data_4GSV # _model_server_result.job_id EpQjZRW90JMTyaQWwW8-gw _model_server_result.datetime_utc '2024-11-15 12:50:49' _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 4gsv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 4GSV # _exptl.entry_id 4GSV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _entity.pdbx_number_of_molecules 4 _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 4GSV _cell.length_a 90.711 _cell.length_b 90.711 _cell.length_c 69.658 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GSV _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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 1,2,3 B,F,G,H,J 2 1,4,5 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 45.3555 -78.55803 0 3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 90.711 0 0 4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 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 F N N ? 2 G 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 ND1 HIS 101 A HIS 101 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc2 A OD2 ASP 124 A ASP 124 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc3 A OD1 ASP 124 A ASP 124 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc4 A ND1 HIS 126 A HIS 126 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc5 A OD2 ASP 128 A ASP 128 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? metalc ? metalc6 A OD2 ASP 232 A ASP 232 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc7 A OD2 ASP 232 A ASP 232 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc8 A OD1 ASP 234 A ASP 234 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc9 A OD2 ASP 234 A ASP 234 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc10 C NI NI . A NI 401 1_555 E O1 ABH . A ABH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc11 C NI NI . A NI 401 1_555 E O2 ABH . A ABH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc12 D NI NI . A NI 402 1_555 E O1 ABH . A ABH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc13 B ND1 HIS 101 B HIS 101 1_555 F NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.25 ? metalc ? metalc14 B OD2 ASP 124 B ASP 124 1_555 F NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc15 B OD1 ASP 124 B ASP 124 1_555 G NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc16 B ND1 HIS 126 B HIS 126 1_555 G NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc17 B OD2 ASP 128 B ASP 128 1_555 F NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc18 B OD2 ASP 232 B ASP 232 1_555 F NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc19 B OD2 ASP 232 B ASP 232 1_555 G NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc20 B OD1 ASP 234 B ASP 234 1_555 G NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? metalc ? metalc21 B OD2 ASP 234 B ASP 234 1_555 G NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc22 F NI NI . B NI 401 1_555 H O1 ABH . B ABH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc23 F NI NI . B NI 401 1_555 H O2 ABH . B ABH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.408 ? metalc ? metalc24 G NI NI . B NI 402 1_555 H O1 ABH . B ABH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? # _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 4GSV _atom_sites.fract_transf_matrix[1][1] 0.011024 _atom_sites.fract_transf_matrix[1][2] 0.006365 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012729 _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] 0.014356 _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 NI A 1 401 400 NI NI . D 2 NI A 1 402 401 NI NI . E 3 ABH A 1 403 500 ABH AB5 . F 2 NI B 1 401 400 NI NI . G 2 NI B 1 402 401 NI NI . H 3 ABH B 1 403 500 ABH AB5 . I 4 HOH A 1 501 1 HOH HOH . I 4 HOH A 2 502 2 HOH HOH . I 4 HOH A 3 503 3 HOH HOH . I 4 HOH A 4 504 4 HOH HOH . I 4 HOH A 5 505 6 HOH HOH . I 4 HOH A 6 506 9 HOH HOH . I 4 HOH A 7 507 10 HOH HOH . I 4 HOH A 8 508 12 HOH HOH . I 4 HOH A 9 509 13 HOH HOH . I 4 HOH A 10 510 14 HOH HOH . I 4 HOH A 11 511 15 HOH HOH . I 4 HOH A 12 512 16 HOH HOH . I 4 HOH A 13 513 17 HOH HOH . I 4 HOH A 14 514 18 HOH HOH . I 4 HOH A 15 515 19 HOH HOH . I 4 HOH A 16 516 20 HOH HOH . I 4 HOH A 17 517 22 HOH HOH . I 4 HOH A 18 518 24 HOH HOH . I 4 HOH A 19 519 25 HOH HOH . I 4 HOH A 20 520 27 HOH HOH . I 4 HOH A 21 521 28 HOH HOH . I 4 HOH A 22 522 29 HOH HOH . I 4 HOH A 23 523 30 HOH HOH . I 4 HOH A 24 524 34 HOH HOH . I 4 HOH A 25 525 39 HOH HOH . I 4 HOH A 26 526 41 HOH HOH . I 4 HOH A 27 527 42 HOH HOH . I 4 HOH A 28 528 43 HOH HOH . I 4 HOH A 29 529 44 HOH HOH . I 4 HOH A 30 530 49 HOH HOH . I 4 HOH A 31 531 50 HOH HOH . I 4 HOH A 32 532 55 HOH HOH . I 4 HOH A 33 533 57 HOH HOH . I 4 HOH A 34 534 58 HOH HOH . I 4 HOH A 35 535 59 HOH HOH . I 4 HOH A 36 536 63 HOH HOH . I 4 HOH A 37 537 66 HOH HOH . I 4 HOH A 38 538 67 HOH HOH . I 4 HOH A 39 539 70 HOH HOH . I 4 HOH A 40 540 71 HOH HOH . I 4 HOH A 41 541 72 HOH HOH . I 4 HOH A 42 542 74 HOH HOH . I 4 HOH A 43 543 75 HOH HOH . I 4 HOH A 44 544 76 HOH HOH . I 4 HOH A 45 545 79 HOH HOH . I 4 HOH A 46 546 81 HOH HOH . I 4 HOH A 47 547 83 HOH HOH . I 4 HOH A 48 548 84 HOH HOH . I 4 HOH A 49 549 85 HOH HOH . I 4 HOH A 50 550 86 HOH HOH . I 4 HOH A 51 551 87 HOH HOH . I 4 HOH A 52 552 88 HOH HOH . I 4 HOH A 53 553 92 HOH HOH . I 4 HOH A 54 554 95 HOH HOH . I 4 HOH A 55 555 96 HOH HOH . I 4 HOH A 56 556 98 HOH HOH . I 4 HOH A 57 557 99 HOH HOH . I 4 HOH A 58 558 101 HOH HOH . I 4 HOH A 59 559 104 HOH HOH . I 4 HOH A 60 560 106 HOH HOH . I 4 HOH A 61 561 108 HOH HOH . I 4 HOH A 62 562 109 HOH HOH . I 4 HOH A 63 563 110 HOH HOH . I 4 HOH A 64 564 111 HOH HOH . I 4 HOH A 65 565 114 HOH HOH . I 4 HOH A 66 566 116 HOH HOH . I 4 HOH A 67 567 117 HOH HOH . I 4 HOH A 68 568 118 HOH HOH . I 4 HOH A 69 569 119 HOH HOH . I 4 HOH A 70 570 121 HOH HOH . I 4 HOH A 71 571 126 HOH HOH . I 4 HOH A 72 572 127 HOH HOH . I 4 HOH A 73 573 129 HOH HOH . I 4 HOH A 74 574 131 HOH HOH . I 4 HOH A 75 575 134 HOH HOH . I 4 HOH A 76 576 135 HOH HOH . I 4 HOH A 77 577 137 HOH HOH . I 4 HOH A 78 578 138 HOH HOH . I 4 HOH A 79 579 142 HOH HOH . I 4 HOH A 80 580 143 HOH HOH . I 4 HOH A 81 581 144 HOH HOH . I 4 HOH A 82 582 146 HOH HOH . I 4 HOH A 83 583 147 HOH HOH . I 4 HOH A 84 584 148 HOH HOH . I 4 HOH A 85 585 150 HOH HOH . I 4 HOH A 86 586 151 HOH HOH . I 4 HOH A 87 587 152 HOH HOH . I 4 HOH A 88 588 155 HOH HOH . I 4 HOH A 89 589 157 HOH HOH . I 4 HOH A 90 590 158 HOH HOH . I 4 HOH A 91 591 161 HOH HOH . I 4 HOH A 92 592 163 HOH HOH . I 4 HOH A 93 593 165 HOH HOH . I 4 HOH A 94 594 166 HOH HOH . I 4 HOH A 95 595 168 HOH HOH . I 4 HOH A 96 596 170 HOH HOH . I 4 HOH A 97 597 172 HOH HOH . I 4 HOH A 98 598 174 HOH HOH . I 4 HOH A 99 599 176 HOH HOH . I 4 HOH A 100 600 178 HOH HOH . I 4 HOH A 101 601 183 HOH HOH . I 4 HOH A 102 602 184 HOH HOH . I 4 HOH A 103 603 185 HOH HOH . I 4 HOH A 104 604 186 HOH HOH . I 4 HOH A 105 605 191 HOH HOH . I 4 HOH A 106 606 195 HOH HOH . I 4 HOH A 107 607 196 HOH HOH . I 4 HOH A 108 608 197 HOH HOH . I 4 HOH A 109 609 198 HOH HOH . J 4 HOH B 1 501 5 HOH HOH . J 4 HOH B 2 502 7 HOH HOH . J 4 HOH B 3 503 8 HOH HOH . J 4 HOH B 4 504 11 HOH HOH . J 4 HOH B 5 505 21 HOH HOH . J 4 HOH B 6 506 23 HOH HOH . J 4 HOH B 7 507 26 HOH HOH . J 4 HOH B 8 508 31 HOH HOH . J 4 HOH B 9 509 32 HOH HOH . J 4 HOH B 10 510 33 HOH HOH . J 4 HOH B 11 511 35 HOH HOH . J 4 HOH B 12 512 36 HOH HOH . J 4 HOH B 13 513 37 HOH HOH . J 4 HOH B 14 514 38 HOH HOH . J 4 HOH B 15 515 40 HOH HOH . J 4 HOH B 16 516 45 HOH HOH . J 4 HOH B 17 517 46 HOH HOH . J 4 HOH B 18 518 47 HOH HOH . J 4 HOH B 19 519 48 HOH HOH . J 4 HOH B 20 520 51 HOH HOH . J 4 HOH B 21 521 52 HOH HOH . J 4 HOH B 22 522 53 HOH HOH . J 4 HOH B 23 523 54 HOH HOH . J 4 HOH B 24 524 56 HOH HOH . J 4 HOH B 25 525 60 HOH HOH . J 4 HOH B 26 526 61 HOH HOH . J 4 HOH B 27 527 62 HOH HOH . J 4 HOH B 28 528 64 HOH HOH . J 4 HOH B 29 529 65 HOH HOH . J 4 HOH B 30 530 68 HOH HOH . J 4 HOH B 31 531 69 HOH HOH . J 4 HOH B 32 532 73 HOH HOH . J 4 HOH B 33 533 77 HOH HOH . J 4 HOH B 34 534 78 HOH HOH . J 4 HOH B 35 535 80 HOH HOH . J 4 HOH B 36 536 82 HOH HOH . J 4 HOH B 37 537 89 HOH HOH . J 4 HOH B 38 538 90 HOH HOH . J 4 HOH B 39 539 91 HOH HOH . J 4 HOH B 40 540 93 HOH HOH . J 4 HOH B 41 541 94 HOH HOH . J 4 HOH B 42 542 97 HOH HOH . J 4 HOH B 43 543 100 HOH HOH . J 4 HOH B 44 544 102 HOH HOH . J 4 HOH B 45 545 103 HOH HOH . J 4 HOH B 46 546 105 HOH HOH . J 4 HOH B 47 547 107 HOH HOH . J 4 HOH B 48 548 112 HOH HOH . J 4 HOH B 49 549 113 HOH HOH . J 4 HOH B 50 550 115 HOH HOH . J 4 HOH B 51 551 120 HOH HOH . J 4 HOH B 52 552 122 HOH HOH . J 4 HOH B 53 553 123 HOH HOH . J 4 HOH B 54 554 124 HOH HOH . J 4 HOH B 55 555 125 HOH HOH . J 4 HOH B 56 556 128 HOH HOH . J 4 HOH B 57 557 130 HOH HOH . J 4 HOH B 58 558 132 HOH HOH . J 4 HOH B 59 559 133 HOH HOH . J 4 HOH B 60 560 136 HOH HOH . J 4 HOH B 61 561 139 HOH HOH . J 4 HOH B 62 562 140 HOH HOH . J 4 HOH B 63 563 141 HOH HOH . J 4 HOH B 64 564 145 HOH HOH . J 4 HOH B 65 565 149 HOH HOH . J 4 HOH B 66 566 153 HOH HOH . J 4 HOH B 67 567 154 HOH HOH . J 4 HOH B 68 568 156 HOH HOH . J 4 HOH B 69 569 159 HOH HOH . J 4 HOH B 70 570 160 HOH HOH . J 4 HOH B 71 571 162 HOH HOH . J 4 HOH B 72 572 164 HOH HOH . J 4 HOH B 73 573 167 HOH HOH . J 4 HOH B 74 574 169 HOH HOH . J 4 HOH B 75 575 171 HOH HOH . J 4 HOH B 76 576 173 HOH HOH . J 4 HOH B 77 577 175 HOH HOH . J 4 HOH B 78 578 177 HOH HOH . J 4 HOH B 79 579 179 HOH HOH . J 4 HOH B 80 580 180 HOH HOH . J 4 HOH B 81 581 181 HOH HOH . J 4 HOH B 82 582 182 HOH HOH . J 4 HOH B 83 583 187 HOH HOH . J 4 HOH B 84 584 188 HOH HOH . J 4 HOH B 85 585 189 HOH HOH . J 4 HOH B 86 586 190 HOH HOH . J 4 HOH B 87 587 192 HOH HOH . J 4 HOH B 88 588 193 HOH HOH . J 4 HOH B 89 589 194 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 F _atom_site.label_entity_id 2 _atom_site.Cartn_x 15.79 _atom_site.Cartn_y -16.323 _atom_site.Cartn_z -31.274 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 18.4 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 401 _atom_site.auth_asym_id B _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 43 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 1 #