data_4NDD # _model_server_result.job_id GNqG6OLfMYRlFUYjFMvjoA _model_server_result.datetime_utc '2025-03-25 18:56:26' _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 4ndd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 4NDD # _exptl.entry_id 4NDD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 40.078 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'CALCIUM ION' _entity.pdbx_number_of_molecules 6 _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 4NDD _cell.length_a 46.806 _cell.length_b 69.387 _cell.length_c 133.466 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NDD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 ? 2 C N N ? 2 D N N ? 2 E N N ? 2 F N N ? 2 G N N ? 2 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 44 A ASP 23 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc2 A OD1 ASN 46 A ASN 25 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc3 A OD1 ASP 48 A ASP 27 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc4 A O VAL 50 A VAL 29 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc5 A OD2 ASP 55 A ASP 34 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? metalc ? metalc6 A OD1 ASP 55 A ASP 34 1_555 C CA CA . A CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc7 A OD1 ASP 95 A ASP 74 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? metalc ? metalc8 A OD1 ASN 97 A ASN 76 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc9 A OD1 ASP 99 A ASP 78 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc10 A O GLN 101 A GLN 80 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc11 A OE1 GLU 106 A GLU 85 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.48 ? metalc ? metalc12 A OE2 GLU 106 A GLU 85 1_555 D CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc13 A OD1 ASP 140 A ASP 119 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.731 ? metalc ? metalc14 A OG SER 142 A SER 121 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc15 A OD1 ASP 144 A ASP 123 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc16 A O ILE 146 A ILE 125 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc17 A OE2 GLU 151 A GLU 130 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc18 A OE1 GLU 151 A GLU 130 1_555 E CA CA . A CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.752 ? metalc ? metalc19 C CA CA . A CA 401 1_555 I O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc20 D CA CA . A CA 402 1_555 I O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc21 E CA CA . A CA 403 1_555 I O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc22 B OD1 ASP 44 B ASP 23 1_555 F CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? metalc ? metalc23 B OD1 ASP 48 B ASP 27 1_555 F CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc24 B O VAL 50 B VAL 29 1_555 F CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc25 B OD1 ASP 55 B ASP 34 1_555 F CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc26 B OD2 ASP 55 B ASP 34 1_555 F CA CA . B CA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc27 B OD1 ASP 95 B ASP 74 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc28 B OD1 ASN 97 B ASN 76 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? metalc ? metalc29 B OD1 ASP 99 B ASP 78 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc30 B O GLN 101 B GLN 80 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? metalc ? metalc31 B OE1 GLU 106 B GLU 85 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc32 B OE2 GLU 106 B GLU 85 1_555 G CA CA . B CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc33 B OD1 ASP 140 B ASP 119 1_555 H CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.687 ? metalc ? metalc34 B OD1 ASP 144 B ASP 123 1_555 H CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? metalc ? metalc35 B O ILE 146 B ILE 125 1_555 H CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc36 B OE2 GLU 151 B GLU 130 1_555 H CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc37 B OE1 GLU 151 B GLU 130 1_555 H CA CA . B CA 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc38 F CA CA . B CA 401 1_555 J O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc39 G CA CA . B CA 402 1_555 J O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc40 H CA CA . B CA 403 1_555 J O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.651 ? # _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 4NDD _atom_sites.fract_transf_matrix[1][1] 0.021365 _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] 0.014412 _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] 0.007493 _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 CA A 1 401 401 CA CA . D 2 CA A 1 402 402 CA CA . E 2 CA A 1 403 403 CA CA . F 2 CA B 1 401 401 CA CA . G 2 CA B 1 402 402 CA CA . H 2 CA B 1 403 403 CA CA . I 3 HOH A 1 501 501 HOH HOH . I 3 HOH A 2 502 502 HOH HOH . I 3 HOH A 3 503 503 HOH HOH . I 3 HOH A 4 504 508 HOH HOH . I 3 HOH A 5 505 512 HOH HOH . I 3 HOH A 6 506 517 HOH HOH . I 3 HOH A 7 507 518 HOH HOH . I 3 HOH A 8 508 529 HOH HOH . I 3 HOH A 9 509 533 HOH HOH . I 3 HOH A 10 510 536 HOH HOH . I 3 HOH A 11 511 537 HOH HOH . I 3 HOH A 12 512 539 HOH HOH . I 3 HOH A 13 513 541 HOH HOH . I 3 HOH A 14 514 555 HOH HOH . I 3 HOH A 15 515 559 HOH HOH . I 3 HOH A 16 516 567 HOH HOH . I 3 HOH A 17 517 568 HOH HOH . I 3 HOH A 18 518 570 HOH HOH . I 3 HOH A 19 519 573 HOH HOH . I 3 HOH A 20 520 576 HOH HOH . I 3 HOH A 21 521 577 HOH HOH . I 3 HOH A 22 522 579 HOH HOH . I 3 HOH A 23 523 580 HOH HOH . I 3 HOH A 24 524 594 HOH HOH . I 3 HOH A 25 525 598 HOH HOH . I 3 HOH A 26 526 600 HOH HOH . I 3 HOH A 27 527 601 HOH HOH . I 3 HOH A 28 528 605 HOH HOH . I 3 HOH A 29 529 606 HOH HOH . I 3 HOH A 30 530 623 HOH HOH . I 3 HOH A 31 531 624 HOH HOH . I 3 HOH A 32 532 625 HOH HOH . I 3 HOH A 33 533 626 HOH HOH . I 3 HOH A 34 534 637 HOH HOH . I 3 HOH A 35 535 639 HOH HOH . I 3 HOH A 36 536 640 HOH HOH . I 3 HOH A 37 537 643 HOH HOH . I 3 HOH A 38 538 646 HOH HOH . I 3 HOH A 39 539 647 HOH HOH . I 3 HOH A 40 540 648 HOH HOH . I 3 HOH A 41 541 649 HOH HOH . I 3 HOH A 42 542 652 HOH HOH . I 3 HOH A 43 543 654 HOH HOH . I 3 HOH A 44 544 655 HOH HOH . I 3 HOH A 45 545 656 HOH HOH . I 3 HOH A 46 546 674 HOH HOH . I 3 HOH A 47 547 677 HOH HOH . J 3 HOH B 1 501 504 HOH HOH . J 3 HOH B 2 502 505 HOH HOH . J 3 HOH B 3 503 506 HOH HOH . J 3 HOH B 4 504 511 HOH HOH . J 3 HOH B 5 505 513 HOH HOH . J 3 HOH B 6 506 522 HOH HOH . J 3 HOH B 7 507 524 HOH HOH . J 3 HOH B 8 508 527 HOH HOH . J 3 HOH B 9 509 528 HOH HOH . J 3 HOH B 10 510 542 HOH HOH . J 3 HOH B 11 511 543 HOH HOH . J 3 HOH B 12 512 550 HOH HOH . J 3 HOH B 13 513 551 HOH HOH . J 3 HOH B 14 514 552 HOH HOH . J 3 HOH B 15 515 553 HOH HOH . J 3 HOH B 16 516 560 HOH HOH . J 3 HOH B 17 517 562 HOH HOH . J 3 HOH B 18 518 563 HOH HOH . J 3 HOH B 19 519 565 HOH HOH . J 3 HOH B 20 520 572 HOH HOH . J 3 HOH B 21 521 584 HOH HOH . J 3 HOH B 22 522 586 HOH HOH . J 3 HOH B 23 523 589 HOH HOH . J 3 HOH B 24 524 593 HOH HOH . J 3 HOH B 25 525 596 HOH HOH . J 3 HOH B 26 526 608 HOH HOH . J 3 HOH B 27 527 611 HOH HOH . J 3 HOH B 28 528 612 HOH HOH . J 3 HOH B 29 529 613 HOH HOH . J 3 HOH B 30 530 614 HOH HOH . J 3 HOH B 31 531 615 HOH HOH . J 3 HOH B 32 532 618 HOH HOH . J 3 HOH B 33 533 619 HOH HOH . J 3 HOH B 34 534 620 HOH HOH . J 3 HOH B 35 535 621 HOH HOH . J 3 HOH B 36 536 622 HOH HOH . J 3 HOH B 37 537 627 HOH HOH . J 3 HOH B 38 538 629 HOH HOH . J 3 HOH B 39 539 630 HOH HOH . J 3 HOH B 40 540 631 HOH HOH . J 3 HOH B 41 541 632 HOH HOH . J 3 HOH B 42 542 633 HOH HOH . J 3 HOH B 43 543 634 HOH HOH . J 3 HOH B 44 544 635 HOH HOH . J 3 HOH B 45 545 636 HOH HOH . J 3 HOH B 46 546 638 HOH HOH . J 3 HOH B 47 547 641 HOH HOH . J 3 HOH B 48 548 644 HOH HOH . J 3 HOH B 49 549 645 HOH HOH . J 3 HOH B 50 550 650 HOH HOH . J 3 HOH B 51 551 651 HOH HOH . J 3 HOH B 52 552 653 HOH HOH . J 3 HOH B 53 553 657 HOH HOH . J 3 HOH B 54 554 658 HOH HOH . J 3 HOH B 55 555 659 HOH HOH . J 3 HOH B 56 556 660 HOH HOH . J 3 HOH B 57 557 661 HOH HOH . J 3 HOH B 58 558 662 HOH HOH . J 3 HOH B 59 559 663 HOH HOH . J 3 HOH B 60 560 664 HOH HOH . J 3 HOH B 61 561 665 HOH HOH . J 3 HOH B 62 562 666 HOH HOH . J 3 HOH B 63 563 667 HOH HOH . J 3 HOH B 64 564 668 HOH HOH . J 3 HOH B 65 565 669 HOH HOH . J 3 HOH B 66 566 670 HOH HOH . J 3 HOH B 67 567 671 HOH HOH . J 3 HOH B 68 568 672 HOH HOH . J 3 HOH B 69 569 673 HOH HOH . J 3 HOH B 70 570 675 HOH HOH . J 3 HOH B 71 571 676 HOH HOH . J 3 HOH B 72 572 678 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 C _atom_site.label_entity_id 2 _atom_site.Cartn_x 0.752 _atom_site.Cartn_y -4.902 _atom_site.Cartn_z 5.973 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 15.59 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id CA _atom_site.auth_comp_id CA _atom_site.auth_seq_id 401 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 1 #