data_6D5P
#
_model_server_result.job_id            F7e4dehCsBXeUpQuV1ieMw 
_model_server_result.datetime_utc      '2024-11-23 04:59:37' 
_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          6d5p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":404}' 
#
_entry.id    6D5P 
#
_exptl.entry_id    6D5P 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CALCIUM ION' 
_entity.pdbx_number_of_molecules    4 
_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            6D5P 
_cell.length_a            93.307 
_cell.length_b            93.307 
_cell.length_c            129.125 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6D5P 
_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    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,H,I,J,K,L 
_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
? 5 E N N 
? 5 F N N 
? 5 G N N 
? 5 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 OD1 ASP 57 A ASP 57 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? 
metalc ? metalc2 A OD2 ASP 57 A ASP 57 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc3 A OD1 ASP 59 A ASP 59 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc4 A O GLN 61 A GLN 61 1_555 F CA CA . A CA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? 
metalc ? metalc5 A OD2 ASP 138 A ASP 138 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? 
metalc ? metalc6 A NE2 HIS 142 A HIS 142 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc7 A NE2 HIS 146 A HIS 146 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? 
metalc ? metalc8 A OE2 GLU 166 A GLU 166 1_555 D ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? 
metalc ? metalc9 A OE1 GLU 177 A GLU 177 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? 
metalc ? metalc10 A OE2 GLU 177 A GLU 177 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc11 A OE2 GLU 177 A GLU 177 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? 
metalc ? metalc12 A O ASN 183 A ASN 183 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc13 A OD1 ASP 185 A ASP 185 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.748 ? 
metalc ? metalc14 A OD2 ASP 185 A ASP 185 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc15 A O GLU 187 A GLU 187 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? 
metalc ? metalc16 A OE1 GLU 190 A GLU 190 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? 
metalc ? metalc17 A OE2 GLU 190 A GLU 190 1_555 E CA CA . A CA 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc18 A OE2 GLU 190 A GLU 190 1_555 H CA CA . A CA 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc19 A O TYR 193 A TYR 193 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc20 A O THR 194 A THR 194 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc21 A OG1 THR 194 A THR 194 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? 
metalc ? metalc22 A O ILE 197 A ILE 197 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc23 A OD1 ASP 200 A ASP 200 1_555 G CA CA . A CA 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? 
metalc ? metalc24 D ZN ZN . A ZN 403 1_555 L O HOH . A HOH 526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? 
metalc ? metalc25 E CA CA . A CA 404 1_555 L O HOH . A HOH 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? 
metalc ? metalc26 F CA CA . A CA 405 1_555 L O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
metalc ? metalc27 F CA CA . A CA 405 1_555 L O HOH . A HOH 569 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? 
metalc ? metalc28 G CA CA . A CA 406 1_555 L O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? 
metalc ? metalc29 G CA CA . A CA 406 1_555 L O HOH . A HOH 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? 
#
_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                     6D5P 
_atom_sites.fract_transf_matrix[1][1]    0.010717 
_atom_sites.fract_transf_matrix[1][2]    0.006188 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012375 
_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]    0.007744 
_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 VAL A 1 401 401 VAL VAL . 
C 3 LYS A 1 402 402 LYS LYS . 
D 4 ZN A 1 403 403 ZN ZN . 
E 5 CA A 1 404 404 CA CA . 
F 5 CA A 1 405 405 CA CA . 
G 5 CA A 1 406 406 CA CA . 
H 5 CA A 1 407 407 CA CA . 
I 6 XYP A 1 408 408 XYP XYP . 
J 6 XYP A 1 409 409 XYP XYP . 
K 6 XYP A 1 410 410 XYP XYP . 
L 7 HOH A 1 501 501 HOH HOH . 
L 7 HOH A 2 502 502 HOH HOH . 
L 7 HOH A 3 503 503 HOH HOH . 
L 7 HOH A 4 504 504 HOH HOH . 
L 7 HOH A 5 505 505 HOH HOH . 
L 7 HOH A 6 506 506 HOH HOH . 
L 7 HOH A 7 507 507 HOH HOH . 
L 7 HOH A 8 508 508 HOH HOH . 
L 7 HOH A 9 509 509 HOH HOH . 
L 7 HOH A 10 510 510 HOH HOH . 
L 7 HOH A 11 511 511 HOH HOH . 
L 7 HOH A 12 512 512 HOH HOH . 
L 7 HOH A 13 513 513 HOH HOH . 
L 7 HOH A 14 514 514 HOH HOH . 
L 7 HOH A 15 515 515 HOH HOH . 
L 7 HOH A 16 516 516 HOH HOH . 
L 7 HOH A 17 517 517 HOH HOH . 
L 7 HOH A 18 518 518 HOH HOH . 
L 7 HOH A 19 519 519 HOH HOH . 
L 7 HOH A 20 520 521 HOH HOH . 
L 7 HOH A 21 521 520 HOH HOH . 
L 7 HOH A 22 522 522 HOH HOH . 
L 7 HOH A 23 523 523 HOH HOH . 
L 7 HOH A 24 524 524 HOH HOH . 
L 7 HOH A 25 525 525 HOH HOH . 
L 7 HOH A 26 526 526 HOH HOH . 
L 7 HOH A 27 527 527 HOH HOH . 
L 7 HOH A 28 528 528 HOH HOH . 
L 7 HOH A 29 529 529 HOH HOH . 
L 7 HOH A 30 530 530 HOH HOH . 
L 7 HOH A 31 531 534 HOH HOH . 
L 7 HOH A 32 532 533 HOH HOH . 
L 7 HOH A 33 533 531 HOH HOH . 
L 7 HOH A 34 534 535 HOH HOH . 
L 7 HOH A 35 535 532 HOH HOH . 
L 7 HOH A 36 536 536 HOH HOH . 
L 7 HOH A 37 537 537 HOH HOH . 
L 7 HOH A 38 538 539 HOH HOH . 
L 7 HOH A 39 539 538 HOH HOH . 
L 7 HOH A 40 540 540 HOH HOH . 
L 7 HOH A 41 541 541 HOH HOH . 
L 7 HOH A 42 542 542 HOH HOH . 
L 7 HOH A 43 543 544 HOH HOH . 
L 7 HOH A 44 544 543 HOH HOH . 
L 7 HOH A 45 545 545 HOH HOH . 
L 7 HOH A 46 546 546 HOH HOH . 
L 7 HOH A 47 547 547 HOH HOH . 
L 7 HOH A 48 548 548 HOH HOH . 
L 7 HOH A 49 549 549 HOH HOH . 
L 7 HOH A 50 550 550 HOH HOH . 
L 7 HOH A 51 551 551 HOH HOH . 
L 7 HOH A 52 552 552 HOH HOH . 
L 7 HOH A 53 553 553 HOH HOH . 
L 7 HOH A 54 554 554 HOH HOH . 
L 7 HOH A 55 555 555 HOH HOH . 
L 7 HOH A 56 556 556 HOH HOH . 
L 7 HOH A 57 557 557 HOH HOH . 
L 7 HOH A 58 558 559 HOH HOH . 
L 7 HOH A 59 559 558 HOH HOH . 
L 7 HOH A 60 560 560 HOH HOH . 
L 7 HOH A 61 561 561 HOH HOH . 
L 7 HOH A 62 562 562 HOH HOH . 
L 7 HOH A 63 563 563 HOH HOH . 
L 7 HOH A 64 564 564 HOH HOH . 
L 7 HOH A 65 565 567 HOH HOH . 
L 7 HOH A 66 566 565 HOH HOH . 
L 7 HOH A 67 567 566 HOH HOH . 
L 7 HOH A 68 568 568 HOH HOH . 
L 7 HOH A 69 569 569 HOH HOH . 
L 7 HOH A 70 570 570 HOH HOH . 
L 7 HOH A 71 571 572 HOH HOH . 
L 7 HOH A 72 572 571 HOH HOH . 
L 7 HOH A 73 573 573 HOH HOH . 
L 7 HOH A 74 574 574 HOH HOH . 
L 7 HOH A 75 575 575 HOH HOH . 
L 7 HOH A 76 576 576 HOH HOH . 
L 7 HOH A 77 577 577 HOH HOH . 
L 7 HOH A 78 578 578 HOH HOH . 
L 7 HOH A 79 579 580 HOH HOH . 
L 7 HOH A 80 580 579 HOH HOH . 
L 7 HOH A 81 581 581 HOH HOH . 
L 7 HOH A 82 582 582 HOH HOH . 
L 7 HOH A 83 583 583 HOH HOH . 
L 7 HOH A 84 584 584 HOH HOH . 
L 7 HOH A 85 585 585 HOH HOH . 
L 7 HOH A 86 586 586 HOH HOH . 
L 7 HOH A 87 587 587 HOH HOH . 
L 7 HOH A 88 588 588 HOH HOH . 
L 7 HOH A 89 589 589 HOH HOH . 
L 7 HOH A 90 590 590 HOH HOH . 
L 7 HOH A 91 591 591 HOH HOH . 
L 7 HOH A 92 592 592 HOH HOH . 
L 7 HOH A 93 593 593 HOH HOH . 
L 7 HOH A 94 594 594 HOH HOH . 
L 7 HOH A 95 595 595 HOH HOH . 
L 7 HOH A 96 596 596 HOH HOH . 
L 7 HOH A 97 597 597 HOH HOH . 
L 7 HOH A 98 598 598 HOH HOH . 
L 7 HOH A 99 599 599 HOH HOH . 
L 7 HOH A 100 600 600 HOH HOH . 
L 7 HOH A 101 601 601 HOH HOH . 
L 7 HOH A 102 602 602 HOH HOH . 
L 7 HOH A 103 603 604 HOH HOH . 
L 7 HOH A 104 604 603 HOH HOH . 
L 7 HOH A 105 605 605 HOH HOH . 
L 7 HOH A 106 606 606 HOH HOH . 
L 7 HOH A 107 607 607 HOH HOH . 
L 7 HOH A 108 608 608 HOH HOH . 
L 7 HOH A 109 609 610 HOH HOH . 
L 7 HOH A 110 610 609 HOH HOH . 
L 7 HOH A 111 611 611 HOH HOH . 
L 7 HOH A 112 612 612 HOH HOH . 
L 7 HOH A 113 613 613 HOH HOH . 
L 7 HOH A 114 614 614 HOH HOH . 
L 7 HOH A 115 615 615 HOH HOH . 
L 7 HOH A 116 616 616 HOH HOH . 
L 7 HOH A 117 617 617 HOH HOH . 
L 7 HOH A 118 618 618 HOH HOH . 
L 7 HOH A 119 619 619 HOH HOH . 
L 7 HOH A 120 620 620 HOH HOH . 
L 7 HOH A 121 621 621 HOH HOH . 
L 7 HOH A 122 622 622 HOH HOH . 
L 7 HOH A 123 623 623 HOH HOH . 
L 7 HOH A 124 624 624 HOH HOH . 
L 7 HOH A 125 625 625 HOH HOH . 
L 7 HOH A 126 626 626 HOH HOH . 
L 7 HOH A 127 627 628 HOH HOH . 
L 7 HOH A 128 628 627 HOH HOH . 
L 7 HOH A 129 629 629 HOH HOH . 
L 7 HOH A 130 630 630 HOH HOH . 
L 7 HOH A 131 631 631 HOH HOH . 
L 7 HOH A 132 632 633 HOH HOH . 
L 7 HOH A 133 633 632 HOH HOH . 
L 7 HOH A 134 634 634 HOH HOH . 
L 7 HOH A 135 635 635 HOH HOH . 
L 7 HOH A 136 636 636 HOH HOH . 
L 7 HOH A 137 637 637 HOH HOH . 
L 7 HOH A 138 638 638 HOH HOH . 
L 7 HOH A 139 639 639 HOH HOH . 
L 7 HOH A 140 640 640 HOH HOH . 
L 7 HOH A 141 641 641 HOH HOH . 
L 7 HOH A 142 642 642 HOH HOH . 
L 7 HOH A 143 643 643 HOH HOH . 
L 7 HOH A 144 644 644 HOH HOH . 
L 7 HOH A 145 645 645 HOH HOH . 
L 7 HOH A 146 646 646 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         E 
_atom_site.label_entity_id       5 
_atom_site.Cartn_x               4.619 
_atom_site.Cartn_y               -31.296 
_atom_site.Cartn_z               -4.402 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        19.57 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           404 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#