data_6V1R
#
_model_server_result.job_id            5ZVr_tUho9xuqBDSUNigOg 
_model_server_result.datetime_utc      '2024-11-16 17:30:17' 
_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          6v1r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":303}' 
#
_entry.id    6V1R 
#
_exptl.entry_id    6V1R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              145.246 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            SPERMIDINE 
_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            6V1R 
_cell.length_a            46.76 
_cell.length_b            65.781 
_cell.length_c            96.592 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6V1R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
#
_chem_comp.formula           'C7 H19 N3' 
_chem_comp.formula_weight    145.246 
_chem_comp.id                SPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              SPERMIDINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) 
#
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 C2 SPD sing 348 n n 
N1 HN11 SPD sing 349 n n 
N1 HN12 SPD sing 350 n n 
C2 C3 SPD sing 351 n n 
C2 H21 SPD sing 352 n n 
C2 H22 SPD sing 353 n n 
C3 C4 SPD sing 354 n n 
C3 H31 SPD sing 355 n n 
C3 H32 SPD sing 356 n n 
C4 C5 SPD sing 357 n n 
C4 H41 SPD sing 358 n n 
C4 H42 SPD sing 359 n n 
C5 N6 SPD sing 360 n n 
C5 H51 SPD sing 361 n n 
C5 H52 SPD sing 362 n n 
N6 C7 SPD sing 363 n n 
N6 HN6 SPD sing 364 n n 
C7 C8 SPD sing 365 n n 
C7 H71 SPD sing 366 n n 
C7 H72 SPD sing 367 n n 
C8 C9 SPD sing 368 n n 
C8 H81 SPD sing 369 n n 
C8 H82 SPD sing 370 n n 
C9 N10 SPD sing 371 n n 
C9 H91 SPD sing 372 n n 
C9 H92 SPD sing 373 n n 
N10 H101 SPD sing 374 n n 
N10 H102 SPD sing 375 n n 
#
_atom_sites.entry_id                     6V1R 
_atom_sites.fract_transf_matrix[1][1]    0.021386 
_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]    0.015202 
_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]    0.010353 
_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 ACH A 1 301 301 ACH ACH . 
C 3 NHE A 1 302 401 NHE NHE . 
D 4 SPD A 1 303 501 SPD SPD . 
E 5 PEG A 1 304 601 PEG PEG . 
F 6 HOH A 1 401 172 HOH HOH . 
F 6 HOH A 2 402 143 HOH HOH . 
F 6 HOH A 3 403 182 HOH HOH . 
F 6 HOH A 4 404 52 HOH HOH . 
F 6 HOH A 5 405 16 HOH HOH . 
F 6 HOH A 6 406 44 HOH HOH . 
F 6 HOH A 7 407 113 HOH HOH . 
F 6 HOH A 8 408 41 HOH HOH . 
F 6 HOH A 9 409 178 HOH HOH . 
F 6 HOH A 10 410 167 HOH HOH . 
F 6 HOH A 11 411 47 HOH HOH . 
F 6 HOH A 12 412 62 HOH HOH . 
F 6 HOH A 13 413 24 HOH HOH . 
F 6 HOH A 14 414 31 HOH HOH . 
F 6 HOH A 15 415 79 HOH HOH . 
F 6 HOH A 16 416 141 HOH HOH . 
F 6 HOH A 17 417 102 HOH HOH . 
F 6 HOH A 18 418 65 HOH HOH . 
F 6 HOH A 19 419 138 HOH HOH . 
F 6 HOH A 20 420 145 HOH HOH . 
F 6 HOH A 21 421 124 HOH HOH . 
F 6 HOH A 22 422 110 HOH HOH . 
F 6 HOH A 23 423 49 HOH HOH . 
F 6 HOH A 24 424 88 HOH HOH . 
F 6 HOH A 25 425 112 HOH HOH . 
F 6 HOH A 26 426 72 HOH HOH . 
F 6 HOH A 27 427 43 HOH HOH . 
F 6 HOH A 28 428 59 HOH HOH . 
F 6 HOH A 29 429 153 HOH HOH . 
F 6 HOH A 30 430 67 HOH HOH . 
F 6 HOH A 31 431 108 HOH HOH . 
F 6 HOH A 32 432 28 HOH HOH . 
F 6 HOH A 33 433 192 HOH HOH . 
F 6 HOH A 34 434 111 HOH HOH . 
F 6 HOH A 35 435 57 HOH HOH . 
F 6 HOH A 36 436 38 HOH HOH . 
F 6 HOH A 37 437 163 HOH HOH . 
F 6 HOH A 38 438 132 HOH HOH . 
F 6 HOH A 39 439 70 HOH HOH . 
F 6 HOH A 40 440 86 HOH HOH . 
F 6 HOH A 41 441 157 HOH HOH . 
F 6 HOH A 42 442 9 HOH HOH . 
F 6 HOH A 43 443 114 HOH HOH . 
F 6 HOH A 44 444 73 HOH HOH . 
F 6 HOH A 45 445 91 HOH HOH . 
F 6 HOH A 46 446 13 HOH HOH . 
F 6 HOH A 47 447 33 HOH HOH . 
F 6 HOH A 48 448 45 HOH HOH . 
F 6 HOH A 49 449 107 HOH HOH . 
F 6 HOH A 50 450 131 HOH HOH . 
F 6 HOH A 51 451 94 HOH HOH . 
F 6 HOH A 52 452 64 HOH HOH . 
F 6 HOH A 53 453 117 HOH HOH . 
F 6 HOH A 54 454 199 HOH HOH . 
F 6 HOH A 55 455 104 HOH HOH . 
F 6 HOH A 56 456 90 HOH HOH . 
F 6 HOH A 57 457 18 HOH HOH . 
F 6 HOH A 58 458 21 HOH HOH . 
F 6 HOH A 59 459 4 HOH HOH . 
F 6 HOH A 60 460 32 HOH HOH . 
F 6 HOH A 61 461 58 HOH HOH . 
F 6 HOH A 62 462 84 HOH HOH . 
F 6 HOH A 63 463 161 HOH HOH . 
F 6 HOH A 64 464 55 HOH HOH . 
F 6 HOH A 65 465 183 HOH HOH . 
F 6 HOH A 66 466 89 HOH HOH . 
F 6 HOH A 67 467 48 HOH HOH . 
F 6 HOH A 68 468 1 HOH HOH . 
F 6 HOH A 69 469 99 HOH HOH . 
F 6 HOH A 70 470 97 HOH HOH . 
F 6 HOH A 71 471 171 HOH HOH . 
F 6 HOH A 72 472 2 HOH HOH . 
F 6 HOH A 73 473 87 HOH HOH . 
F 6 HOH A 74 474 30 HOH HOH . 
F 6 HOH A 75 475 53 HOH HOH . 
F 6 HOH A 76 476 6 HOH HOH . 
F 6 HOH A 77 477 126 HOH HOH . 
F 6 HOH A 78 478 14 HOH HOH . 
F 6 HOH A 79 479 34 HOH HOH . 
F 6 HOH A 80 480 205 HOH HOH . 
F 6 HOH A 81 481 175 HOH HOH . 
F 6 HOH A 82 482 76 HOH HOH . 
F 6 HOH A 83 483 12 HOH HOH . 
F 6 HOH A 84 484 69 HOH HOH . 
F 6 HOH A 85 485 36 HOH HOH . 
F 6 HOH A 86 486 50 HOH HOH . 
F 6 HOH A 87 487 22 HOH HOH . 
F 6 HOH A 88 488 63 HOH HOH . 
F 6 HOH A 89 489 37 HOH HOH . 
F 6 HOH A 90 490 127 HOH HOH . 
F 6 HOH A 91 491 42 HOH HOH . 
F 6 HOH A 92 492 92 HOH HOH . 
F 6 HOH A 93 493 96 HOH HOH . 
F 6 HOH A 94 494 129 HOH HOH . 
F 6 HOH A 95 495 133 HOH HOH . 
F 6 HOH A 96 496 5 HOH HOH . 
F 6 HOH A 97 497 95 HOH HOH . 
F 6 HOH A 98 498 121 HOH HOH . 
F 6 HOH A 99 499 27 HOH HOH . 
F 6 HOH A 100 500 118 HOH HOH . 
F 6 HOH A 101 501 29 HOH HOH . 
F 6 HOH A 102 502 81 HOH HOH . 
F 6 HOH A 103 503 82 HOH HOH . 
F 6 HOH A 104 504 17 HOH HOH . 
F 6 HOH A 105 505 39 HOH HOH . 
F 6 HOH A 106 506 26 HOH HOH . 
F 6 HOH A 107 507 177 HOH HOH . 
F 6 HOH A 108 508 128 HOH HOH . 
F 6 HOH A 109 509 151 HOH HOH . 
F 6 HOH A 110 510 11 HOH HOH . 
F 6 HOH A 111 511 173 HOH HOH . 
F 6 HOH A 112 512 135 HOH HOH . 
F 6 HOH A 113 513 19 HOH HOH . 
F 6 HOH A 114 514 56 HOH HOH . 
F 6 HOH A 115 515 187 HOH HOH . 
F 6 HOH A 116 516 25 HOH HOH . 
F 6 HOH A 117 517 40 HOH HOH . 
F 6 HOH A 118 518 83 HOH HOH . 
F 6 HOH A 119 519 71 HOH HOH . 
F 6 HOH A 120 520 142 HOH HOH . 
F 6 HOH A 121 521 156 HOH HOH . 
F 6 HOH A 122 522 10 HOH HOH . 
F 6 HOH A 123 523 3 HOH HOH . 
F 6 HOH A 124 524 75 HOH HOH . 
F 6 HOH A 125 525 194 HOH HOH . 
F 6 HOH A 126 526 60 HOH HOH . 
F 6 HOH A 127 527 51 HOH HOH . 
F 6 HOH A 128 528 190 HOH HOH . 
F 6 HOH A 129 529 189 HOH HOH . 
F 6 HOH A 130 530 198 HOH HOH . 
F 6 HOH A 131 531 35 HOH HOH . 
F 6 HOH A 132 532 85 HOH HOH . 
F 6 HOH A 133 533 7 HOH HOH . 
F 6 HOH A 134 534 200 HOH HOH . 
F 6 HOH A 135 535 162 HOH HOH . 
F 6 HOH A 136 536 202 HOH HOH . 
F 6 HOH A 137 537 103 HOH HOH . 
F 6 HOH A 138 538 139 HOH HOH . 
F 6 HOH A 139 539 195 HOH HOH . 
F 6 HOH A 140 540 77 HOH HOH . 
F 6 HOH A 141 541 46 HOH HOH . 
F 6 HOH A 142 542 61 HOH HOH . 
F 6 HOH A 143 543 15 HOH HOH . 
F 6 HOH A 144 544 174 HOH HOH . 
F 6 HOH A 145 545 123 HOH HOH . 
F 6 HOH A 146 546 74 HOH HOH . 
F 6 HOH A 147 547 146 HOH HOH . 
F 6 HOH A 148 548 105 HOH HOH . 
F 6 HOH A 149 549 203 HOH HOH . 
F 6 HOH A 150 550 122 HOH HOH . 
F 6 HOH A 151 551 100 HOH HOH . 
F 6 HOH A 152 552 54 HOH HOH . 
F 6 HOH A 153 553 159 HOH HOH . 
F 6 HOH A 154 554 8 HOH HOH . 
F 6 HOH A 155 555 188 HOH HOH . 
F 6 HOH A 156 556 166 HOH HOH . 
F 6 HOH A 157 557 152 HOH HOH . 
F 6 HOH A 158 558 179 HOH HOH . 
F 6 HOH A 159 559 134 HOH HOH . 
F 6 HOH A 160 560 197 HOH HOH . 
F 6 HOH A 161 561 98 HOH HOH . 
F 6 HOH A 162 562 147 HOH HOH . 
F 6 HOH A 163 563 149 HOH HOH . 
F 6 HOH A 164 564 176 HOH HOH . 
F 6 HOH A 165 565 158 HOH HOH . 
F 6 HOH A 166 566 119 HOH HOH . 
F 6 HOH A 167 567 115 HOH HOH . 
F 6 HOH A 168 568 150 HOH HOH . 
F 6 HOH A 169 569 201 HOH HOH . 
F 6 HOH A 170 570 204 HOH HOH . 
F 6 HOH A 171 571 148 HOH HOH . 
F 6 HOH A 172 572 101 HOH HOH . 
F 6 HOH A 173 573 181 HOH HOH . 
F 6 HOH A 174 574 184 HOH HOH . 
F 6 HOH A 175 575 164 HOH HOH . 
F 6 HOH A 176 576 106 HOH HOH . 
F 6 HOH A 177 577 109 HOH HOH . 
F 6 HOH A 178 578 169 HOH HOH . 
F 6 HOH A 179 579 165 HOH HOH . 
F 6 HOH A 180 580 78 HOH HOH . 
F 6 HOH A 181 581 125 HOH HOH . 
F 6 HOH A 182 582 191 HOH HOH . 
F 6 HOH A 183 583 20 HOH HOH . 
F 6 HOH A 184 584 196 HOH HOH . 
F 6 HOH A 185 585 193 HOH HOH . 
F 6 HOH A 186 586 130 HOH HOH . 
F 6 HOH A 187 587 23 HOH HOH . 
F 6 HOH A 188 588 120 HOH HOH . 
F 6 HOH A 189 589 93 HOH HOH . 
F 6 HOH A 190 590 144 HOH HOH . 
F 6 HOH A 191 591 206 HOH HOH . 
F 6 HOH A 192 592 116 HOH HOH . 
F 6 HOH A 193 593 155 HOH HOH . 
F 6 HOH A 194 594 66 HOH HOH . 
F 6 HOH A 195 595 168 HOH HOH . 
F 6 HOH A 196 596 80 HOH HOH . 
F 6 HOH A 197 597 160 HOH HOH . 
F 6 HOH A 198 598 154 HOH HOH . 
F 6 HOH A 199 599 68 HOH HOH . 
F 6 HOH A 200 600 137 HOH HOH . 
F 6 HOH A 201 601 185 HOH HOH . 
F 6 HOH A 202 602 186 HOH HOH . 
F 6 HOH A 203 603 136 HOH HOH . 
F 6 HOH A 204 604 140 HOH HOH . 
F 6 HOH A 205 605 180 HOH HOH . 
F 6 HOH A 206 606 170 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 SPD . . . D 4 -1.354 4.272 24.265 0.48 21.23 ? N1 SPD 303 A 1 
HETATM 2 C C2 SPD . . . D 4 -1.277 3.361 25.392 0.52 24.18 ? C2 SPD 303 A 1 
HETATM 3 C C3 SPD . . . D 4 -1.94 3.855 26.659 0.71 25.66 ? C3 SPD 303 A 1 
HETATM 4 C C4 SPD . . . D 4 -2.707 2.686 27.227 1 31.8 ? C4 SPD 303 A 1 
HETATM 5 C C5 SPD . . . D 4 -3.832 2.409 26.255 0.3 34.78 ? C5 SPD 303 A 1 
HETATM 6 N N6 SPD . . . D 4 -4.791 1.503 26.819 0.92 33.47 ? N6 SPD 303 A 1 
HETATM 7 C C7 SPD . . . D 4 -5.672 2.396 27.523 0.67 30.31 ? C7 SPD 303 A 1 
HETATM 8 C C8 SPD . . . D 4 -7.069 2.487 26.909 0.97 25.52 ? C8 SPD 303 A 1 
HETATM 9 C C9 SPD . . . D 4 -7.311 3.958 26.6 0.39 25.73 ? C9 SPD 303 A 1 
HETATM 10 N N10 SPD . . . D 4 -8.459 4.176 25.744 0.8 31.94 ? N10 SPD 303 A 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           478 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           10 
#