data_9EBM # _model_server_result.job_id iHGQ0Mo7Fa5IVJPjhSbpFA _model_server_result.datetime_utc '2025-06-27 19:49:45' _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 9ebm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":502}' # _entry.id 9EBM # _exptl.entry_id 9EBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 148.16 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N~5~-hydroxy-L-ornithine _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 120 _cell.entry_id 9EBM _cell.length_a 67.002 _cell.length_b 67.002 _cell.length_c 479.001 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9EBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall 'P 61 2 (x,y,z+5/12)' _symmetry.space_group_name_H-M 'P 61 2 2' # _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,G,H,I,J _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 H N 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 metalc ? metalc1 A NE2 HIS 66 B HIS 66 1_555 C FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc2 C FE HEM . B HEM 501 1_555 D NE ONH . B ONH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc3 B NE2 HIS 66 A HIS 66 1_555 E FE HEM . A HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc4 E FE HEM . A HEM 301 1_555 H NE ONH . A ONH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.969 ? metalc ? metalc5 E FE HEM . A HEM 301 1_555 H OZ ONH . A ONH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? # _chem_comp.formula 'C5 H12 N2 O3' _chem_comp.formula_weight 148.16 _chem_comp.id ONH _chem_comp.mon_nstd_flag n _chem_comp.name N~5~-hydroxy-L-ornithine _chem_comp.type 'l-peptide linking' _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 O C ONH doub 332 n n C OXT ONH sing 333 n n C CA ONH sing 334 n n N CA ONH sing 335 n n N HN ONH sing 336 n n N HNA ONH sing 337 n n CB CA ONH sing 338 n n CA HA ONH sing 339 n n CB CG ONH sing 340 n n CB HB ONH sing 341 n n CB HBA ONH sing 342 n n CD CG ONH sing 343 n n CD NE ONH sing 344 n n CD HD ONH sing 345 n n CD HDA ONH sing 346 n n OZ NE ONH sing 347 n n CG HG ONH sing 348 n n CG HGA ONH sing 349 n n OXT HOXT ONH sing 350 n n OZ HOZ ONH sing 351 n n NE HNE ONH sing 352 n n # _atom_sites.entry_id 9EBM _atom_sites.fract_transf_matrix[1][1] 0.014925 _atom_sites.fract_transf_matrix[1][2] 0.008617 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017234 _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] 0.002088 _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 2 HEM B 1 501 501 HEM HEM . D 3 ONH B 1 502 1 ONH OOH . E 2 HEM A 1 301 502 HEM HEM . F 4 GOL A 1 302 1 GOL GOL . G 4 GOL A 1 303 2 GOL GOL . H 3 ONH A 1 304 2 ONH OOH . I 5 HOH B 1 601 171 HOH HOH . I 5 HOH B 2 602 105 HOH HOH . I 5 HOH B 3 603 280 HOH HOH . I 5 HOH B 4 604 73 HOH HOH . I 5 HOH B 5 605 112 HOH HOH . I 5 HOH B 6 606 145 HOH HOH . I 5 HOH B 7 607 181 HOH HOH . I 5 HOH B 8 608 102 HOH HOH . I 5 HOH B 9 609 271 HOH HOH . I 5 HOH B 10 610 70 HOH HOH . I 5 HOH B 11 611 47 HOH HOH . I 5 HOH B 12 612 179 HOH HOH . I 5 HOH B 13 613 58 HOH HOH . I 5 HOH B 14 614 27 HOH HOH . I 5 HOH B 15 615 85 HOH HOH . I 5 HOH B 16 616 115 HOH HOH . I 5 HOH B 17 617 84 HOH HOH . I 5 HOH B 18 618 37 HOH HOH . I 5 HOH B 19 619 2 HOH HOH . I 5 HOH B 20 620 182 HOH HOH . I 5 HOH B 21 621 278 HOH HOH . I 5 HOH B 22 622 20 HOH HOH . I 5 HOH B 23 623 15 HOH HOH . I 5 HOH B 24 624 133 HOH HOH . I 5 HOH B 25 625 38 HOH HOH . I 5 HOH B 26 626 183 HOH HOH . I 5 HOH B 27 627 60 HOH HOH . I 5 HOH B 28 628 71 HOH HOH . I 5 HOH B 29 629 28 HOH HOH . I 5 HOH B 30 630 114 HOH HOH . I 5 HOH B 31 631 22 HOH HOH . I 5 HOH B 32 632 146 HOH HOH . I 5 HOH B 33 633 269 HOH HOH . I 5 HOH B 34 634 90 HOH HOH . I 5 HOH B 35 635 268 HOH HOH . I 5 HOH B 36 636 23 HOH HOH . I 5 HOH B 37 637 118 HOH HOH . I 5 HOH B 38 638 193 HOH HOH . I 5 HOH B 39 639 195 HOH HOH . I 5 HOH B 40 640 140 HOH HOH . I 5 HOH B 41 641 78 HOH HOH . I 5 HOH B 42 642 31 HOH HOH . I 5 HOH B 43 643 96 HOH HOH . I 5 HOH B 44 644 43 HOH HOH . I 5 HOH B 45 645 12 HOH HOH . I 5 HOH B 46 646 95 HOH HOH . I 5 HOH B 47 647 190 HOH HOH . I 5 HOH B 48 648 134 HOH HOH . I 5 HOH B 49 649 110 HOH HOH . I 5 HOH B 50 650 304 HOH HOH . I 5 HOH B 51 651 234 HOH HOH . I 5 HOH B 52 652 192 HOH HOH . I 5 HOH B 53 653 274 HOH HOH . I 5 HOH B 54 654 270 HOH HOH . I 5 HOH B 55 655 77 HOH HOH . I 5 HOH B 56 656 109 HOH HOH . I 5 HOH B 57 657 175 HOH HOH . I 5 HOH B 58 658 276 HOH HOH . I 5 HOH B 59 659 98 HOH HOH . I 5 HOH B 60 660 89 HOH HOH . I 5 HOH B 61 661 231 HOH HOH . I 5 HOH B 62 662 125 HOH HOH . I 5 HOH B 63 663 14 HOH HOH . I 5 HOH B 64 664 237 HOH HOH . I 5 HOH B 65 665 199 HOH HOH . I 5 HOH B 66 666 50 HOH HOH . I 5 HOH B 67 667 40 HOH HOH . I 5 HOH B 68 668 36 HOH HOH . I 5 HOH B 69 669 188 HOH HOH . I 5 HOH B 70 670 1 HOH HOH . I 5 HOH B 71 671 218 HOH HOH . I 5 HOH B 72 672 99 HOH HOH . I 5 HOH B 73 673 295 HOH HOH . I 5 HOH B 74 674 18 HOH HOH . I 5 HOH B 75 675 170 HOH HOH . I 5 HOH B 76 676 86 HOH HOH . I 5 HOH B 77 677 239 HOH HOH . I 5 HOH B 78 678 32 HOH HOH . I 5 HOH B 79 679 7 HOH HOH . I 5 HOH B 80 680 254 HOH HOH . I 5 HOH B 81 681 126 HOH HOH . I 5 HOH B 82 682 298 HOH HOH . I 5 HOH B 83 683 8 HOH HOH . I 5 HOH B 84 684 267 HOH HOH . I 5 HOH B 85 685 24 HOH HOH . I 5 HOH B 86 686 163 HOH HOH . I 5 HOH B 87 687 297 HOH HOH . I 5 HOH B 88 688 292 HOH HOH . I 5 HOH B 89 689 194 HOH HOH . I 5 HOH B 90 690 240 HOH HOH . I 5 HOH B 91 691 198 HOH HOH . I 5 HOH B 92 692 164 HOH HOH . I 5 HOH B 93 693 277 HOH HOH . I 5 HOH B 94 694 92 HOH HOH . I 5 HOH B 95 695 174 HOH HOH . I 5 HOH B 96 696 205 HOH HOH . I 5 HOH B 97 697 100 HOH HOH . I 5 HOH B 98 698 162 HOH HOH . I 5 HOH B 99 699 82 HOH HOH . I 5 HOH B 100 700 287 HOH HOH . I 5 HOH B 101 701 299 HOH HOH . I 5 HOH B 102 702 35 HOH HOH . I 5 HOH B 103 703 169 HOH HOH . I 5 HOH B 104 704 294 HOH HOH . J 5 HOH A 1 401 248 HOH HOH . J 5 HOH A 2 402 309 HOH HOH . J 5 HOH A 3 403 310 HOH HOH . J 5 HOH A 4 404 5 HOH HOH . J 5 HOH A 5 405 226 HOH HOH . J 5 HOH A 6 406 155 HOH HOH . J 5 HOH A 7 407 160 HOH HOH . J 5 HOH A 8 408 201 HOH HOH . J 5 HOH A 9 409 220 HOH HOH . J 5 HOH A 10 410 56 HOH HOH . J 5 HOH A 11 411 290 HOH HOH . J 5 HOH A 12 412 122 HOH HOH . J 5 HOH A 13 413 135 HOH HOH . J 5 HOH A 14 414 215 HOH HOH . J 5 HOH A 15 415 147 HOH HOH . J 5 HOH A 16 416 168 HOH HOH . J 5 HOH A 17 417 284 HOH HOH . J 5 HOH A 18 418 57 HOH HOH . J 5 HOH A 19 419 53 HOH HOH . J 5 HOH A 20 420 221 HOH HOH . J 5 HOH A 21 421 4 HOH HOH . J 5 HOH A 22 422 186 HOH HOH . J 5 HOH A 23 423 258 HOH HOH . J 5 HOH A 24 424 301 HOH HOH . J 5 HOH A 25 425 196 HOH HOH . J 5 HOH A 26 426 216 HOH HOH . J 5 HOH A 27 427 83 HOH HOH . J 5 HOH A 28 428 88 HOH HOH . J 5 HOH A 29 429 111 HOH HOH . J 5 HOH A 30 430 232 HOH HOH . J 5 HOH A 31 431 124 HOH HOH . J 5 HOH A 32 432 144 HOH HOH . J 5 HOH A 33 433 103 HOH HOH . J 5 HOH A 34 434 49 HOH HOH . J 5 HOH A 35 435 44 HOH HOH . J 5 HOH A 36 436 61 HOH HOH . J 5 HOH A 37 437 306 HOH HOH . J 5 HOH A 38 438 10 HOH HOH . J 5 HOH A 39 439 200 HOH HOH . J 5 HOH A 40 440 187 HOH HOH . J 5 HOH A 41 441 104 HOH HOH . J 5 HOH A 42 442 273 HOH HOH . J 5 HOH A 43 443 25 HOH HOH . J 5 HOH A 44 444 149 HOH HOH . J 5 HOH A 45 445 264 HOH HOH . J 5 HOH A 46 446 26 HOH HOH . J 5 HOH A 47 447 121 HOH HOH . J 5 HOH A 48 448 210 HOH HOH . J 5 HOH A 49 449 101 HOH HOH . J 5 HOH A 50 450 65 HOH HOH . J 5 HOH A 51 451 13 HOH HOH . J 5 HOH A 52 452 263 HOH HOH . J 5 HOH A 53 453 34 HOH HOH . J 5 HOH A 54 454 117 HOH HOH . J 5 HOH A 55 455 72 HOH HOH . J 5 HOH A 56 456 211 HOH HOH . J 5 HOH A 57 457 79 HOH HOH . J 5 HOH A 58 458 21 HOH HOH . J 5 HOH A 59 459 41 HOH HOH . J 5 HOH A 60 460 17 HOH HOH . J 5 HOH A 61 461 52 HOH HOH . J 5 HOH A 62 462 108 HOH HOH . J 5 HOH A 63 463 67 HOH HOH . J 5 HOH A 64 464 120 HOH HOH . J 5 HOH A 65 465 46 HOH HOH . J 5 HOH A 66 466 137 HOH HOH . J 5 HOH A 67 467 223 HOH HOH . J 5 HOH A 68 468 141 HOH HOH . J 5 HOH A 69 469 128 HOH HOH . J 5 HOH A 70 470 45 HOH HOH . J 5 HOH A 71 471 48 HOH HOH . J 5 HOH A 72 472 106 HOH HOH . J 5 HOH A 73 473 54 HOH HOH . J 5 HOH A 74 474 16 HOH HOH . J 5 HOH A 75 475 127 HOH HOH . J 5 HOH A 76 476 132 HOH HOH . J 5 HOH A 77 477 64 HOH HOH . J 5 HOH A 78 478 289 HOH HOH . J 5 HOH A 79 479 123 HOH HOH . J 5 HOH A 80 480 227 HOH HOH . J 5 HOH A 81 481 76 HOH HOH . J 5 HOH A 82 482 19 HOH HOH . J 5 HOH A 83 483 116 HOH HOH . J 5 HOH A 84 484 253 HOH HOH . J 5 HOH A 85 485 94 HOH HOH . J 5 HOH A 86 486 245 HOH HOH . J 5 HOH A 87 487 69 HOH HOH . J 5 HOH A 88 488 51 HOH HOH . J 5 HOH A 89 489 214 HOH HOH . J 5 HOH A 90 490 39 HOH HOH . J 5 HOH A 91 491 257 HOH HOH . J 5 HOH A 92 492 282 HOH HOH . J 5 HOH A 93 493 279 HOH HOH . J 5 HOH A 94 494 303 HOH HOH . J 5 HOH A 95 495 230 HOH HOH . J 5 HOH A 96 496 260 HOH HOH . J 5 HOH A 97 497 11 HOH HOH . J 5 HOH A 98 498 296 HOH HOH . J 5 HOH A 99 499 130 HOH HOH . J 5 HOH A 100 500 91 HOH HOH . J 5 HOH A 101 501 247 HOH HOH . J 5 HOH A 102 502 219 HOH HOH . J 5 HOH A 103 503 293 HOH HOH . J 5 HOH A 104 504 291 HOH HOH . J 5 HOH A 105 505 233 HOH HOH . J 5 HOH A 106 506 286 HOH HOH . J 5 HOH A 107 507 6 HOH HOH . J 5 HOH A 108 508 142 HOH HOH . J 5 HOH A 109 509 97 HOH HOH . J 5 HOH A 110 510 243 HOH HOH . J 5 HOH A 111 511 259 HOH HOH . J 5 HOH A 112 512 136 HOH HOH . J 5 HOH A 113 513 241 HOH HOH . J 5 HOH A 114 514 66 HOH HOH . J 5 HOH A 115 515 250 HOH HOH . J 5 HOH A 116 516 3 HOH HOH . J 5 HOH A 117 517 59 HOH HOH . J 5 HOH A 118 518 308 HOH HOH . J 5 HOH A 119 519 159 HOH HOH . J 5 HOH A 120 520 302 HOH HOH . J 5 HOH A 121 521 265 HOH HOH . J 5 HOH A 122 522 212 HOH HOH . J 5 HOH A 123 523 262 HOH HOH . J 5 HOH A 124 524 197 HOH HOH . J 5 HOH A 125 525 177 HOH HOH . J 5 HOH A 126 526 256 HOH HOH . J 5 HOH A 127 527 178 HOH HOH . J 5 HOH A 128 528 213 HOH HOH . J 5 HOH A 129 529 42 HOH HOH . J 5 HOH A 130 530 165 HOH HOH . J 5 HOH A 131 531 261 HOH HOH . J 5 HOH A 132 532 80 HOH HOH . J 5 HOH A 133 533 242 HOH HOH . J 5 HOH A 134 534 173 HOH HOH . J 5 HOH A 135 535 29 HOH HOH . J 5 HOH A 136 536 172 HOH HOH . J 5 HOH A 137 537 166 HOH HOH . J 5 HOH A 138 538 30 HOH HOH . J 5 HOH A 139 539 235 HOH HOH . J 5 HOH A 140 540 228 HOH HOH . J 5 HOH A 141 541 300 HOH HOH . J 5 HOH A 142 542 307 HOH HOH . J 5 HOH A 143 543 167 HOH HOH . J 5 HOH A 144 544 191 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 C ONH . . . D 3 -33.566 12.361 -28.672 1 65.72 ? C ONH 502 B 1 HETATM 2 N N ONH . . . D 3 -33.068 14.849 -28.766 1 61.51 ? N ONH 502 B 1 HETATM 3 O O ONH . . . D 3 -34.168 12.725 -27.649 1 61.61 ? O ONH 502 B 1 HETATM 4 C CA ONH . . . D 3 -32.473 13.516 -29.222 1 59.68 ? CA ONH 502 B 1 HETATM 5 C CB ONH . . . D 3 -31.047 13.299 -28.672 1 50.23 ? CB ONH 502 B 1 HETATM 6 C CD ONH . . . D 3 -29.765 11.974 -26.913 1 41.54 ? CD ONH 502 B 1 HETATM 7 N NE ONH . . . D 3 -28.797 13.009 -26.407 1 41.88 ? NE ONH 502 B 1 HETATM 8 C CG ONH . . . D 3 -31.074 12.721 -27.251 1 45.43 ? CG ONH 502 B 1 HETATM 9 O OZ ONH . . . D 3 -29.425 13.593 -25.335 1 64.92 ? OZ ONH 502 B 1 HETATM 10 O OXT ONH . . . D 3 -33.601 11.35 -29.365 1 66.18 ? OXT ONH 502 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 10 #