data_4LXL # _model_server_result.job_id QQfHdM0hScp9QY83mnnMuA _model_server_result.datetime_utc '2024-12-26 16:20:01' _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 4lxl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":402}' # _entry.id 4LXL # _exptl.entry_id 4LXL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _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 4LXL _cell.length_a 54.364 _cell.length_b 78.475 _cell.length_c 83.893 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LXL _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 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 _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 D _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 covale ? covale1 B C ARG 2 D ARG 8 1_555 B N M3L 3 D M3L 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 B C M3L 3 D M3L 9 1_555 B N SER 4 D SER 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? metalc ? metalc1 A NE2 HIS 209 A HIS 189 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc2 A OE2 GLU 211 A GLU 191 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc3 A SG CYS 255 A CYS 235 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc4 A NE2 HIS 261 A HIS 241 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc5 A NE2 HIS 297 A HIS 277 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc6 A SG CYS 327 A CYS 307 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc7 A SG CYS 329 A CYS 309 1_555 E ZN ZN . A ZN 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? metalc ? metalc8 C N1 PD2 . A PD2 401 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc9 C O22 PD2 . A PD2 401 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc10 D NI NI . A NI 402 1_555 F O HOH . A HOH 752 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4LXL _atom_sites.fract_transf_matrix[1][1] 0.018395 _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] 0.012743 _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] 0.01192 _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 3 PD2 A 1 401 1 PD2 PD2 . D 4 NI A 1 402 1 NI NI . E 5 ZN A 1 403 1 ZN ZN . F 6 HOH A 1 501 1 HOH HOH . F 6 HOH A 2 502 2 HOH HOH . F 6 HOH A 3 503 3 HOH HOH . F 6 HOH A 4 504 4 HOH HOH . F 6 HOH A 5 505 5 HOH HOH . F 6 HOH A 6 506 6 HOH HOH . F 6 HOH A 7 507 7 HOH HOH . F 6 HOH A 8 508 8 HOH HOH . F 6 HOH A 9 509 9 HOH HOH . F 6 HOH A 10 510 10 HOH HOH . F 6 HOH A 11 511 12 HOH HOH . F 6 HOH A 12 512 13 HOH HOH . F 6 HOH A 13 513 14 HOH HOH . F 6 HOH A 14 514 15 HOH HOH . F 6 HOH A 15 515 16 HOH HOH . F 6 HOH A 16 516 17 HOH HOH . F 6 HOH A 17 517 18 HOH HOH . F 6 HOH A 18 518 20 HOH HOH . F 6 HOH A 19 519 21 HOH HOH . F 6 HOH A 20 520 22 HOH HOH . F 6 HOH A 21 521 23 HOH HOH . F 6 HOH A 22 522 24 HOH HOH . F 6 HOH A 23 523 25 HOH HOH . F 6 HOH A 24 524 26 HOH HOH . F 6 HOH A 25 525 27 HOH HOH . F 6 HOH A 26 526 28 HOH HOH . F 6 HOH A 27 527 29 HOH HOH . F 6 HOH A 28 528 30 HOH HOH . F 6 HOH A 29 529 31 HOH HOH . F 6 HOH A 30 530 32 HOH HOH . F 6 HOH A 31 531 33 HOH HOH . F 6 HOH A 32 532 34 HOH HOH . F 6 HOH A 33 533 35 HOH HOH . F 6 HOH A 34 534 36 HOH HOH . F 6 HOH A 35 535 37 HOH HOH . F 6 HOH A 36 536 38 HOH HOH . F 6 HOH A 37 537 39 HOH HOH . F 6 HOH A 38 538 40 HOH HOH . F 6 HOH A 39 539 41 HOH HOH . F 6 HOH A 40 540 42 HOH HOH . F 6 HOH A 41 541 43 HOH HOH . F 6 HOH A 42 542 44 HOH HOH . F 6 HOH A 43 543 45 HOH HOH . F 6 HOH A 44 544 46 HOH HOH . F 6 HOH A 45 545 47 HOH HOH . F 6 HOH A 46 546 48 HOH HOH . F 6 HOH A 47 547 49 HOH HOH . F 6 HOH A 48 548 50 HOH HOH . F 6 HOH A 49 549 51 HOH HOH . F 6 HOH A 50 550 52 HOH HOH . F 6 HOH A 51 551 53 HOH HOH . F 6 HOH A 52 552 54 HOH HOH . F 6 HOH A 53 553 56 HOH HOH . F 6 HOH A 54 554 57 HOH HOH . F 6 HOH A 55 555 58 HOH HOH . F 6 HOH A 56 556 59 HOH HOH . F 6 HOH A 57 557 60 HOH HOH . F 6 HOH A 58 558 61 HOH HOH . F 6 HOH A 59 559 62 HOH HOH . F 6 HOH A 60 560 63 HOH HOH . F 6 HOH A 61 561 64 HOH HOH . F 6 HOH A 62 562 65 HOH HOH . F 6 HOH A 63 563 66 HOH HOH . F 6 HOH A 64 564 67 HOH HOH . F 6 HOH A 65 565 68 HOH HOH . F 6 HOH A 66 566 69 HOH HOH . F 6 HOH A 67 567 70 HOH HOH . F 6 HOH A 68 568 71 HOH HOH . F 6 HOH A 69 569 72 HOH HOH . F 6 HOH A 70 570 73 HOH HOH . F 6 HOH A 71 571 74 HOH HOH . F 6 HOH A 72 572 75 HOH HOH . F 6 HOH A 73 573 76 HOH HOH . F 6 HOH A 74 574 77 HOH HOH . F 6 HOH A 75 575 78 HOH HOH . F 6 HOH A 76 576 79 HOH HOH . F 6 HOH A 77 577 80 HOH HOH . F 6 HOH A 78 578 82 HOH HOH . F 6 HOH A 79 579 83 HOH HOH . F 6 HOH A 80 580 84 HOH HOH . F 6 HOH A 81 581 85 HOH HOH . F 6 HOH A 82 582 86 HOH HOH . F 6 HOH A 83 583 87 HOH HOH . F 6 HOH A 84 584 88 HOH HOH . F 6 HOH A 85 585 89 HOH HOH . F 6 HOH A 86 586 90 HOH HOH . F 6 HOH A 87 587 91 HOH HOH . F 6 HOH A 88 588 92 HOH HOH . F 6 HOH A 89 589 93 HOH HOH . F 6 HOH A 90 590 94 HOH HOH . F 6 HOH A 91 591 95 HOH HOH . F 6 HOH A 92 592 96 HOH HOH . F 6 HOH A 93 593 97 HOH HOH . F 6 HOH A 94 594 98 HOH HOH . F 6 HOH A 95 595 99 HOH HOH . F 6 HOH A 96 596 100 HOH HOH . F 6 HOH A 97 597 101 HOH HOH . F 6 HOH A 98 598 102 HOH HOH . F 6 HOH A 99 599 103 HOH HOH . F 6 HOH A 100 600 104 HOH HOH . F 6 HOH A 101 601 105 HOH HOH . F 6 HOH A 102 602 106 HOH HOH . F 6 HOH A 103 603 108 HOH HOH . F 6 HOH A 104 604 110 HOH HOH . F 6 HOH A 105 605 112 HOH HOH . F 6 HOH A 106 606 113 HOH HOH . F 6 HOH A 107 607 114 HOH HOH . F 6 HOH A 108 608 115 HOH HOH . F 6 HOH A 109 609 116 HOH HOH . F 6 HOH A 110 610 117 HOH HOH . F 6 HOH A 111 611 119 HOH HOH . F 6 HOH A 112 612 121 HOH HOH . F 6 HOH A 113 613 122 HOH HOH . F 6 HOH A 114 614 123 HOH HOH . F 6 HOH A 115 615 124 HOH HOH . F 6 HOH A 116 616 125 HOH HOH . F 6 HOH A 117 617 126 HOH HOH . F 6 HOH A 118 618 127 HOH HOH . F 6 HOH A 119 619 129 HOH HOH . F 6 HOH A 120 620 130 HOH HOH . F 6 HOH A 121 621 131 HOH HOH . F 6 HOH A 122 622 132 HOH HOH . F 6 HOH A 123 623 133 HOH HOH . F 6 HOH A 124 624 134 HOH HOH . F 6 HOH A 125 625 135 HOH HOH . F 6 HOH A 126 626 136 HOH HOH . F 6 HOH A 127 627 137 HOH HOH . F 6 HOH A 128 628 139 HOH HOH . F 6 HOH A 129 629 140 HOH HOH . F 6 HOH A 130 630 141 HOH HOH . F 6 HOH A 131 631 142 HOH HOH . F 6 HOH A 132 632 143 HOH HOH . F 6 HOH A 133 633 144 HOH HOH . F 6 HOH A 134 634 145 HOH HOH . F 6 HOH A 135 635 146 HOH HOH . F 6 HOH A 136 636 147 HOH HOH . F 6 HOH A 137 637 148 HOH HOH . F 6 HOH A 138 638 149 HOH HOH . F 6 HOH A 139 639 150 HOH HOH . F 6 HOH A 140 640 152 HOH HOH . F 6 HOH A 141 641 153 HOH HOH . F 6 HOH A 142 642 154 HOH HOH . F 6 HOH A 143 643 155 HOH HOH . F 6 HOH A 144 644 156 HOH HOH . F 6 HOH A 145 645 157 HOH HOH . F 6 HOH A 146 646 158 HOH HOH . F 6 HOH A 147 647 159 HOH HOH . F 6 HOH A 148 648 160 HOH HOH . F 6 HOH A 149 649 161 HOH HOH . F 6 HOH A 150 650 162 HOH HOH . F 6 HOH A 151 651 165 HOH HOH . F 6 HOH A 152 652 166 HOH HOH . F 6 HOH A 153 653 167 HOH HOH . F 6 HOH A 154 654 168 HOH HOH . F 6 HOH A 155 655 169 HOH HOH . F 6 HOH A 156 656 170 HOH HOH . F 6 HOH A 157 657 171 HOH HOH . F 6 HOH A 158 658 172 HOH HOH . F 6 HOH A 159 659 173 HOH HOH . F 6 HOH A 160 660 174 HOH HOH . F 6 HOH A 161 661 175 HOH HOH . F 6 HOH A 162 662 176 HOH HOH . F 6 HOH A 163 663 177 HOH HOH . F 6 HOH A 164 664 178 HOH HOH . F 6 HOH A 165 665 179 HOH HOH . F 6 HOH A 166 666 180 HOH HOH . F 6 HOH A 167 667 181 HOH HOH . F 6 HOH A 168 668 182 HOH HOH . F 6 HOH A 169 669 183 HOH HOH . F 6 HOH A 170 670 184 HOH HOH . F 6 HOH A 171 671 186 HOH HOH . F 6 HOH A 172 672 188 HOH HOH . F 6 HOH A 173 673 189 HOH HOH . F 6 HOH A 174 674 190 HOH HOH . F 6 HOH A 175 675 191 HOH HOH . F 6 HOH A 176 676 192 HOH HOH . F 6 HOH A 177 677 193 HOH HOH . F 6 HOH A 178 678 194 HOH HOH . F 6 HOH A 179 679 195 HOH HOH . F 6 HOH A 180 680 196 HOH HOH . F 6 HOH A 181 681 197 HOH HOH . F 6 HOH A 182 682 198 HOH HOH . F 6 HOH A 183 683 199 HOH HOH . F 6 HOH A 184 684 200 HOH HOH . F 6 HOH A 185 685 201 HOH HOH . F 6 HOH A 186 686 202 HOH HOH . F 6 HOH A 187 687 203 HOH HOH . F 6 HOH A 188 688 204 HOH HOH . F 6 HOH A 189 689 205 HOH HOH . F 6 HOH A 190 690 206 HOH HOH . F 6 HOH A 191 691 207 HOH HOH . F 6 HOH A 192 692 208 HOH HOH . F 6 HOH A 193 693 209 HOH HOH . F 6 HOH A 194 694 210 HOH HOH . F 6 HOH A 195 695 211 HOH HOH . F 6 HOH A 196 696 212 HOH HOH . F 6 HOH A 197 697 213 HOH HOH . F 6 HOH A 198 698 214 HOH HOH . F 6 HOH A 199 699 215 HOH HOH . F 6 HOH A 200 700 216 HOH HOH . F 6 HOH A 201 701 217 HOH HOH . F 6 HOH A 202 702 218 HOH HOH . F 6 HOH A 203 703 219 HOH HOH . F 6 HOH A 204 704 220 HOH HOH . F 6 HOH A 205 705 221 HOH HOH . F 6 HOH A 206 706 222 HOH HOH . F 6 HOH A 207 707 223 HOH HOH . F 6 HOH A 208 708 224 HOH HOH . F 6 HOH A 209 709 225 HOH HOH . F 6 HOH A 210 710 226 HOH HOH . F 6 HOH A 211 711 227 HOH HOH . F 6 HOH A 212 712 229 HOH HOH . F 6 HOH A 213 713 230 HOH HOH . F 6 HOH A 214 714 231 HOH HOH . F 6 HOH A 215 715 232 HOH HOH . F 6 HOH A 216 716 233 HOH HOH . F 6 HOH A 217 717 234 HOH HOH . F 6 HOH A 218 718 235 HOH HOH . F 6 HOH A 219 719 237 HOH HOH . F 6 HOH A 220 720 238 HOH HOH . F 6 HOH A 221 721 239 HOH HOH . F 6 HOH A 222 722 240 HOH HOH . F 6 HOH A 223 723 241 HOH HOH . F 6 HOH A 224 724 242 HOH HOH . F 6 HOH A 225 725 243 HOH HOH . F 6 HOH A 226 726 244 HOH HOH . F 6 HOH A 227 727 245 HOH HOH . F 6 HOH A 228 728 249 HOH HOH . F 6 HOH A 229 729 250 HOH HOH . F 6 HOH A 230 730 251 HOH HOH . F 6 HOH A 231 731 252 HOH HOH . F 6 HOH A 232 732 253 HOH HOH . F 6 HOH A 233 733 254 HOH HOH . F 6 HOH A 234 734 255 HOH HOH . F 6 HOH A 235 735 257 HOH HOH . F 6 HOH A 236 736 259 HOH HOH . F 6 HOH A 237 737 260 HOH HOH . F 6 HOH A 238 738 261 HOH HOH . F 6 HOH A 239 739 262 HOH HOH . F 6 HOH A 240 740 263 HOH HOH . F 6 HOH A 241 741 264 HOH HOH . F 6 HOH A 242 742 267 HOH HOH . F 6 HOH A 243 743 269 HOH HOH . F 6 HOH A 244 744 270 HOH HOH . F 6 HOH A 245 745 272 HOH HOH . F 6 HOH A 246 746 274 HOH HOH . F 6 HOH A 247 747 275 HOH HOH . F 6 HOH A 248 748 276 HOH HOH . F 6 HOH A 249 749 281 HOH HOH . F 6 HOH A 250 750 282 HOH HOH . F 6 HOH A 251 751 284 HOH HOH . F 6 HOH A 252 752 285 HOH HOH . G 6 HOH D 1 101 11 HOH HOH . G 6 HOH D 2 102 19 HOH HOH . G 6 HOH D 3 103 55 HOH HOH . G 6 HOH D 4 104 81 HOH HOH . G 6 HOH D 5 105 107 HOH HOH . G 6 HOH D 6 106 128 HOH HOH . G 6 HOH D 7 107 163 HOH HOH . G 6 HOH D 8 108 164 HOH HOH . G 6 HOH D 9 109 236 HOH HOH . G 6 HOH D 10 110 247 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id D _atom_site.label_entity_id 4 _atom_site.Cartn_x -2.395 _atom_site.Cartn_y -0.633 _atom_site.Cartn_z -10.409 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 15.8 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 402 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 347 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #