data_3NV4
#
_model_server_result.job_id            ok3bn7aRpjMp9dqVmp5caw 
_model_server_result.datetime_utc      '2024-12-21 16:39:43' 
_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          3nv4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    3NV4 
#
_exptl.entry_id    3NV4 
_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            3NV4 
_cell.length_a            70.766 
_cell.length_b            70.766 
_cell.length_c            50.48 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3NV4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        173 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 63' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D 
_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 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 2 2 1 GAL BGC C1 O1 . O4 HO4 . sing 
2 ? 2 3 2 SIA GAL C2 O2 . O3 HO3 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n B BGC 1 B 1 BGC L 502 GLC 
2 n B GAL 2 B 2 GAL L 501 GAL 
2 n B SIA 3 B 3 SIA L 500 SIA 
#
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 O4 BGC . B BGC 1 1_555 B C1 GAL . B GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? 
covale ? covale2 B O3 GAL . B GAL 2 1_555 B C2 SIA . B SIA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? 
metalc ? metalc1 D O HOH . A HOH 12 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? 
metalc ? metalc2 A NE2 HIS 135 A HIS 320 1_555 C NI NI . A NI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? 
#
_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                     3NV4 
_atom_sites.fract_transf_matrix[1][1]    0.014131 
_atom_sites.fract_transf_matrix[1][2]    0.008159 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016317 
_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]    0.01981 
_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 1 401 401 NI NI2 . 
D 4 HOH A 1 1 1 HOH HOH . 
D 4 HOH A 2 2 2 HOH HOH . 
D 4 HOH A 3 3 3 HOH HOH . 
D 4 HOH A 4 4 4 HOH HOH . 
D 4 HOH A 5 5 5 HOH HOH . 
D 4 HOH A 6 6 6 HOH HOH . 
D 4 HOH A 7 7 7 HOH HOH . 
D 4 HOH A 8 8 8 HOH HOH . 
D 4 HOH A 9 9 9 HOH HOH . 
D 4 HOH A 10 10 10 HOH HOH . 
D 4 HOH A 11 11 11 HOH HOH . 
D 4 HOH A 12 12 12 HOH HOH . 
D 4 HOH A 13 13 13 HOH HOH . 
D 4 HOH A 14 14 14 HOH HOH . 
D 4 HOH A 15 15 15 HOH HOH . 
D 4 HOH A 16 16 16 HOH HOH . 
D 4 HOH A 17 17 17 HOH HOH . 
D 4 HOH A 18 18 18 HOH HOH . 
D 4 HOH A 19 19 19 HOH HOH . 
D 4 HOH A 20 20 20 HOH HOH . 
D 4 HOH A 21 21 21 HOH HOH . 
D 4 HOH A 22 22 22 HOH HOH . 
D 4 HOH A 23 23 23 HOH HOH . 
D 4 HOH A 24 24 24 HOH HOH . 
D 4 HOH A 25 25 25 HOH HOH . 
D 4 HOH A 26 26 26 HOH HOH . 
D 4 HOH A 27 27 27 HOH HOH . 
D 4 HOH A 28 28 28 HOH HOH . 
D 4 HOH A 29 29 29 HOH HOH . 
D 4 HOH A 30 30 30 HOH HOH . 
D 4 HOH A 31 31 31 HOH HOH . 
D 4 HOH A 32 32 32 HOH HOH . 
D 4 HOH A 33 33 33 HOH HOH . 
D 4 HOH A 34 34 34 HOH HOH . 
D 4 HOH A 35 35 35 HOH HOH . 
D 4 HOH A 36 36 36 HOH HOH . 
D 4 HOH A 37 37 37 HOH HOH . 
D 4 HOH A 38 38 38 HOH HOH . 
D 4 HOH A 39 39 39 HOH HOH . 
D 4 HOH A 40 40 40 HOH HOH . 
D 4 HOH A 41 41 41 HOH HOH . 
D 4 HOH A 42 42 42 HOH HOH . 
D 4 HOH A 43 43 43 HOH HOH . 
D 4 HOH A 44 44 44 HOH HOH . 
D 4 HOH A 45 45 45 HOH HOH . 
D 4 HOH A 46 46 46 HOH HOH . 
D 4 HOH A 47 47 47 HOH HOH . 
D 4 HOH A 48 48 48 HOH HOH . 
D 4 HOH A 49 49 49 HOH HOH . 
D 4 HOH A 50 50 50 HOH HOH . 
D 4 HOH A 51 51 51 HOH HOH . 
D 4 HOH A 52 52 52 HOH HOH . 
D 4 HOH A 53 53 53 HOH HOH . 
D 4 HOH A 54 54 54 HOH HOH . 
D 4 HOH A 55 55 55 HOH HOH . 
D 4 HOH A 56 56 56 HOH HOH . 
D 4 HOH A 57 57 57 HOH HOH . 
D 4 HOH A 58 58 58 HOH HOH . 
D 4 HOH A 59 59 59 HOH HOH . 
D 4 HOH A 60 60 60 HOH HOH . 
D 4 HOH A 61 61 61 HOH HOH . 
D 4 HOH A 62 62 62 HOH HOH . 
D 4 HOH A 63 63 63 HOH HOH . 
D 4 HOH A 64 64 64 HOH HOH . 
D 4 HOH A 65 65 65 HOH HOH . 
D 4 HOH A 66 66 66 HOH HOH . 
D 4 HOH A 67 67 67 HOH HOH . 
D 4 HOH A 68 68 68 HOH HOH . 
D 4 HOH A 69 69 69 HOH HOH . 
D 4 HOH A 70 70 70 HOH HOH . 
D 4 HOH A 71 71 71 HOH HOH . 
D 4 HOH A 72 72 72 HOH HOH . 
D 4 HOH A 73 73 73 HOH HOH . 
D 4 HOH A 74 74 74 HOH HOH . 
D 4 HOH A 75 75 75 HOH HOH . 
D 4 HOH A 76 76 76 HOH HOH . 
D 4 HOH A 77 77 77 HOH HOH . 
D 4 HOH A 78 78 78 HOH HOH . 
D 4 HOH A 79 79 79 HOH HOH . 
D 4 HOH A 80 80 80 HOH HOH . 
D 4 HOH A 81 81 81 HOH HOH . 
D 4 HOH A 82 82 82 HOH HOH . 
D 4 HOH A 83 83 83 HOH HOH . 
D 4 HOH A 84 84 84 HOH HOH . 
D 4 HOH A 85 85 85 HOH HOH . 
D 4 HOH A 86 86 86 HOH HOH . 
D 4 HOH A 87 87 87 HOH HOH . 
D 4 HOH A 88 88 88 HOH HOH . 
D 4 HOH A 89 89 89 HOH HOH . 
D 4 HOH A 90 90 90 HOH HOH . 
D 4 HOH A 91 91 91 HOH HOH . 
D 4 HOH A 92 92 92 HOH HOH . 
D 4 HOH A 93 93 93 HOH HOH . 
D 4 HOH A 94 94 94 HOH HOH . 
D 4 HOH A 95 95 95 HOH HOH . 
D 4 HOH A 96 96 96 HOH HOH . 
D 4 HOH A 97 97 97 HOH HOH . 
D 4 HOH A 98 98 98 HOH HOH . 
D 4 HOH A 99 99 99 HOH HOH . 
D 4 HOH A 100 100 100 HOH HOH . 
D 4 HOH A 101 101 101 HOH HOH . 
D 4 HOH A 102 102 102 HOH HOH . 
D 4 HOH A 103 103 103 HOH HOH . 
D 4 HOH A 104 104 104 HOH HOH . 
D 4 HOH A 105 105 105 HOH HOH . 
D 4 HOH A 106 106 106 HOH HOH . 
D 4 HOH A 107 107 107 HOH HOH . 
D 4 HOH A 108 108 108 HOH HOH . 
D 4 HOH A 109 109 109 HOH HOH . 
D 4 HOH A 110 110 110 HOH HOH . 
D 4 HOH A 111 111 111 HOH HOH . 
D 4 HOH A 112 112 112 HOH HOH . 
D 4 HOH A 113 113 113 HOH HOH . 
D 4 HOH A 114 114 114 HOH HOH . 
D 4 HOH A 115 115 115 HOH HOH . 
D 4 HOH A 116 116 116 HOH HOH . 
D 4 HOH A 117 117 117 HOH HOH . 
D 4 HOH A 118 118 118 HOH HOH . 
D 4 HOH A 119 119 119 HOH HOH . 
D 4 HOH A 120 120 120 HOH HOH . 
D 4 HOH A 121 121 121 HOH HOH . 
D 4 HOH A 122 122 122 HOH HOH . 
D 4 HOH A 123 123 123 HOH HOH . 
D 4 HOH A 124 124 124 HOH HOH . 
D 4 HOH A 125 125 125 HOH HOH . 
D 4 HOH A 126 126 126 HOH HOH . 
D 4 HOH A 127 127 127 HOH HOH . 
D 4 HOH A 128 128 128 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               0 
_atom_site.Cartn_y               40.857 
_atom_site.Cartn_z               21.623 
_atom_site.occupancy             0.5 
_atom_site.B_iso_or_equiv        20.39 
_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          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              53 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           356 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           1 
#