data_3KVB
#
_model_server_result.job_id            f6qJlmgGqrdhhAxR7qSFVQ 
_model_server_result.datetime_utc      '2024-12-03 14:55:06' 
_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          3kvb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":490}' 
#
_entry.id    3KVB 
#
_exptl.entry_id    3KVB 
_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    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         120 
_cell.entry_id            3KVB 
_cell.length_a            78.3 
_cell.length_b            78.3 
_cell.length_c            289.1 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3KVB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 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
? monomeric 1 author_defined_assembly 1 
PISA dimeric 2 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,B,C,D,E,F 1 1 
A,B,C,D,E,F 2 1,2 
#
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' 12_565 x,x-y+1,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -39.15 67.809789 48.183333 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 B N N 
? 2 C 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 NE2 HIS 191 A HIS 282 1_555 B NI NI . A NI 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.482 ? 
metalc ? metalc2 A OD1 ASP 193 A ASP 284 1_555 B NI NI . A NI 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? 
metalc ? metalc3 A NE2 HIS 263 A HIS 354 1_555 B NI NI . A NI 489 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? 
metalc ? metalc4 B NI NI . A NI 489 1_555 E O2' OGA . A OGA 5798 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? 
metalc ? metalc5 B NI NI . A NI 489 1_555 E O2 OGA . A OGA 5798 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
#
_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                     3KVB 
_atom_sites.fract_transf_matrix[1][1]    0.012771 
_atom_sites.fract_transf_matrix[1][2]    0.007374 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014747 
_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]    0.003459 
_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
B 2 NI A 1 489 480 NI NI . 
C 2 NI A 1 490 481 NI NI . 
D 3 OXY A 1 491 482 OXY OXY . 
E 4 OGA A 1 5798 5798 OGA OGA . 
F 5 HOH A 1 1 1 HOH TIP . 
F 5 HOH A 2 2 2 HOH TIP . 
F 5 HOH A 3 3 3 HOH TIP . 
F 5 HOH A 4 4 4 HOH TIP . 
F 5 HOH A 5 5 5 HOH TIP . 
F 5 HOH A 6 6 6 HOH TIP . 
F 5 HOH A 7 7 7 HOH TIP . 
F 5 HOH A 8 8 8 HOH TIP . 
F 5 HOH A 9 9 9 HOH TIP . 
F 5 HOH A 10 10 10 HOH TIP . 
F 5 HOH A 11 11 11 HOH TIP . 
F 5 HOH A 12 12 12 HOH TIP . 
F 5 HOH A 13 13 13 HOH TIP . 
F 5 HOH A 14 14 14 HOH TIP . 
F 5 HOH A 15 15 15 HOH TIP . 
F 5 HOH A 16 16 16 HOH TIP . 
F 5 HOH A 17 17 17 HOH TIP . 
F 5 HOH A 18 18 18 HOH TIP . 
F 5 HOH A 19 19 19 HOH TIP . 
F 5 HOH A 20 20 20 HOH TIP . 
F 5 HOH A 21 21 21 HOH TIP . 
F 5 HOH A 22 22 22 HOH TIP . 
F 5 HOH A 23 23 23 HOH TIP . 
F 5 HOH A 24 24 24 HOH TIP . 
F 5 HOH A 25 25 25 HOH TIP . 
F 5 HOH A 26 26 26 HOH TIP . 
F 5 HOH A 27 27 27 HOH TIP . 
F 5 HOH A 28 28 28 HOH TIP . 
F 5 HOH A 29 29 29 HOH TIP . 
F 5 HOH A 30 30 30 HOH TIP . 
F 5 HOH A 31 31 31 HOH TIP . 
F 5 HOH A 32 33 33 HOH TIP . 
F 5 HOH A 33 34 34 HOH TIP . 
F 5 HOH A 34 35 35 HOH TIP . 
F 5 HOH A 35 36 36 HOH TIP . 
F 5 HOH A 36 38 38 HOH TIP . 
F 5 HOH A 37 39 39 HOH TIP . 
F 5 HOH A 38 40 40 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         C 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               -29.067 
_atom_site.Cartn_y               32.258 
_atom_site.Cartn_z               6.829 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        68.08 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           490 
_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           13 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          12 
_model_server_stats.element_count           1 
#