data_4Q6P # _model_server_result.job_id cJZag3hhovBk0VuUQEOOvw _model_server_result.datetime_utc '2024-12-02 02:32:50' _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 4q6p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":510}' # _entry.id 4Q6P # _exptl.entry_id 4Q6P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 190.197 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2,6-DIAMINOPIMELIC ACID' _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 4Q6P _cell.length_a 53.023 _cell.length_b 66.555 _cell.length_c 144.055 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4Q6P _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _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,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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id K _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 GLN 45 A GLN 46 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? metalc ? metalc2 A OE2 GLU 48 A GLU 49 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc3 A OE1 GLU 48 A GLU 49 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? metalc ? metalc4 A ND1 HIS 61 A HIS 62 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? metalc ? metalc5 A OD2 ASP 99 A ASP 100 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc6 A ND1 HIS 127 A HIS 128 1_555 B ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc7 A NE2 HIS 189 A HIS 190 1_555 G ZN ZN . A ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc8 A OD2 ASP 253 A ASP 254 1_555 C ZN ZN . A ZN 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.361 ? metalc ? metalc9 A ND1 HIS 262 A HIS 263 1_555 D ZN ZN . A ZN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc10 A NE2 GLN 319 A GLN 320 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc11 A OE1 GLN 319 A GLN 320 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.557 ? metalc ? metalc12 A OE2 GLU 320 A GLU 321 1_555 E ZN ZN . A ZN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc13 A ND1 HIS 373 A HIS 374 1_555 H ZN ZN . A ZN 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? metalc ? metalc14 A OD1 ASN 381 A ASN 382 1_555 J CA CA . A CA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc15 A O VAL 382 A VAL 383 1_555 J CA CA . A CA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc16 A O PHE 385 A PHE 386 1_555 J CA CA . A CA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc17 A OE2 GLU 395 A GLU 396 1_555 J CA CA . A CA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc18 A OE1 GLU 395 A GLU 396 1_555 J CA CA . A CA 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? metalc ? metalc19 C ZN ZN . A ZN 502 1_555 L O HOH . A HOH 662 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc20 D ZN ZN . A ZN 503 1_555 L O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.419 ? metalc ? metalc21 D ZN ZN . A ZN 503 1_555 L O HOH . A HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc22 D ZN ZN . A ZN 503 1_555 L O HOH . A HOH 713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc23 G ZN ZN . A ZN 506 1_555 L O HOH . A HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc24 H ZN ZN . A ZN 507 1_555 L O HOH . A HOH 649 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc25 H ZN ZN . A ZN 507 1_555 L O HOH . A HOH 676 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc26 J CA CA . A CA 509 1_555 L O HOH . A HOH 688 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? # _chem_comp.formula 'C7 H14 N2 O4' _chem_comp.formula_weight 190.197 _chem_comp.id API _chem_comp.mon_nstd_flag n _chem_comp.name '2,6-DIAMINOPIMELIC ACID' _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 C CA API sing 13 n n C O API doub 14 n n C OXT API sing 15 n n CA C3 API sing 16 n n CA N API sing 17 n n CA HA API sing 18 n n C3 C4 API sing 19 n n C3 H31 API sing 20 n n C3 H32 API sing 21 n n C4 C5 API sing 22 n n C4 H41 API sing 23 n n C4 H42 API sing 24 n n C5 C6 API sing 25 n n C5 H51 API sing 26 n n C5 H52 API sing 27 n n C6 C7 API sing 28 n n C6 N6 API sing 29 n n C6 H6 API sing 30 n n C7 O3 API doub 31 n n C7 O4 API sing 32 n n OXT HXT API sing 33 n n O4 HO4 API sing 34 n n N H API sing 35 n n N H2 API sing 36 n n N6 HN61 API sing 37 n n N6 HN62 API sing 38 n n # _atom_sites.entry_id 4Q6P _atom_sites.fract_transf_matrix[1][1] 0.01886 _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] 0.015025 _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] 0.006942 _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 ZN A 1 501 1 ZN ZN . C 2 ZN A 1 502 2 ZN ZN . D 2 ZN A 1 503 3 ZN ZN . E 2 ZN A 1 504 4 ZN ZN . F 2 ZN A 1 505 5 ZN ZN . G 2 ZN A 1 506 6 ZN ZN . H 2 ZN A 1 507 7 ZN ZN . I 2 ZN A 1 508 8 ZN ZN . J 3 CA A 1 509 9 CA CA . K 4 API A 1 510 1 API API . L 5 HOH A 1 601 1 HOH HOH . L 5 HOH A 2 602 3 HOH HOH . L 5 HOH A 3 603 4 HOH HOH . L 5 HOH A 4 604 5 HOH HOH . L 5 HOH A 5 605 6 HOH HOH . L 5 HOH A 6 606 7 HOH HOH . L 5 HOH A 7 607 8 HOH HOH . L 5 HOH A 8 608 9 HOH HOH . L 5 HOH A 9 609 10 HOH HOH . L 5 HOH A 10 610 11 HOH HOH . L 5 HOH A 11 611 12 HOH HOH . L 5 HOH A 12 612 13 HOH HOH . L 5 HOH A 13 613 14 HOH HOH . L 5 HOH A 14 614 15 HOH HOH . L 5 HOH A 15 615 16 HOH HOH . L 5 HOH A 16 616 17 HOH HOH . L 5 HOH A 17 617 18 HOH HOH . L 5 HOH A 18 618 19 HOH HOH . L 5 HOH A 19 619 20 HOH HOH . L 5 HOH A 20 620 21 HOH HOH . L 5 HOH A 21 621 22 HOH HOH . L 5 HOH A 22 622 23 HOH HOH . L 5 HOH A 23 623 24 HOH HOH . L 5 HOH A 24 624 25 HOH HOH . L 5 HOH A 25 625 26 HOH HOH . L 5 HOH A 26 626 27 HOH HOH . L 5 HOH A 27 627 28 HOH HOH . L 5 HOH A 28 628 29 HOH HOH . L 5 HOH A 29 629 30 HOH HOH . L 5 HOH A 30 630 31 HOH HOH . L 5 HOH A 31 631 32 HOH HOH . L 5 HOH A 32 632 33 HOH HOH . L 5 HOH A 33 633 34 HOH HOH . L 5 HOH A 34 634 35 HOH HOH . L 5 HOH A 35 635 36 HOH HOH . L 5 HOH A 36 636 37 HOH HOH . L 5 HOH A 37 637 38 HOH HOH . L 5 HOH A 38 638 40 HOH HOH . L 5 HOH A 39 639 41 HOH HOH . L 5 HOH A 40 640 42 HOH HOH . L 5 HOH A 41 641 43 HOH HOH . L 5 HOH A 42 642 44 HOH HOH . L 5 HOH A 43 643 45 HOH HOH . L 5 HOH A 44 644 46 HOH HOH . L 5 HOH A 45 645 47 HOH HOH . L 5 HOH A 46 646 48 HOH HOH . L 5 HOH A 47 647 49 HOH HOH . L 5 HOH A 48 648 50 HOH HOH . L 5 HOH A 49 649 52 HOH HOH . L 5 HOH A 50 650 54 HOH HOH . L 5 HOH A 51 651 55 HOH HOH . L 5 HOH A 52 652 56 HOH HOH . L 5 HOH A 53 653 57 HOH HOH . L 5 HOH A 54 654 58 HOH HOH . L 5 HOH A 55 655 59 HOH HOH . L 5 HOH A 56 656 60 HOH HOH . L 5 HOH A 57 657 61 HOH HOH . L 5 HOH A 58 658 62 HOH HOH . L 5 HOH A 59 659 63 HOH HOH . L 5 HOH A 60 660 65 HOH HOH . L 5 HOH A 61 661 66 HOH HOH . L 5 HOH A 62 662 67 HOH HOH . L 5 HOH A 63 663 68 HOH HOH . L 5 HOH A 64 664 69 HOH HOH . L 5 HOH A 65 665 71 HOH HOH . L 5 HOH A 66 666 72 HOH HOH . L 5 HOH A 67 667 73 HOH HOH . L 5 HOH A 68 668 74 HOH HOH . L 5 HOH A 69 669 75 HOH HOH . L 5 HOH A 70 670 76 HOH HOH . L 5 HOH A 71 671 77 HOH HOH . L 5 HOH A 72 672 78 HOH HOH . L 5 HOH A 73 673 79 HOH HOH . L 5 HOH A 74 674 80 HOH HOH . L 5 HOH A 75 675 81 HOH HOH . L 5 HOH A 76 676 82 HOH HOH . L 5 HOH A 77 677 83 HOH HOH . L 5 HOH A 78 678 84 HOH HOH . L 5 HOH A 79 679 85 HOH HOH . L 5 HOH A 80 680 86 HOH HOH . L 5 HOH A 81 681 87 HOH HOH . L 5 HOH A 82 682 88 HOH HOH . L 5 HOH A 83 683 89 HOH HOH . L 5 HOH A 84 684 90 HOH HOH . L 5 HOH A 85 685 91 HOH HOH . L 5 HOH A 86 686 92 HOH HOH . L 5 HOH A 87 687 93 HOH HOH . L 5 HOH A 88 688 94 HOH HOH . L 5 HOH A 89 689 95 HOH HOH . L 5 HOH A 90 690 96 HOH HOH . L 5 HOH A 91 691 97 HOH HOH . L 5 HOH A 92 692 98 HOH HOH . L 5 HOH A 93 693 99 HOH HOH . L 5 HOH A 94 694 100 HOH HOH . L 5 HOH A 95 695 101 HOH HOH . L 5 HOH A 96 696 102 HOH HOH . L 5 HOH A 97 697 103 HOH HOH . L 5 HOH A 98 698 104 HOH HOH . L 5 HOH A 99 699 105 HOH HOH . L 5 HOH A 100 700 106 HOH HOH . L 5 HOH A 101 701 107 HOH HOH . L 5 HOH A 102 702 108 HOH HOH . L 5 HOH A 103 703 109 HOH HOH . L 5 HOH A 104 704 110 HOH HOH . L 5 HOH A 105 705 111 HOH HOH . L 5 HOH A 106 706 113 HOH HOH . L 5 HOH A 107 707 114 HOH HOH . L 5 HOH A 108 708 115 HOH HOH . L 5 HOH A 109 709 116 HOH HOH . L 5 HOH A 110 710 117 HOH HOH . L 5 HOH A 111 711 118 HOH HOH . L 5 HOH A 112 712 119 HOH HOH . L 5 HOH A 113 713 120 HOH HOH . L 5 HOH A 114 714 121 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 API . . . K 4 -28.469 -8.008 -6.322 1 55.42 ? C API 510 A 1 HETATM 2 C CA API . . . K 4 -27.039 -7.605 -5.89 1 54.2 ? CA API 510 A 1 HETATM 3 C C3 API . . . K 4 -26.616 -6.523 -6.877 1 54.38 ? C3 API 510 A 1 HETATM 4 C C4 API . . . K 4 -26.954 -5.174 -6.214 1 55.37 ? C4 API 510 A 1 HETATM 5 C C5 API . . . K 4 -28.044 -4.454 -7.031 1 54.77 ? C5 API 510 A 1 HETATM 6 C C6 API . . . K 4 -28.176 -2.963 -6.623 1 54.21 ? C6 API 510 A 1 HETATM 7 C C7 API . . . K 4 -28.979 -2.73 -5.298 1 55.18 ? C7 API 510 A 1 HETATM 8 O O API . . . K 4 -28.617 -9.08 -6.963 1 54.69 ? O API 510 A 1 HETATM 9 O OXT API . . . K 4 -29.38 -7.193 -6.022 1 56.49 ? OXT API 510 A 1 HETATM 10 O O3 API . . . K 4 -28.913 -1.589 -4.784 1 53.99 ? O3 API 510 A 1 HETATM 11 O O4 API . . . K 4 -29.63 -3.681 -4.811 1 57.45 ? O4 API 510 A 1 HETATM 12 N N API . . . K 4 -26.115 -8.77 -5.819 1 51.1 ? N API 510 A 1 HETATM 13 N N6 API . . . K 4 -28.824 -2.227 -7.723 1 51.46 ? N6 API 510 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 13 #