data_1S3M
#
_model_server_result.job_id            UC9_01s1sSNhxleVs3RE1A 
_model_server_result.datetime_utc      '2025-04-09 00:54:09' 
_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          1s3m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":504}' 
#
_entry.id    1S3M 
#
_exptl.entry_id    1S3M 
_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         90 
_cell.entry_id            1S3M 
_cell.length_a            70.106 
_cell.length_b            70.106 
_cell.length_c            196.173 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1S3M 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 41' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_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 
B,E,F,H 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
? 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 OD1 ASP 33 A ASP 8 1_555 D NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? 
metalc ? metalc2 A NE2 HIS 35 A HIS 10 1_555 D NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc3 A OD1 ASP 61 A ASP 36 1_555 D NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? 
metalc ? metalc4 A OD1 ASN 84 A ASN 59 1_555 C NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? 
metalc ? metalc5 A NE2 HIS 122 A HIS 97 1_555 C NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? 
metalc ? metalc6 A ND1 HIS 145 A HIS 120 1_555 C NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.775 ? 
metalc ? metalc7 A NE2 HIS 147 A HIS 122 1_555 D NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? 
metalc ? metalc8 C NI NI . A NI 503 1_555 G O HOH . A HOH 647 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? 
metalc ? metalc9 B OD1 ASP 33 B ASP 208 1_555 F NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? 
metalc ? metalc10 B NE2 HIS 35 B HIS 210 1_555 F NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.319 ? 
metalc ? metalc11 B OD1 ASP 61 B ASP 236 1_555 F NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? 
metalc ? metalc12 B OD1 ASN 84 B ASN 259 1_555 E NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
metalc ? metalc13 B NE2 HIS 122 B HIS 297 1_555 E NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc14 B ND1 HIS 145 B HIS 320 1_555 E NI NI . B NI 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? 
metalc ? metalc15 B NE2 HIS 147 B HIS 322 1_555 F NI NI . B NI 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
metalc ? metalc16 F NI NI . B NI 502 1_555 H O HOH . B HOH 646 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? 
#
_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                     1S3M 
_atom_sites.fract_transf_matrix[1][1]    0.014264 
_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]    0.014264 
_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]    0.005098 
_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 1 503 503 NI NI . 
D 2 NI A 1 504 504 NI NI . 
E 2 NI B 1 501 501 NI NI . 
F 2 NI B 1 502 502 NI NI . 
G 3 HOH A 1 602 602 HOH TIP . 
G 3 HOH A 2 605 605 HOH TIP . 
G 3 HOH A 3 608 608 HOH TIP . 
G 3 HOH A 4 609 609 HOH TIP . 
G 3 HOH A 5 614 614 HOH TIP . 
G 3 HOH A 6 616 616 HOH TIP . 
G 3 HOH A 7 617 617 HOH TIP . 
G 3 HOH A 8 618 618 HOH TIP . 
G 3 HOH A 9 619 619 HOH TIP . 
G 3 HOH A 10 623 623 HOH TIP . 
G 3 HOH A 11 624 624 HOH TIP . 
G 3 HOH A 12 625 625 HOH TIP . 
G 3 HOH A 13 626 626 HOH TIP . 
G 3 HOH A 14 627 627 HOH TIP . 
G 3 HOH A 15 628 628 HOH TIP . 
G 3 HOH A 16 630 630 HOH TIP . 
G 3 HOH A 17 632 632 HOH TIP . 
G 3 HOH A 18 633 633 HOH TIP . 
G 3 HOH A 19 635 635 HOH TIP . 
G 3 HOH A 20 638 638 HOH TIP . 
G 3 HOH A 21 641 641 HOH TIP . 
G 3 HOH A 22 644 644 HOH TIP . 
G 3 HOH A 23 645 645 HOH TIP . 
G 3 HOH A 24 647 647 HOH TIP . 
G 3 HOH A 25 648 648 HOH TIP . 
G 3 HOH A 26 651 651 HOH TIP . 
G 3 HOH A 27 652 652 HOH TIP . 
G 3 HOH A 28 653 653 HOH TIP . 
G 3 HOH A 29 655 655 HOH TIP . 
G 3 HOH A 30 657 657 HOH TIP . 
G 3 HOH A 31 658 658 HOH TIP . 
G 3 HOH A 32 659 659 HOH TIP . 
G 3 HOH A 33 670 670 HOH TIP . 
G 3 HOH A 34 675 675 HOH TIP . 
G 3 HOH A 35 676 676 HOH TIP . 
H 3 HOH B 1 601 601 HOH TIP . 
H 3 HOH B 2 603 603 HOH TIP . 
H 3 HOH B 3 604 604 HOH TIP . 
H 3 HOH B 4 606 606 HOH TIP . 
H 3 HOH B 5 607 607 HOH TIP . 
H 3 HOH B 6 610 610 HOH TIP . 
H 3 HOH B 7 611 611 HOH TIP . 
H 3 HOH B 8 612 612 HOH TIP . 
H 3 HOH B 9 613 613 HOH TIP . 
H 3 HOH B 10 615 615 HOH TIP . 
H 3 HOH B 11 620 620 HOH TIP . 
H 3 HOH B 12 621 621 HOH TIP . 
H 3 HOH B 13 622 622 HOH TIP . 
H 3 HOH B 14 629 629 HOH TIP . 
H 3 HOH B 15 631 631 HOH TIP . 
H 3 HOH B 16 634 634 HOH TIP . 
H 3 HOH B 17 636 636 HOH TIP . 
H 3 HOH B 18 637 637 HOH TIP . 
H 3 HOH B 19 639 639 HOH TIP . 
H 3 HOH B 20 640 640 HOH TIP . 
H 3 HOH B 21 642 642 HOH TIP . 
H 3 HOH B 22 643 643 HOH TIP . 
H 3 HOH B 23 646 646 HOH TIP . 
H 3 HOH B 24 649 649 HOH TIP . 
H 3 HOH B 25 650 650 HOH TIP . 
H 3 HOH B 26 654 654 HOH TIP . 
H 3 HOH B 27 656 656 HOH TIP . 
H 3 HOH B 28 671 671 HOH TIP . 
H 3 HOH B 29 672 672 HOH TIP . 
H 3 HOH B 30 673 673 HOH TIP . 
H 3 HOH B 31 674 674 HOH TIP . 
H 3 HOH B 32 677 677 HOH TIP . 
H 3 HOH B 33 678 678 HOH TIP . 
H 3 HOH B 34 679 679 HOH TIP . 
#
_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               66.763 
_atom_site.Cartn_y               27.119 
_atom_site.Cartn_z               0.76 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        46.83 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           504 
_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           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           323 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           1 
#