 1 39.14 ? C5' M8M 368 A 1 
HETATM 8 C C4' M8M . . . D 4 -14.865 -7.612 6.426 1 39.68 ? C4' M8M 368 A 1 
HETATM 9 O O4' M8M . . . D 4 -15.633 -7.218 5.233 1 39.5 ? O4' M8M 368 A 1 
HETATM 10 C C1' M8M . . . D 4 -15.234 -5.924 5.062 1 39.16 ? C1' M8M 368 A 1 
HETATM 11 N N5 M8M . . . D 4 -16.528 -5.076 4.783 1 41.28 ? N5 M8M 368 A 1 
HETATM 12 C C11 M8M . . . D 4 -17.657 -5.294 5.574 1 42.39 ? C11 M8M 368 A 1 
HETATM 13 N N4 M8M . . . D 4 -17.812 -6.172 6.593 1 43.32 ? N4 M8M 368 A 1 
HETATM 14 C C10 M8M . . . D 4 -19.044 -6.096 7.123 1 43.65 ? C10 M8M 368 A 1 
HETATM 15 N N3 M8M . . . D 4 -20.067 -5.296 6.774 1 43.08 ? N3 M8M 368 A 1 
HETATM 16 C C9 M8M . . . D 4 -19.884 -4.424 5.747 1 43.12 ? C9 M8M 368 A 1 
HETATM 17 N N7 M8M . . . D 4 -20.896 -3.628 5.398 1 43.95 ? N7 M8M 368 A 1 
HETATM 18 C C12 M8M . . . D 4 -18.623 -4.407 5.098 1 43.19 ? C12 M8M 368 A 1 
HETATM 19 N N6 M8M . . . D 4 -18.128 -3.654 4.042 1 42.93 ? N6 M8M 368 A 1 
HETATM 20 C C7 M8M . . . D 4 -16.894 -4.084 3.892 1 42.13 ? C7 M8M 368 A 1 
HETATM 21 C C2' M8M . . . D 4 -14.396 -5.376 5.953 1 39.01 ? C2' M8M 368 A 1 
HETATM 22 O O2' M8M . . . D 4 -13.509 -4.335 5.6 1 37.72 ? O2' M8M 368 A 1 
HETATM 23 C C3' M8M . . . D 4 -13.726 -6.614 6.502 1 39.51 ? C3' M8M 368 A 1 
HETATM 24 O O3' M8M . . . D 4 -12.657 -6.999 5.637 1 39.61 ? O3' M8M 368 A 1 
HETATM 25 C C8 M8M . . . D 4 -15.905 -3.597 2.873 1 40.89 ? C8 M8M 368 A 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           25 
#