data_2Q8D # _model_server_result.job_id ijZ0Uu0yZJ65sSQhmZnF4A _model_server_result.datetime_utc '2024-12-03 19:26:08' _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 2q8d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":502}' # _entry.id 2Q8D # _exptl.entry_id 2Q8D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 2 _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 2Q8D _cell.length_a 100.857 _cell.length_b 148.642 _cell.length_c 57.346 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Q8D _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,E,F,G,K 1 1 B,D,H,I,J,L 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 ? 3 E N N ? 3 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 covale ? covale1 C C VAL 10 F VAL 35 1_555 C N MLY 11 F MLY 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 D C VAL 10 G VAL 35 1_555 D N MLY 11 G MLY 36 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? metalc ? metalc1 A NE2 HIS 190 A HIS 188 1_555 E NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc2 A OE1 GLU 192 A GLU 190 1_555 E NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc3 A SG CYS 236 A CYS 234 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? metalc ? metalc4 A NE2 HIS 242 A HIS 240 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc5 A NE2 HIS 278 A HIS 276 1_555 E NI NI . A NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc6 A SG CYS 308 A CYS 306 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc7 A SG CYS 310 A CYS 308 1_555 F ZN ZN . A ZN 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? metalc ? metalc8 E NI NI . A NI 501 1_555 G O1 SIN . A SIN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc9 E NI NI . A NI 501 1_555 G O2 SIN . A SIN 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc10 B NE2 HIS 190 B HIS 188 1_555 H NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc11 B OE1 GLU 192 B GLU 190 1_555 H NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc12 B SG CYS 236 B CYS 234 1_555 I ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc13 B NE2 HIS 242 B HIS 240 1_555 I ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc14 B NE2 HIS 278 B HIS 276 1_555 H NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc15 B SG CYS 308 B CYS 306 1_555 I ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc16 B SG CYS 310 B CYS 308 1_555 I ZN ZN . B ZN 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc17 H NI NI . B NI 502 1_555 J O1 SIN . B SIN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc18 H NI NI . B NI 502 1_555 J O2 SIN . B SIN 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? # _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 2Q8D _atom_sites.fract_transf_matrix[1][1] 0.009915 _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] 0.006728 _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] 0.017438 _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 E 3 NI A 1 501 1 NI NI . F 4 ZN A 1 505 1 ZN ZN . G 5 SIN A 1 503 1 SIN SIN . H 3 NI B 1 502 2 NI NI . I 4 ZN B 1 506 2 ZN ZN . J 5 SIN B 1 504 2 SIN SIN . K 6 HOH A 1 506 3 HOH HOH . K 6 HOH A 2 507 4 HOH HOH . K 6 HOH A 3 508 5 HOH HOH . K 6 HOH A 4 509 7 HOH HOH . K 6 HOH A 5 510 8 HOH HOH . K 6 HOH A 6 511 9 HOH HOH . K 6 HOH A 7 512 11 HOH HOH . K 6 HOH A 8 513 12 HOH HOH . K 6 HOH A 9 514 14 HOH HOH . K 6 HOH A 10 515 16 HOH HOH . K 6 HOH A 11 516 18 HOH HOH . K 6 HOH A 12 517 20 HOH HOH . K 6 HOH A 13 518 21 HOH HOH . K 6 HOH A 14 519 22 HOH HOH . K 6 HOH A 15 520 25 HOH HOH . K 6 HOH A 16 521 34 HOH HOH . K 6 HOH A 17 522 35 HOH HOH . K 6 HOH A 18 523 37 HOH HOH . K 6 HOH A 19 524 38 HOH HOH . K 6 HOH A 20 525 39 HOH HOH . K 6 HOH A 21 526 41 HOH HOH . K 6 HOH A 22 527 42 HOH HOH . K 6 HOH A 23 528 44 HOH HOH . K 6 HOH A 24 529 47 HOH HOH . K 6 HOH A 25 530 48 HOH HOH . K 6 HOH A 26 531 49 HOH HOH . K 6 HOH A 27 532 52 HOH HOH . K 6 HOH A 28 533 55 HOH HOH . K 6 HOH A 29 534 56 HOH HOH . K 6 HOH A 30 535 59 HOH HOH . K 6 HOH A 31 536 63 HOH HOH . K 6 HOH A 32 537 65 HOH HOH . K 6 HOH A 33 538 66 HOH HOH . K 6 HOH A 34 539 67 HOH HOH . K 6 HOH A 35 540 68 HOH HOH . K 6 HOH A 36 541 75 HOH HOH . K 6 HOH A 37 542 76 HOH HOH . K 6 HOH A 38 543 78 HOH HOH . K 6 HOH A 39 544 79 HOH HOH . K 6 HOH A 40 545 80 HOH HOH . K 6 HOH A 41 546 82 HOH HOH . K 6 HOH A 42 547 83 HOH HOH . K 6 HOH A 43 548 85 HOH HOH . K 6 HOH A 44 549 86 HOH HOH . K 6 HOH A 45 550 87 HOH HOH . K 6 HOH A 46 551 88 HOH HOH . K 6 HOH A 47 552 89 HOH HOH . K 6 HOH A 48 553 90 HOH HOH . K 6 HOH A 49 554 91 HOH HOH . K 6 HOH A 50 555 92 HOH HOH . K 6 HOH A 51 556 93 HOH HOH . K 6 HOH A 52 557 94 HOH HOH . K 6 HOH A 53 558 96 HOH HOH . K 6 HOH A 54 559 97 HOH HOH . K 6 HOH A 55 560 100 HOH HOH . K 6 HOH A 56 561 101 HOH HOH . K 6 HOH A 57 562 102 HOH HOH . K 6 HOH A 58 563 105 HOH HOH . K 6 HOH A 59 564 106 HOH HOH . K 6 HOH A 60 565 110 HOH HOH . K 6 HOH A 61 566 111 HOH HOH . K 6 HOH A 62 567 113 HOH HOH . K 6 HOH A 63 568 114 HOH HOH . K 6 HOH A 64 569 117 HOH HOH . K 6 HOH A 65 570 118 HOH HOH . K 6 HOH A 66 571 119 HOH HOH . K 6 HOH A 67 572 122 HOH HOH . K 6 HOH A 68 573 124 HOH HOH . K 6 HOH A 69 574 126 HOH HOH . K 6 HOH A 70 575 127 HOH HOH . K 6 HOH A 71 576 129 HOH HOH . K 6 HOH A 72 577 131 HOH HOH . K 6 HOH A 73 578 134 HOH HOH . K 6 HOH A 74 579 136 HOH HOH . K 6 HOH A 75 580 139 HOH HOH . K 6 HOH A 76 581 143 HOH HOH . K 6 HOH A 77 582 145 HOH HOH . K 6 HOH A 78 583 146 HOH HOH . K 6 HOH A 79 584 148 HOH HOH . K 6 HOH A 80 585 150 HOH HOH . K 6 HOH A 81 586 152 HOH HOH . K 6 HOH A 82 587 157 HOH HOH . K 6 HOH A 83 588 166 HOH HOH . K 6 HOH A 84 589 171 HOH HOH . K 6 HOH A 85 590 172 HOH HOH . K 6 HOH A 86 591 173 HOH HOH . K 6 HOH A 87 592 175 HOH HOH . K 6 HOH A 88 593 176 HOH HOH . K 6 HOH A 89 594 180 HOH HOH . K 6 HOH A 90 595 182 HOH HOH . K 6 HOH A 91 596 183 HOH HOH . K 6 HOH A 92 597 184 HOH HOH . K 6 HOH A 93 598 187 HOH HOH . K 6 HOH A 94 599 188 HOH HOH . K 6 HOH A 95 600 193 HOH HOH . K 6 HOH A 96 601 199 HOH HOH . K 6 HOH A 97 602 204 HOH HOH . K 6 HOH A 98 603 206 HOH HOH . K 6 HOH A 99 604 215 HOH HOH . K 6 HOH A 100 605 217 HOH HOH . K 6 HOH A 101 606 218 HOH HOH . K 6 HOH A 102 607 223 HOH HOH . K 6 HOH A 103 608 225 HOH HOH . K 6 HOH A 104 609 226 HOH HOH . K 6 HOH A 105 610 228 HOH HOH . K 6 HOH A 106 611 230 HOH HOH . K 6 HOH A 107 612 231 HOH HOH . K 6 HOH A 108 613 234 HOH HOH . K 6 HOH A 109 614 235 HOH HOH . K 6 HOH A 110 615 242 HOH HOH . K 6 HOH A 111 616 246 HOH HOH . K 6 HOH A 112 617 248 HOH HOH . L 6 HOH B 1 507 1 HOH HOH . L 6 HOH B 2 508 2 HOH HOH . L 6 HOH B 3 509 6 HOH HOH . L 6 HOH B 4 510 10 HOH HOH . L 6 HOH B 5 511 13 HOH HOH . L 6 HOH B 6 512 15 HOH HOH . L 6 HOH B 7 513 17 HOH HOH . L 6 HOH B 8 514 19 HOH HOH . L 6 HOH B 9 515 23 HOH HOH . L 6 HOH B 10 516 24 HOH HOH . L 6 HOH B 11 517 26 HOH HOH . L 6 HOH B 12 518 27 HOH HOH . L 6 HOH B 13 519 28 HOH HOH . L 6 HOH B 14 520 29 HOH HOH . L 6 HOH B 15 521 30 HOH HOH . L 6 HOH B 16 522 32 HOH HOH . L 6 HOH B 17 523 33 HOH HOH . L 6 HOH B 18 524 36 HOH HOH . L 6 HOH B 19 525 40 HOH HOH . L 6 HOH B 20 526 43 HOH HOH . L 6 HOH B 21 527 45 HOH HOH . L 6 HOH B 22 528 46 HOH HOH . L 6 HOH B 23 529 50 HOH HOH . L 6 HOH B 24 530 51 HOH HOH . L 6 HOH B 25 531 53 HOH HOH . L 6 HOH B 26 532 54 HOH HOH . L 6 HOH B 27 533 57 HOH HOH . L 6 HOH B 28 534 58 HOH HOH . L 6 HOH B 29 535 60 HOH HOH . L 6 HOH B 30 536 61 HOH HOH . L 6 HOH B 31 537 62 HOH HOH . L 6 HOH B 32 538 64 HOH HOH . L 6 HOH B 33 539 69 HOH HOH . L 6 HOH B 34 540 70 HOH HOH . L 6 HOH B 35 541 71 HOH HOH . L 6 HOH B 36 542 72 HOH HOH . L 6 HOH B 37 543 73 HOH HOH . L 6 HOH B 38 544 74 HOH HOH . L 6 HOH B 39 545 77 HOH HOH . L 6 HOH B 40 546 81 HOH HOH . L 6 HOH B 41 547 84 HOH HOH . L 6 HOH B 42 548 95 HOH HOH . L 6 HOH B 43 549 98 HOH HOH . L 6 HOH B 44 550 99 HOH HOH . L 6 HOH B 45 551 103 HOH HOH . L 6 HOH B 46 552 104 HOH HOH . L 6 HOH B 47 553 107 HOH HOH . L 6 HOH B 48 554 108 HOH HOH . L 6 HOH B 49 555 109 HOH HOH . L 6 HOH B 50 556 112 HOH HOH . L 6 HOH B 51 557 115 HOH HOH . L 6 HOH B 52 558 116 HOH HOH . L 6 HOH B 53 559 121 HOH HOH . L 6 HOH B 54 560 123 HOH HOH . L 6 HOH B 55 561 125 HOH HOH . L 6 HOH B 56 562 128 HOH HOH . L 6 HOH B 57 563 130 HOH HOH . L 6 HOH B 58 564 133 HOH HOH . L 6 HOH B 59 565 135 HOH HOH . L 6 HOH B 60 566 138 HOH HOH . L 6 HOH B 61 567 140 HOH HOH . L 6 HOH B 62 568 141 HOH HOH . L 6 HOH B 63 569 142 HOH HOH . L 6 HOH B 64 570 144 HOH HOH . L 6 HOH B 65 571 147 HOH HOH . L 6 HOH B 66 572 149 HOH HOH . L 6 HOH B 67 573 151 HOH HOH . L 6 HOH B 68 574 154 HOH HOH . L 6 HOH B 69 575 155 HOH HOH . L 6 HOH B 70 576 156 HOH HOH . L 6 HOH B 71 577 159 HOH HOH . L 6 HOH B 72 578 160 HOH HOH . L 6 HOH B 73 579 161 HOH HOH . L 6 HOH B 74 580 162 HOH HOH . L 6 HOH B 75 581 163 HOH HOH . L 6 HOH B 76 582 164 HOH HOH . L 6 HOH B 77 583 165 HOH HOH . L 6 HOH B 78 584 167 HOH HOH . L 6 HOH B 79 585 168 HOH HOH . L 6 HOH B 80 586 169 HOH HOH . L 6 HOH B 81 587 170 HOH HOH . L 6 HOH B 82 588 177 HOH HOH . L 6 HOH B 83 589 179 HOH HOH . L 6 HOH B 84 590 181 HOH HOH . L 6 HOH B 85 591 186 HOH HOH . L 6 HOH B 86 592 190 HOH HOH . L 6 HOH B 87 593 192 HOH HOH . L 6 HOH B 88 594 194 HOH HOH . L 6 HOH B 89 595 195 HOH HOH . L 6 HOH B 90 596 196 HOH HOH . L 6 HOH B 91 597 198 HOH HOH . L 6 HOH B 92 598 200 HOH HOH . L 6 HOH B 93 599 201 HOH HOH . L 6 HOH B 94 600 202 HOH HOH . L 6 HOH B 95 601 205 HOH HOH . L 6 HOH B 96 602 207 HOH HOH . L 6 HOH B 97 603 209 HOH HOH . L 6 HOH B 98 604 211 HOH HOH . L 6 HOH B 99 605 213 HOH HOH . L 6 HOH B 100 606 216 HOH HOH . L 6 HOH B 101 607 219 HOH HOH . L 6 HOH B 102 608 222 HOH HOH . L 6 HOH B 103 609 227 HOH HOH . L 6 HOH B 104 610 233 HOH HOH . L 6 HOH B 105 611 237 HOH HOH . L 6 HOH B 106 612 239 HOH HOH . L 6 HOH B 107 613 241 HOH HOH . L 6 HOH B 108 614 243 HOH HOH . L 6 HOH B 109 615 244 HOH HOH . L 6 HOH B 110 616 247 HOH HOH . L 6 HOH B 111 617 249 HOH HOH . L 6 HOH B 112 618 250 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 H _atom_site.label_entity_id 3 _atom_site.Cartn_x -11.317 _atom_site.Cartn_y -19.326 _atom_site.Cartn_z 4.456 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 40.75 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 502 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 325 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 1 #