data_1S6M # _model_server_result.job_id vCS9JroMLQGwmjrayB5xYQ _model_server_result.datetime_utc '2025-03-06 10:15:53' _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 1s6m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 1S6M # _exptl.entry_id 1S6M _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 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 120 _cell.entry_id 1S6M _cell.length_a 92.731 _cell.length_b 92.731 _cell.length_c 208.855 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1S6M _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 3 _struct_asym.id C _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 MSE 1 A MSE 1 1_555 B N LEU 2 A LEU 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 B C HIS 4 A HIS 4 1_555 B N MSE 5 A MSE 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale3 B C MSE 5 A MSE 5 1_555 B N VAL 6 A VAL 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 B C ILE 69 A ILE 69 1_555 B N MSE 70 A MSE 70 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 B C MSE 70 A MSE 70 1_555 B N ARG 71 A ARG 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale6 B C ASN 168 A ASN 168 1_555 B N MSE 169 A MSE 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale7 B C MSE 169 A MSE 169 1_555 B N THR 170 A THR 170 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 B ND1 HIS 150 A HIS 150 1_555 C NI NI . A NI 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc2 B NE2 HIS 161 A HIS 161 1_555 C NI NI . A NI 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc3 B NE2 HIS 163 A HIS 163 1_555 C NI NI . A NI 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc4 C NI NI . A NI 500 1_555 E O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? metalc ? metalc5 C NI NI . A NI 500 1_555 E O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? hydrog WATSON-CRICK hydrog1 A N1 DG 3 B DG 3 1_555 A N3 DC 16 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 3 B DG 3 1_555 A O2 DC 16 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 3 B DG 3 1_555 A N4 DC 16 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N3 DC 4 B DC 4 1_555 A N1 DG 15 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N4 DC 4 B DC 4 1_555 A O6 DG 15 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O2 DC 4 B DC 4 1_555 A N2 DG 15 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N1 DA 5 B DA 5 1_555 A N3 DT 14 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N6 DA 5 B DA 5 1_555 A O4 DT 14 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N3 DC 6 B DC 6 1_555 A N1 DG 13 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N4 DC 6 B DC 6 1_555 A O6 DG 13 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A O2 DC 6 B DC 6 1_555 A N2 DG 13 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A N3 DC 7 B DC 7 1_555 A N1 DG 12 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N4 DC 7 B DC 7 1_555 A O6 DG 12 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A O2 DC 7 B DC 7 1_555 A N2 DG 12 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DA MISPAIR' hydrog15 A N2 DG 8 B DG 8 1_555 A N1 DA 10 B DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 1S6M _atom_sites.fract_transf_matrix[1][1] 0.010784 _atom_sites.fract_transf_matrix[1][2] 0.006226 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012452 _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] 0.004788 _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 NI A 1 500 500 NI NI . D 4 HOH B 1 26 7 HOH HOH . D 4 HOH B 2 27 10 HOH HOH . D 4 HOH B 3 28 11 HOH HOH . D 4 HOH B 4 29 12 HOH HOH . D 4 HOH B 5 30 13 HOH HOH . D 4 HOH B 6 31 22 HOH HOH . D 4 HOH B 7 32 24 HOH HOH . D 4 HOH B 8 33 27 HOH HOH . D 4 HOH B 9 34 29 HOH HOH . D 4 HOH B 10 35 30 HOH HOH . D 4 HOH B 11 36 31 HOH HOH . D 4 HOH B 12 37 34 HOH HOH . D 4 HOH B 13 38 36 HOH HOH . D 4 HOH B 14 39 37 HOH HOH . D 4 HOH B 15 40 41 HOH HOH . D 4 HOH B 16 41 43 HOH HOH . D 4 HOH B 17 42 45 HOH HOH . D 4 HOH B 18 43 52 HOH HOH . D 4 HOH B 19 44 63 HOH HOH . D 4 HOH B 20 45 73 HOH HOH . D 4 HOH B 21 46 80 HOH HOH . D 4 HOH B 22 47 82 HOH HOH . D 4 HOH B 23 48 88 HOH HOH . D 4 HOH B 24 49 94 HOH HOH . D 4 HOH B 25 50 100 HOH HOH . D 4 HOH B 26 51 109 HOH HOH . D 4 HOH B 27 52 111 HOH HOH . D 4 HOH B 28 53 119 HOH HOH . D 4 HOH B 29 54 122 HOH HOH . D 4 HOH B 30 55 124 HOH HOH . D 4 HOH B 31 56 127 HOH HOH . D 4 HOH B 32 57 128 HOH HOH . D 4 HOH B 33 58 130 HOH HOH . D 4 HOH B 34 59 134 HOH HOH . D 4 HOH B 35 60 136 HOH HOH . D 4 HOH B 36 61 139 HOH HOH . D 4 HOH B 37 62 141 HOH HOH . D 4 HOH B 38 63 148 HOH HOH . D 4 HOH B 39 64 168 HOH HOH . E 4 HOH A 1 501 501 HOH HOH . E 4 HOH A 2 502 502 HOH HOH . E 4 HOH A 3 503 2 HOH HOH . E 4 HOH A 4 504 3 HOH HOH . E 4 HOH A 5 505 4 HOH HOH . E 4 HOH A 6 506 5 HOH HOH . E 4 HOH A 7 507 6 HOH HOH . E 4 HOH A 8 508 8 HOH HOH . E 4 HOH A 9 509 9 HOH HOH . E 4 HOH A 10 510 14 HOH HOH . E 4 HOH A 11 511 15 HOH HOH . E 4 HOH A 12 512 16 HOH HOH . E 4 HOH A 13 513 17 HOH HOH . E 4 HOH A 14 514 18 HOH HOH . E 4 HOH A 15 515 19 HOH HOH . E 4 HOH A 16 516 20 HOH HOH . E 4 HOH A 17 517 21 HOH HOH . E 4 HOH A 18 518 23 HOH HOH . E 4 HOH A 19 519 25 HOH HOH . E 4 HOH A 20 520 26 HOH HOH . E 4 HOH A 21 521 28 HOH HOH . E 4 HOH A 22 522 33 HOH HOH . E 4 HOH A 23 523 35 HOH HOH . E 4 HOH A 24 524 38 HOH HOH . E 4 HOH A 25 525 39 HOH HOH . E 4 HOH A 26 526 40 HOH HOH . E 4 HOH A 27 527 42 HOH HOH . E 4 HOH A 28 528 44 HOH HOH . E 4 HOH A 29 529 46 HOH HOH . E 4 HOH A 30 530 47 HOH HOH . E 4 HOH A 31 531 48 HOH HOH . E 4 HOH A 32 532 49 HOH HOH . E 4 HOH A 33 533 50 HOH HOH . E 4 HOH A 34 534 51 HOH HOH . E 4 HOH A 35 535 53 HOH HOH . E 4 HOH A 36 536 54 HOH HOH . E 4 HOH A 37 537 55 HOH HOH . E 4 HOH A 38 538 56 HOH HOH . E 4 HOH A 39 539 57 HOH HOH . E 4 HOH A 40 540 59 HOH HOH . E 4 HOH A 41 541 60 HOH HOH . E 4 HOH A 42 542 61 HOH HOH . E 4 HOH A 43 543 62 HOH HOH . E 4 HOH A 44 544 64 HOH HOH . E 4 HOH A 45 545 65 HOH HOH . E 4 HOH A 46 546 66 HOH HOH . E 4 HOH A 47 547 67 HOH HOH . E 4 HOH A 48 548 68 HOH HOH . E 4 HOH A 49 549 69 HOH HOH . E 4 HOH A 50 550 70 HOH HOH . E 4 HOH A 51 551 71 HOH HOH . E 4 HOH A 52 552 72 HOH HOH . E 4 HOH A 53 553 74 HOH HOH . E 4 HOH A 54 554 75 HOH HOH . E 4 HOH A 55 555 76 HOH HOH . E 4 HOH A 56 556 77 HOH HOH . E 4 HOH A 57 557 78 HOH HOH . E 4 HOH A 58 558 79 HOH HOH . E 4 HOH A 59 559 81 HOH HOH . E 4 HOH A 60 560 83 HOH HOH . E 4 HOH A 61 561 84 HOH HOH . E 4 HOH A 62 562 85 HOH HOH . E 4 HOH A 63 563 86 HOH HOH . E 4 HOH A 64 564 87 HOH HOH . E 4 HOH A 65 565 89 HOH HOH . E 4 HOH A 66 566 90 HOH HOH . E 4 HOH A 67 567 91 HOH HOH . E 4 HOH A 68 568 92 HOH HOH . E 4 HOH A 69 569 93 HOH HOH . E 4 HOH A 70 570 95 HOH HOH . E 4 HOH A 71 571 96 HOH HOH . E 4 HOH A 72 572 97 HOH HOH . E 4 HOH A 73 573 98 HOH HOH . E 4 HOH A 74 574 99 HOH HOH . E 4 HOH A 75 575 101 HOH HOH . E 4 HOH A 76 576 103 HOH HOH . E 4 HOH A 77 577 104 HOH HOH . E 4 HOH A 78 578 105 HOH HOH . E 4 HOH A 79 579 106 HOH HOH . E 4 HOH A 80 580 107 HOH HOH . E 4 HOH A 81 581 108 HOH HOH . E 4 HOH A 82 582 110 HOH HOH . E 4 HOH A 83 583 112 HOH HOH . E 4 HOH A 84 584 115 HOH HOH . E 4 HOH A 85 585 116 HOH HOH . E 4 HOH A 86 586 117 HOH HOH . E 4 HOH A 87 587 118 HOH HOH . E 4 HOH A 88 588 120 HOH HOH . E 4 HOH A 89 589 121 HOH HOH . E 4 HOH A 90 590 123 HOH HOH . E 4 HOH A 91 591 126 HOH HOH . E 4 HOH A 92 592 129 HOH HOH . E 4 HOH A 93 593 131 HOH HOH . E 4 HOH A 94 594 132 HOH HOH . E 4 HOH A 95 595 133 HOH HOH . E 4 HOH A 96 596 135 HOH HOH . E 4 HOH A 97 597 137 HOH HOH . E 4 HOH A 98 598 140 HOH HOH . E 4 HOH A 99 599 142 HOH HOH . E 4 HOH A 100 600 143 HOH HOH . E 4 HOH A 101 601 145 HOH HOH . E 4 HOH A 102 602 146 HOH HOH . E 4 HOH A 103 603 147 HOH HOH . E 4 HOH A 104 604 149 HOH HOH . E 4 HOH A 105 605 150 HOH HOH . E 4 HOH A 106 606 151 HOH HOH . E 4 HOH A 107 607 152 HOH HOH . E 4 HOH A 108 608 153 HOH HOH . E 4 HOH A 109 609 154 HOH HOH . E 4 HOH A 110 610 155 HOH HOH . E 4 HOH A 111 611 156 HOH HOH . E 4 HOH A 112 612 159 HOH HOH . E 4 HOH A 113 613 160 HOH HOH . E 4 HOH A 114 614 163 HOH HOH . E 4 HOH A 115 615 164 HOH HOH . E 4 HOH A 116 616 165 HOH HOH . E 4 HOH A 117 617 166 HOH HOH . E 4 HOH A 118 618 167 HOH HOH . E 4 HOH A 119 619 169 HOH HOH . E 4 HOH A 120 620 170 HOH HOH . E 4 HOH A 121 621 171 HOH HOH . E 4 HOH A 122 622 172 HOH HOH . E 4 HOH A 123 623 173 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 C _atom_site.label_entity_id 3 _atom_site.Cartn_x 20.097 _atom_site.Cartn_y 14.386 _atom_site.Cartn_z 51.713 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 17.79 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 500 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 1 #