data_1DGM
#
_model_server_result.job_id            zQoTKMWocERK_nf1hlieZQ 
_model_server_result.datetime_utc      '2024-12-21 13:04:43' 
_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          1dgm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":375}' 
#
_entry.id    1DGM 
#
_exptl.entry_id    1DGM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              267.241 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            ADENOSINE 
_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          100.3 
_cell.angle_gamma         90 
_cell.entry_id            1DGM 
_cell.length_a            47.55 
_cell.length_b            68.75 
_cell.length_c            57.29 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1DGM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_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
disulf ? disulf1 A SG CYS 340 A CYS 340 1_555 A SG CYS 363 A CYS 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc1 A O ALA 185 A ALA 185 1_555 B MG MG . A MG 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? 
metalc ? metalc2 A O ILE 188 A ILE 188 1_555 B MG MG . A MG 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc3 A O ALA 191 A ALA 191 1_555 B MG MG . A MG 380 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc4 B MG MG . A MG 380 1_555 F O HOH . A HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc5 B MG MG . A MG 380 1_555 F O HOH . A HOH 471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
#
_chem_comp.formula           'C10 H13 N5 O4' 
_chem_comp.formula_weight    267.241 
_chem_comp.id                ADN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              ADENOSINE 
_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
O5' C5' ADN sing 8 n n 
O5' HO5' ADN sing 9 n n 
C5' C4' ADN sing 10 n n 
C5' "H5'1" ADN sing 11 n n 
C5' "H5'2" ADN sing 12 n n 
C4' O4' ADN sing 13 n n 
C4' C3' ADN sing 14 n n 
C4' H4' ADN sing 15 n n 
O4' C1' ADN sing 16 n n 
C3' O3' ADN sing 17 n n 
C3' C2' ADN sing 18 n n 
C3' H3' ADN sing 19 n n 
O3' HO3' ADN sing 20 n n 
C2' O2' ADN sing 21 n n 
C2' C1' ADN sing 22 n n 
C2' H2' ADN sing 23 n n 
O2' HO2' ADN sing 24 n n 
C1' N9 ADN sing 25 n n 
C1' H1' ADN sing 26 n n 
N9 C8 ADN sing 27 n y 
N9 C4 ADN sing 28 n y 
C8 N7 ADN doub 29 n y 
C8 H8 ADN sing 30 n n 
N7 C5 ADN sing 31 n y 
C5 C6 ADN sing 32 n y 
C5 C4 ADN doub 33 n y 
C6 N6 ADN sing 34 n n 
C6 N1 ADN doub 35 n y 
N6 HN61 ADN sing 36 n n 
N6 HN62 ADN sing 37 n n 
N1 C2 ADN sing 38 n y 
C2 N3 ADN doub 39 n y 
C2 H2 ADN sing 40 n n 
N3 C4 ADN sing 41 n y 
#
_atom_sites.entry_id                     1DGM 
_atom_sites.fract_transf_matrix[1][1]    0.02103 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003822 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014545 
_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]    0.017741 
_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 MG A 1 380 380 MG MG2 . 
C 3 CL A 1 385 385 CL CL1 . 
D 4 ADN A 1 375 375 ADN ADO . 
E 5 ACY A 1 370 370 ACY ACY . 
F 6 HOH A 1 401 401 HOH HOH . 
F 6 HOH A 2 402 402 HOH HOH . 
F 6 HOH A 3 403 403 HOH HOH . 
F 6 HOH A 4 404 404 HOH HOH . 
F 6 HOH A 5 405 405 HOH HOH . 
F 6 HOH A 6 406 406 HOH HOH . 
F 6 HOH A 7 407 407 HOH HOH . 
F 6 HOH A 8 408 408 HOH HOH . 
F 6 HOH A 9 409 409 HOH HOH . 
F 6 HOH A 10 410 410 HOH HOH . 
F 6 HOH A 11 411 411 HOH HOH . 
F 6 HOH A 12 412 412 HOH HOH . 
F 6 HOH A 13 413 413 HOH HOH . 
F 6 HOH A 14 414 414 HOH HOH . 
F 6 HOH A 15 415 415 HOH HOH . 
F 6 HOH A 16 416 416 HOH HOH . 
F 6 HOH A 17 417 417 HOH HOH . 
F 6 HOH A 18 418 418 HOH HOH . 
F 6 HOH A 19 419 419 HOH HOH . 
F 6 HOH A 20 420 420 HOH HOH . 
F 6 HOH A 21 421 421 HOH HOH . 
F 6 HOH A 22 422 422 HOH HOH . 
F 6 HOH A 23 423 423 HOH HOH . 
F 6 HOH A 24 424 424 HOH HOH . 
F 6 HOH A 25 425 425 HOH HOH . 
F 6 HOH A 26 426 426 HOH HOH . 
F 6 HOH A 27 427 427 HOH HOH . 
F 6 HOH A 28 428 428 HOH HOH . 
F 6 HOH A 29 429 429 HOH HOH . 
F 6 HOH A 30 430 430 HOH HOH . 
F 6 HOH A 31 431 431 HOH HOH . 
F 6 HOH A 32 432 432 HOH HOH . 
F 6 HOH A 33 433 433 HOH HOH . 
F 6 HOH A 34 434 434 HOH HOH . 
F 6 HOH A 35 435 435 HOH HOH . 
F 6 HOH A 36 436 436 HOH HOH . 
F 6 HOH A 37 437 437 HOH HOH . 
F 6 HOH A 38 438 438 HOH HOH . 
F 6 HOH A 39 439 439 HOH HOH . 
F 6 HOH A 40 440 440 HOH HOH . 
F 6 HOH A 41 441 441 HOH HOH . 
F 6 HOH A 42 442 442 HOH HOH . 
F 6 HOH A 43 443 443 HOH HOH . 
F 6 HOH A 44 444 444 HOH HOH . 
F 6 HOH A 45 445 445 HOH HOH . 
F 6 HOH A 46 446 446 HOH HOH . 
F 6 HOH A 47 447 447 HOH HOH . 
F 6 HOH A 48 448 448 HOH HOH . 
F 6 HOH A 49 449 449 HOH HOH . 
F 6 HOH A 50 450 450 HOH HOH . 
F 6 HOH A 51 451 451 HOH HOH . 
F 6 HOH A 52 452 452 HOH HOH . 
F 6 HOH A 53 453 453 HOH HOH . 
F 6 HOH A 54 454 454 HOH HOH . 
F 6 HOH A 55 455 455 HOH HOH . 
F 6 HOH A 56 456 456 HOH HOH . 
F 6 HOH A 57 457 457 HOH HOH . 
F 6 HOH A 58 458 458 HOH HOH . 
F 6 HOH A 59 459 459 HOH HOH . 
F 6 HOH A 60 460 460 HOH HOH . 
F 6 HOH A 61 461 461 HOH HOH . 
F 6 HOH A 62 462 462 HOH HOH . 
F 6 HOH A 63 463 463 HOH HOH . 
F 6 HOH A 64 464 464 HOH HOH . 
F 6 HOH A 65 465 465 HOH HOH . 
F 6 HOH A 66 466 466 HOH HOH . 
F 6 HOH A 67 467 467 HOH HOH . 
F 6 HOH A 68 468 468 HOH HOH . 
F 6 HOH A 69 469 469 HOH HOH . 
F 6 HOH A 70 470 470 HOH HOH . 
F 6 HOH A 71 471 471 HOH HOH . 
F 6 HOH A 72 472 472 HOH HOH . 
F 6 HOH A 73 473 473 HOH HOH . 
F 6 HOH A 74 474 474 HOH HOH . 
F 6 HOH A 75 475 475 HOH HOH . 
F 6 HOH A 76 476 476 HOH HOH . 
F 6 HOH A 77 477 477 HOH HOH . 
F 6 HOH A 78 478 478 HOH HOH . 
F 6 HOH A 79 479 479 HOH HOH . 
F 6 HOH A 80 480 480 HOH HOH . 
F 6 HOH A 81 481 481 HOH HOH . 
F 6 HOH A 82 482 482 HOH HOH . 
F 6 HOH A 83 483 483 HOH HOH . 
F 6 HOH A 84 484 484 HOH HOH . 
F 6 HOH A 85 485 485 HOH HOH . 
F 6 HOH A 86 486 486 HOH HOH . 
F 6 HOH A 87 487 487 HOH HOH . 
F 6 HOH A 88 488 488 HOH HOH . 
F 6 HOH A 89 489 489 HOH HOH . 
F 6 HOH A 90 490 490 HOH HOH . 
F 6 HOH A 91 491 491 HOH HOH . 
F 6 HOH A 92 492 492 HOH HOH . 
F 6 HOH A 93 493 493 HOH HOH . 
F 6 HOH A 94 494 494 HOH HOH . 
F 6 HOH A 95 495 495 HOH HOH . 
F 6 HOH A 96 496 496 HOH HOH . 
F 6 HOH A 97 497 497 HOH HOH . 
F 6 HOH A 98 498 498 HOH HOH . 
F 6 HOH A 99 499 499 HOH HOH . 
F 6 HOH A 100 500 500 HOH HOH . 
F 6 HOH A 101 501 501 HOH HOH . 
F 6 HOH A 102 502 502 HOH HOH . 
F 6 HOH A 103 503 503 HOH HOH . 
F 6 HOH A 104 504 504 HOH HOH . 
F 6 HOH A 105 505 505 HOH HOH . 
F 6 HOH A 106 506 506 HOH HOH . 
F 6 HOH A 107 507 507 HOH HOH . 
F 6 HOH A 108 508 508 HOH HOH . 
F 6 HOH A 109 509 509 HOH HOH . 
F 6 HOH A 110 510 510 HOH HOH . 
F 6 HOH A 111 511 511 HOH HOH . 
F 6 HOH A 112 512 512 HOH HOH . 
F 6 HOH A 113 513 513 HOH HOH . 
F 6 HOH A 114 514 514 HOH HOH . 
F 6 HOH A 115 515 515 HOH HOH . 
F 6 HOH A 116 516 516 HOH HOH . 
F 6 HOH A 117 517 517 HOH HOH . 
F 6 HOH A 118 518 518 HOH HOH . 
F 6 HOH A 119 519 519 HOH HOH . 
F 6 HOH A 120 520 520 HOH HOH . 
F 6 HOH A 121 521 521 HOH HOH . 
F 6 HOH A 122 522 522 HOH HOH . 
F 6 HOH A 123 523 523 HOH HOH . 
F 6 HOH A 124 524 524 HOH HOH . 
F 6 HOH A 125 525 525 HOH HOH . 
F 6 HOH A 126 526 526 HOH HOH . 
F 6 HOH A 127 527 527 HOH HOH . 
F 6 HOH A 128 528 528 HOH HOH . 
F 6 HOH A 129 529 529 HOH HOH . 
F 6 HOH A 130 530 530 HOH HOH . 
F 6 HOH A 131 531 531 HOH HOH . 
F 6 HOH A 132 532 532 HOH HOH . 
F 6 HOH A 133 533 533 HOH HOH . 
F 6 HOH A 134 534 534 HOH HOH . 
F 6 HOH A 135 535 535 HOH HOH . 
F 6 HOH A 136 536 536 HOH HOH . 
F 6 HOH A 137 537 537 HOH HOH . 
F 6 HOH A 138 538 538 HOH HOH . 
F 6 HOH A 139 539 539 HOH HOH . 
F 6 HOH A 140 540 540 HOH HOH . 
F 6 HOH A 141 541 541 HOH HOH . 
F 6 HOH A 142 542 542 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 O O5' ADN . . . D 4 2.927 7.77 15.444 0.56 25.92 ? O5' ADN 375 A 1 
HETATM 2 C C5' ADN . . . D 4 2.731 9.118 15.024 0.56 27.69 ? C5' ADN 375 A 1 
HETATM 3 C C4' ADN . . . D 4 1.451 9.238 14.227 0.56 28.38 ? C4' ADN 375 A 1 
HETATM 4 O O4' ADN . . . D 4 0.354 8.69 15.005 0.56 28.65 ? O4' ADN 375 A 1 
HETATM 5 C C3' ADN . . . D 4 1.038 10.668 13.918 0.56 28.79 ? C3' ADN 375 A 1 
HETATM 6 O O3' ADN . . . D 4 1.639 11.129 12.712 0.56 30.12 ? O3' ADN 375 A 1 
HETATM 7 C C2' ADN . . . D 4 -0.475 10.559 13.789 0.56 29.14 ? C2' ADN 375 A 1 
HETATM 8 O O2' ADN . . . D 4 -0.903 10.162 12.5 0.56 25.57 ? O2' ADN 375 A 1 
HETATM 9 C C1' ADN . . . D 4 -0.802 9.498 14.846 0.56 29.48 ? C1' ADN 375 A 1 
HETATM 10 N N9 ADN . . . D 4 -1.156 10.044 16.16 0.56 30.02 ? N9 ADN 375 A 1 
HETATM 11 C C8 ADN . . . D 4 -0.749 11.228 16.724 0.56 30.21 ? C8 ADN 375 A 1 
HETATM 12 N N7 ADN . . . D 4 -1.24 11.441 17.922 0.56 30.58 ? N7 ADN 375 A 1 
HETATM 13 C C5 ADN . . . D 4 -2.024 10.322 18.165 0.56 30.54 ? C5 ADN 375 A 1 
HETATM 14 C C6 ADN . . . D 4 -2.818 9.941 19.264 0.56 30.23 ? C6 ADN 375 A 1 
HETATM 15 N N6 ADN . . . D 4 -2.967 10.679 20.366 0.56 30.9 ? N6 ADN 375 A 1 
HETATM 16 N N1 ADN . . . D 4 -3.466 8.761 19.189 0.56 29.3 ? N1 ADN 375 A 1 
HETATM 17 C C2 ADN . . . D 4 -3.328 8.026 18.08 0.56 30.33 ? C2 ADN 375 A 1 
HETATM 18 N N3 ADN . . . D 4 -2.619 8.276 16.983 0.56 30.67 ? N3 ADN 375 A 1 
HETATM 19 C C4 ADN . . . D 4 -1.982 9.454 17.089 0.56 30.23 ? C4 ADN 375 A 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           19 
#