data_4GSM
#
_model_server_result.job_id            4B7QjKikpuLj5tGCLpSgqQ 
_model_server_result.datetime_utc      '2024-11-15 13:05:29' 
_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          4gsm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":402}' 
#
_entry.id    4GSM 
#
_exptl.entry_id    4GSM 
_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            4GSM 
_cell.length_a            90.353 
_cell.length_b            90.353 
_cell.length_c            69.814 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4GSM 
_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,G 1 1,2,3 
B,E,F,H 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 
3 '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 
4 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 45.1765 -78.247993 0 
5 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 90.353 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 E N N 
? 2 F 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 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc2 A OD1 ASP 124 A ASP 124 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
metalc ? metalc3 A OD2 ASP 124 A ASP 124 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc4 A ND1 HIS 126 A HIS 126 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? 
metalc ? metalc5 A OD1 ASP 128 A ASP 128 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc6 A OD2 ASP 232 A ASP 232 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc7 A OD2 ASP 232 A ASP 232 1_555 D NI NI . A NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? 
metalc ? metalc8 A OD1 ASP 234 A ASP 234 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? 
metalc ? metalc9 A OD2 ASP 234 A ASP 234 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc10 C NI NI . A NI 401 1_555 G O HOH . A HOH 589 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc11 D NI NI . A NI 402 1_555 G O HOH . A HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.71 ? 
metalc ? metalc12 D NI NI . A NI 402 1_555 G O HOH . A HOH 589 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc13 B ND1 HIS 101 B HIS 101 1_555 F NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc14 B OD1 ASP 124 B ASP 124 1_555 E NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc15 B OD2 ASP 124 B ASP 124 1_555 F NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? 
metalc ? metalc16 B ND1 HIS 126 B HIS 126 1_555 E NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? 
metalc ? metalc17 B OD1 ASP 128 B ASP 128 1_555 F NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
metalc ? metalc18 B OD2 ASP 232 B ASP 232 1_555 E NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc19 B OD2 ASP 232 B ASP 232 1_555 F NI NI . B NI 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? 
metalc ? metalc20 B OD1 ASP 234 B ASP 234 1_555 E NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc21 B OD2 ASP 234 B ASP 234 1_555 E NI NI . B NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc22 E NI NI . B NI 401 1_555 H O HOH . B HOH 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? 
metalc ? metalc23 F NI NI . B NI 402 1_555 H O HOH . B HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? 
metalc ? metalc24 F NI NI . B NI 402 1_555 H O HOH . B HOH 565 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? 
#
_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                     4GSM 
_atom_sites.fract_transf_matrix[1][1]    0.011068 
_atom_sites.fract_transf_matrix[1][2]    0.00639 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01278 
_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]    0.014324 
_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 1 401 401 NI NI . 
D 2 NI A 1 402 400 NI NI . 
E 2 NI B 1 401 401 NI NI . 
F 2 NI B 1 402 400 NI NI . 
G 3 HOH A 1 501 1 HOH HOH . 
G 3 HOH A 2 502 3 HOH HOH . 
G 3 HOH A 3 503 5 HOH HOH . 
G 3 HOH A 4 504 6 HOH HOH . 
G 3 HOH A 5 505 7 HOH HOH . 
G 3 HOH A 6 506 8 HOH HOH . 
G 3 HOH A 7 507 10 HOH HOH . 
G 3 HOH A 8 508 11 HOH HOH . 
G 3 HOH A 9 509 13 HOH HOH . 
G 3 HOH A 10 510 14 HOH HOH . 
G 3 HOH A 11 511 15 HOH HOH . 
G 3 HOH A 12 512 17 HOH HOH . 
G 3 HOH A 13 513 18 HOH HOH . 
G 3 HOH A 14 514 19 HOH HOH . 
G 3 HOH A 15 515 22 HOH HOH . 
G 3 HOH A 16 516 23 HOH HOH . 
G 3 HOH A 17 517 25 HOH HOH . 
G 3 HOH A 18 518 26 HOH HOH . 
G 3 HOH A 19 519 28 HOH HOH . 
G 3 HOH A 20 520 29 HOH HOH . 
G 3 HOH A 21 521 30 HOH HOH . 
G 3 HOH A 22 522 31 HOH HOH . 
G 3 HOH A 23 523 32 HOH HOH . 
G 3 HOH A 24 524 36 HOH HOH . 
G 3 HOH A 25 525 42 HOH HOH . 
G 3 HOH A 26 526 45 HOH HOH . 
G 3 HOH A 27 527 47 HOH HOH . 
G 3 HOH A 28 528 48 HOH HOH . 
G 3 HOH A 29 529 49 HOH HOH . 
G 3 HOH A 30 530 50 HOH HOH . 
G 3 HOH A 31 531 52 HOH HOH . 
G 3 HOH A 32 532 54 HOH HOH . 
G 3 HOH A 33 533 55 HOH HOH . 
G 3 HOH A 34 534 58 HOH HOH . 
G 3 HOH A 35 535 62 HOH HOH . 
G 3 HOH A 36 536 63 HOH HOH . 
G 3 HOH A 37 537 65 HOH HOH . 
G 3 HOH A 38 538 69 HOH HOH . 
G 3 HOH A 39 539 71 HOH HOH . 
G 3 HOH A 40 540 72 HOH HOH . 
G 3 HOH A 41 541 74 HOH HOH . 
G 3 HOH A 42 542 77 HOH HOH . 
G 3 HOH A 43 543 81 HOH HOH . 
G 3 HOH A 44 544 82 HOH HOH . 
G 3 HOH A 45 545 85 HOH HOH . 
G 3 HOH A 46 546 86 HOH HOH . 
G 3 HOH A 47 547 87 HOH HOH . 
G 3 HOH A 48 548 90 HOH HOH . 
G 3 HOH A 49 549 92 HOH HOH . 
G 3 HOH A 50 550 93 HOH HOH . 
G 3 HOH A 51 551 94 HOH HOH . 
G 3 HOH A 52 552 95 HOH HOH . 
G 3 HOH A 53 553 97 HOH HOH . 
G 3 HOH A 54 554 98 HOH HOH . 
G 3 HOH A 55 555 99 HOH HOH . 
G 3 HOH A 56 556 101 HOH HOH . 
G 3 HOH A 57 557 102 HOH HOH . 
G 3 HOH A 58 558 103 HOH HOH . 
G 3 HOH A 59 559 105 HOH HOH . 
G 3 HOH A 60 560 106 HOH HOH . 
G 3 HOH A 61 561 109 HOH HOH . 
G 3 HOH A 62 562 110 HOH HOH . 
G 3 HOH A 63 563 112 HOH HOH . 
G 3 HOH A 64 564 115 HOH HOH . 
G 3 HOH A 65 565 117 HOH HOH . 
G 3 HOH A 66 566 119 HOH HOH . 
G 3 HOH A 67 567 120 HOH HOH . 
G 3 HOH A 68 568 123 HOH HOH . 
G 3 HOH A 69 569 124 HOH HOH . 
G 3 HOH A 70 570 125 HOH HOH . 
G 3 HOH A 71 571 126 HOH HOH . 
G 3 HOH A 72 572 128 HOH HOH . 
G 3 HOH A 73 573 129 HOH HOH . 
G 3 HOH A 74 574 130 HOH HOH . 
G 3 HOH A 75 575 132 HOH HOH . 
G 3 HOH A 76 576 133 HOH HOH . 
G 3 HOH A 77 577 135 HOH HOH . 
G 3 HOH A 78 578 138 HOH HOH . 
G 3 HOH A 79 579 140 HOH HOH . 
G 3 HOH A 80 580 141 HOH HOH . 
G 3 HOH A 81 581 143 HOH HOH . 
G 3 HOH A 82 582 144 HOH HOH . 
G 3 HOH A 83 583 146 HOH HOH . 
G 3 HOH A 84 584 147 HOH HOH . 
G 3 HOH A 85 585 148 HOH HOH . 
G 3 HOH A 86 586 149 HOH HOH . 
G 3 HOH A 87 587 151 HOH HOH . 
G 3 HOH A 88 588 152 HOH HOH . 
G 3 HOH A 89 589 153 HOH HOH . 
G 3 HOH A 90 590 154 HOH HOH . 
G 3 HOH A 91 591 156 HOH HOH . 
G 3 HOH A 92 592 157 HOH HOH . 
H 3 HOH B 1 501 2 HOH HOH . 
H 3 HOH B 2 502 4 HOH HOH . 
H 3 HOH B 3 503 9 HOH HOH . 
H 3 HOH B 4 504 12 HOH HOH . 
H 3 HOH B 5 505 16 HOH HOH . 
H 3 HOH B 6 506 20 HOH HOH . 
H 3 HOH B 7 507 21 HOH HOH . 
H 3 HOH B 8 508 24 HOH HOH . 
H 3 HOH B 9 509 27 HOH HOH . 
H 3 HOH B 10 510 33 HOH HOH . 
H 3 HOH B 11 511 34 HOH HOH . 
H 3 HOH B 12 512 35 HOH HOH . 
H 3 HOH B 13 513 37 HOH HOH . 
H 3 HOH B 14 514 38 HOH HOH . 
H 3 HOH B 15 515 39 HOH HOH . 
H 3 HOH B 16 516 40 HOH HOH . 
H 3 HOH B 17 517 41 HOH HOH . 
H 3 HOH B 18 518 43 HOH HOH . 
H 3 HOH B 19 519 44 HOH HOH . 
H 3 HOH B 20 520 46 HOH HOH . 
H 3 HOH B 21 521 51 HOH HOH . 
H 3 HOH B 22 522 53 HOH HOH . 
H 3 HOH B 23 523 56 HOH HOH . 
H 3 HOH B 24 524 57 HOH HOH . 
H 3 HOH B 25 525 59 HOH HOH . 
H 3 HOH B 26 526 60 HOH HOH . 
H 3 HOH B 27 527 61 HOH HOH . 
H 3 HOH B 28 528 64 HOH HOH . 
H 3 HOH B 29 529 66 HOH HOH . 
H 3 HOH B 30 530 67 HOH HOH . 
H 3 HOH B 31 531 68 HOH HOH . 
H 3 HOH B 32 532 70 HOH HOH . 
H 3 HOH B 33 533 73 HOH HOH . 
H 3 HOH B 34 534 75 HOH HOH . 
H 3 HOH B 35 535 76 HOH HOH . 
H 3 HOH B 36 536 78 HOH HOH . 
H 3 HOH B 37 537 79 HOH HOH . 
H 3 HOH B 38 538 80 HOH HOH . 
H 3 HOH B 39 539 83 HOH HOH . 
H 3 HOH B 40 540 84 HOH HOH . 
H 3 HOH B 41 541 88 HOH HOH . 
H 3 HOH B 42 542 89 HOH HOH . 
H 3 HOH B 43 543 91 HOH HOH . 
H 3 HOH B 44 544 96 HOH HOH . 
H 3 HOH B 45 545 100 HOH HOH . 
H 3 HOH B 46 546 104 HOH HOH . 
H 3 HOH B 47 547 107 HOH HOH . 
H 3 HOH B 48 548 108 HOH HOH . 
H 3 HOH B 49 549 111 HOH HOH . 
H 3 HOH B 50 550 113 HOH HOH . 
H 3 HOH B 51 551 114 HOH HOH . 
H 3 HOH B 52 552 116 HOH HOH . 
H 3 HOH B 53 553 118 HOH HOH . 
H 3 HOH B 54 554 121 HOH HOH . 
H 3 HOH B 55 555 122 HOH HOH . 
H 3 HOH B 56 556 127 HOH HOH . 
H 3 HOH B 57 557 131 HOH HOH . 
H 3 HOH B 58 558 134 HOH HOH . 
H 3 HOH B 59 559 136 HOH HOH . 
H 3 HOH B 60 560 137 HOH HOH . 
H 3 HOH B 61 561 139 HOH HOH . 
H 3 HOH B 62 562 142 HOH HOH . 
H 3 HOH B 63 563 145 HOH HOH . 
H 3 HOH B 64 564 150 HOH HOH . 
H 3 HOH B 65 565 155 HOH HOH . 
H 3 HOH B 66 566 158 HOH HOH . 
H 3 HOH B 67 567 159 HOH HOH . 
H 3 HOH B 68 568 160 HOH HOH . 
H 3 HOH B 69 569 161 HOH HOH . 
H 3 HOH B 70 570 162 HOH HOH . 
H 3 HOH B 71 571 163 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       2 
_atom_site.Cartn_x               20.999 
_atom_site.Cartn_y               -8.258 
_atom_site.Cartn_z               -2.971 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        18.24 
_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              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#