data_5D3K
#
_model_server_result.job_id            x6sWGKzQNJY7XuHsQd05MA 
_model_server_result.datetime_utc      '2024-12-26 13:32:43' 
_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          5d3k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":305}' 
#
_entry.id    5D3K 
#
_exptl.entry_id    5D3K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CALCIUM ION' 
_entity.pdbx_number_of_molecules    3 
_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            5D3K 
_cell.length_a            112.92 
_cell.length_b            112.92 
_cell.length_c            42.97 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5D3K 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        150 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 3 2 1' 
#
_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,G 
_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 E N N 
? 3 F 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 O VAL 13 A VAL 27 1_555 D CA CA . A CA 303 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc2 A OD2 ASP 35 A ASP 49 1_555 D CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc3 A OE1 GLU 93 A GLU 107 1_555 F CA CA . A CA 305 2_865 ? ? ? ? ? ? ? ? ? ? ? ? 2.44 ? 
metalc ? metalc4 A OE2 GLU 93 A GLU 107 1_555 F CA CA . A CA 305 2_865 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? 
metalc ? metalc5 A OE2 GLU 94 A GLU 108 1_555 E CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc6 A OD2 ASP 185 A ASP 199 1_555 E CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc7 A OD1 ASP 261 A ASP 275 1_555 F CA CA . A CA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc8 A O GLY 265 A GLY 279 1_555 E CA CA . A CA 304 3_785 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? 
metalc ? metalc9 A O GLY 267 A GLY 281 1_555 E CA CA . A CA 304 3_785 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc10 D CA CA . A CA 303 1_555 G O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? 
metalc ? metalc11 D CA CA . A CA 303 1_555 G O HOH . A HOH 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc12 E CA CA . A CA 304 1_555 G O HOH . A HOH 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.374 ? 
metalc ? metalc13 E CA CA . A CA 304 1_555 G O HOH . A HOH 540 2_865 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? 
metalc ? metalc14 F CA CA . A CA 305 1_555 G O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc15 F CA CA . A CA 305 1_555 G O HOH . A HOH 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc16 F CA CA . A CA 305 1_555 G O HOH . A HOH 469 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc17 F CA CA . A CA 305 1_555 G O HOH . A HOH 575 3_785 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? 
#
_chem_comp.formula           'Ca 2' 
_chem_comp.formula_weight    40.078 
_chem_comp.id                CA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CALCIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5D3K 
_atom_sites.fract_transf_matrix[1][1]    0.008856 
_atom_sites.fract_transf_matrix[1][2]    0.005113 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010226 
_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]    0.023272 
_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 1PE A 1 301 3 1PE PE8 . 
C 2 1PE A 1 302 4 1PE PE8 . 
D 3 CA A 1 303 2 CA CA . 
E 3 CA A 1 304 3 CA CA . 
F 3 CA A 1 305 4 CA CA . 
G 4 HOH A 1 401 246 HOH HOH . 
G 4 HOH A 2 402 81 HOH HOH . 
G 4 HOH A 3 403 250 HOH HOH . 
G 4 HOH A 4 404 253 HOH HOH . 
G 4 HOH A 5 405 212 HOH HOH . 
G 4 HOH A 6 406 117 HOH HOH . 
G 4 HOH A 7 407 220 HOH HOH . 
G 4 HOH A 8 408 14 HOH HOH . 
G 4 HOH A 9 409 95 HOH HOH . 
G 4 HOH A 10 410 110 HOH HOH . 
G 4 HOH A 11 411 44 HOH HOH . 
G 4 HOH A 12 412 16 HOH HOH . 
G 4 HOH A 13 413 62 HOH HOH . 
G 4 HOH A 14 414 211 HOH HOH . 
G 4 HOH A 15 415 61 HOH HOH . 
G 4 HOH A 16 416 191 HOH HOH . 
G 4 HOH A 17 417 200 HOH HOH . 
G 4 HOH A 18 418 77 HOH HOH . 
G 4 HOH A 19 419 34 HOH HOH . 
G 4 HOH A 20 420 66 HOH HOH . 
G 4 HOH A 21 421 102 HOH HOH . 
G 4 HOH A 22 422 105 HOH HOH . 
G 4 HOH A 23 423 93 HOH HOH . 
G 4 HOH A 24 424 71 HOH HOH . 
G 4 HOH A 25 425 100 HOH HOH . 
G 4 HOH A 26 426 48 HOH HOH . 
G 4 HOH A 27 427 218 HOH HOH . 
G 4 HOH A 28 428 177 HOH HOH . 
G 4 HOH A 29 429 78 HOH HOH . 
G 4 HOH A 30 430 51 HOH HOH . 
G 4 HOH A 31 431 89 HOH HOH . 
G 4 HOH A 32 432 116 HOH HOH . 
G 4 HOH A 33 433 13 HOH HOH . 
G 4 HOH A 34 434 189 HOH HOH . 
G 4 HOH A 35 435 114 HOH HOH . 
G 4 HOH A 36 436 57 HOH HOH . 
G 4 HOH A 37 437 223 HOH HOH . 
G 4 HOH A 38 438 74 HOH HOH . 
G 4 HOH A 39 439 69 HOH HOH . 
G 4 HOH A 40 440 76 HOH HOH . 
G 4 HOH A 41 441 22 HOH HOH . 
G 4 HOH A 42 442 50 HOH HOH . 
G 4 HOH A 43 443 249 HOH HOH . 
G 4 HOH A 44 444 38 HOH HOH . 
G 4 HOH A 45 445 124 HOH HOH . 
G 4 HOH A 46 446 19 HOH HOH . 
G 4 HOH A 47 447 41 HOH HOH . 
G 4 HOH A 48 448 73 HOH HOH . 
G 4 HOH A 49 449 88 HOH HOH . 
G 4 HOH A 50 450 148 HOH HOH . 
G 4 HOH A 51 451 112 HOH HOH . 
G 4 HOH A 52 452 25 HOH HOH . 
G 4 HOH A 53 453 2 HOH HOH . 
G 4 HOH A 54 454 118 HOH HOH . 
G 4 HOH A 55 455 33 HOH HOH . 
G 4 HOH A 56 456 46 HOH HOH . 
G 4 HOH A 57 457 185 HOH HOH . 
G 4 HOH A 58 458 145 HOH HOH . 
G 4 HOH A 59 459 72 HOH HOH . 
G 4 HOH A 60 460 54 HOH HOH . 
G 4 HOH A 61 461 217 HOH HOH . 
G 4 HOH A 62 462 214 HOH HOH . 
G 4 HOH A 63 463 63 HOH HOH . 
G 4 HOH A 64 464 8 HOH HOH . 
G 4 HOH A 65 465 21 HOH HOH . 
G 4 HOH A 66 466 147 HOH HOH . 
G 4 HOH A 67 467 10 HOH HOH . 
G 4 HOH A 68 468 12 HOH HOH . 
G 4 HOH A 69 469 15 HOH HOH . 
G 4 HOH A 70 470 111 HOH HOH . 
G 4 HOH A 71 471 115 HOH HOH . 
G 4 HOH A 72 472 18 HOH HOH . 
G 4 HOH A 73 473 238 HOH HOH . 
G 4 HOH A 74 474 86 HOH HOH . 
G 4 HOH A 75 475 165 HOH HOH . 
G 4 HOH A 76 476 35 HOH HOH . 
G 4 HOH A 77 477 146 HOH HOH . 
G 4 HOH A 78 478 166 HOH HOH . 
G 4 HOH A 79 479 236 HOH HOH . 
G 4 HOH A 80 480 45 HOH HOH . 
G 4 HOH A 81 481 138 HOH HOH . 
G 4 HOH A 82 482 187 HOH HOH . 
G 4 HOH A 83 483 30 HOH HOH . 
G 4 HOH A 84 484 121 HOH HOH . 
G 4 HOH A 85 485 4 HOH HOH . 
G 4 HOH A 86 486 247 HOH HOH . 
G 4 HOH A 87 487 135 HOH HOH . 
G 4 HOH A 88 488 32 HOH HOH . 
G 4 HOH A 89 489 210 HOH HOH . 
G 4 HOH A 90 490 43 HOH HOH . 
G 4 HOH A 91 491 83 HOH HOH . 
G 4 HOH A 92 492 113 HOH HOH . 
G 4 HOH A 93 493 252 HOH HOH . 
G 4 HOH A 94 494 132 HOH HOH . 
G 4 HOH A 95 495 60 HOH HOH . 
G 4 HOH A 96 496 153 HOH HOH . 
G 4 HOH A 97 497 251 HOH HOH . 
G 4 HOH A 98 498 36 HOH HOH . 
G 4 HOH A 99 499 7 HOH HOH . 
G 4 HOH A 100 500 144 HOH HOH . 
G 4 HOH A 101 501 203 HOH HOH . 
G 4 HOH A 102 502 216 HOH HOH . 
G 4 HOH A 103 503 65 HOH HOH . 
G 4 HOH A 104 504 39 HOH HOH . 
G 4 HOH A 105 505 42 HOH HOH . 
G 4 HOH A 106 506 59 HOH HOH . 
G 4 HOH A 107 507 97 HOH HOH . 
G 4 HOH A 108 508 103 HOH HOH . 
G 4 HOH A 109 509 26 HOH HOH . 
G 4 HOH A 110 510 201 HOH HOH . 
G 4 HOH A 111 511 228 HOH HOH . 
G 4 HOH A 112 512 248 HOH HOH . 
G 4 HOH A 113 513 94 HOH HOH . 
G 4 HOH A 114 514 101 HOH HOH . 
G 4 HOH A 115 515 6 HOH HOH . 
G 4 HOH A 116 516 129 HOH HOH . 
G 4 HOH A 117 517 162 HOH HOH . 
G 4 HOH A 118 518 31 HOH HOH . 
G 4 HOH A 119 519 119 HOH HOH . 
G 4 HOH A 120 520 192 HOH HOH . 
G 4 HOH A 121 521 84 HOH HOH . 
G 4 HOH A 122 522 75 HOH HOH . 
G 4 HOH A 123 523 229 HOH HOH . 
G 4 HOH A 124 524 143 HOH HOH . 
G 4 HOH A 125 525 150 HOH HOH . 
G 4 HOH A 126 526 70 HOH HOH . 
G 4 HOH A 127 527 127 HOH HOH . 
G 4 HOH A 128 528 37 HOH HOH . 
G 4 HOH A 129 529 3 HOH HOH . 
G 4 HOH A 130 530 11 HOH HOH . 
G 4 HOH A 131 531 140 HOH HOH . 
G 4 HOH A 132 532 1 HOH HOH . 
G 4 HOH A 133 533 207 HOH HOH . 
G 4 HOH A 134 534 234 HOH HOH . 
G 4 HOH A 135 535 222 HOH HOH . 
G 4 HOH A 136 536 53 HOH HOH . 
G 4 HOH A 137 537 131 HOH HOH . 
G 4 HOH A 138 538 106 HOH HOH . 
G 4 HOH A 139 539 90 HOH HOH . 
G 4 HOH A 140 540 20 HOH HOH . 
G 4 HOH A 141 541 125 HOH HOH . 
G 4 HOH A 142 542 17 HOH HOH . 
G 4 HOH A 143 543 56 HOH HOH . 
G 4 HOH A 144 544 188 HOH HOH . 
G 4 HOH A 145 545 156 HOH HOH . 
G 4 HOH A 146 546 160 HOH HOH . 
G 4 HOH A 147 547 80 HOH HOH . 
G 4 HOH A 148 548 199 HOH HOH . 
G 4 HOH A 149 549 99 HOH HOH . 
G 4 HOH A 150 550 87 HOH HOH . 
G 4 HOH A 151 551 40 HOH HOH . 
G 4 HOH A 152 552 161 HOH HOH . 
G 4 HOH A 153 553 64 HOH HOH . 
G 4 HOH A 154 554 68 HOH HOH . 
G 4 HOH A 155 555 241 HOH HOH . 
G 4 HOH A 156 556 183 HOH HOH . 
G 4 HOH A 157 557 29 HOH HOH . 
G 4 HOH A 158 558 128 HOH HOH . 
G 4 HOH A 159 559 235 HOH HOH . 
G 4 HOH A 160 560 198 HOH HOH . 
G 4 HOH A 161 561 104 HOH HOH . 
G 4 HOH A 162 562 91 HOH HOH . 
G 4 HOH A 163 563 108 HOH HOH . 
G 4 HOH A 164 564 134 HOH HOH . 
G 4 HOH A 165 565 27 HOH HOH . 
G 4 HOH A 166 566 126 HOH HOH . 
G 4 HOH A 167 567 96 HOH HOH . 
G 4 HOH A 168 568 173 HOH HOH . 
G 4 HOH A 169 569 24 HOH HOH . 
G 4 HOH A 170 570 186 HOH HOH . 
G 4 HOH A 171 571 243 HOH HOH . 
G 4 HOH A 172 572 206 HOH HOH . 
G 4 HOH A 173 573 184 HOH HOH . 
G 4 HOH A 174 574 176 HOH HOH . 
G 4 HOH A 175 575 23 HOH HOH . 
G 4 HOH A 176 576 230 HOH HOH . 
G 4 HOH A 177 577 109 HOH HOH . 
G 4 HOH A 178 578 79 HOH HOH . 
G 4 HOH A 179 579 215 HOH HOH . 
G 4 HOH A 180 580 123 HOH HOH . 
G 4 HOH A 181 581 92 HOH HOH . 
G 4 HOH A 182 582 195 HOH HOH . 
G 4 HOH A 183 583 221 HOH HOH . 
G 4 HOH A 184 584 194 HOH HOH . 
G 4 HOH A 185 585 136 HOH HOH . 
G 4 HOH A 186 586 182 HOH HOH . 
G 4 HOH A 187 587 139 HOH HOH . 
G 4 HOH A 188 588 226 HOH HOH . 
G 4 HOH A 189 589 193 HOH HOH . 
G 4 HOH A 190 591 142 HOH HOH . 
G 4 HOH A 191 592 219 HOH HOH . 
G 4 HOH A 192 593 141 HOH HOH . 
G 4 HOH A 193 594 178 HOH HOH . 
G 4 HOH A 194 595 168 HOH HOH . 
G 4 HOH A 195 596 224 HOH HOH . 
G 4 HOH A 196 597 209 HOH HOH . 
G 4 HOH A 197 598 169 HOH HOH . 
G 4 HOH A 198 599 233 HOH HOH . 
G 4 HOH A 199 600 240 HOH HOH . 
G 4 HOH A 200 601 151 HOH HOH . 
G 4 HOH A 201 602 175 HOH HOH . 
G 4 HOH A 202 603 196 HOH HOH . 
G 4 HOH A 203 604 181 HOH HOH . 
G 4 HOH A 204 605 197 HOH HOH . 
G 4 HOH A 205 606 167 HOH HOH . 
G 4 HOH A 206 607 170 HOH HOH . 
G 4 HOH A 207 608 204 HOH HOH . 
G 4 HOH A 208 609 213 HOH HOH . 
G 4 HOH A 209 610 120 HOH HOH . 
G 4 HOH A 210 611 232 HOH HOH . 
G 4 HOH A 211 612 67 HOH HOH . 
G 4 HOH A 212 613 174 HOH HOH . 
G 4 HOH A 213 614 163 HOH HOH . 
G 4 HOH A 214 615 157 HOH HOH . 
G 4 HOH A 215 616 154 HOH HOH . 
G 4 HOH A 216 617 28 HOH HOH . 
G 4 HOH A 217 618 202 HOH HOH . 
G 4 HOH A 218 619 179 HOH HOH . 
G 4 HOH A 219 620 149 HOH HOH . 
G 4 HOH A 220 621 242 HOH HOH . 
G 4 HOH A 221 622 133 HOH HOH . 
G 4 HOH A 222 623 159 HOH HOH . 
G 4 HOH A 223 624 85 HOH HOH . 
G 4 HOH A 224 625 237 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           CA 
_atom_site.label_atom_id         CA 
_atom_site.label_comp_id         CA 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         F 
_atom_site.label_entity_id       3 
_atom_site.Cartn_x               131.33 
_atom_site.Cartn_y               134.265 
_atom_site.Cartn_z               47.529 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        11.9 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           305 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#