data_1D39
#
_model_server_result.job_id            OxsAUBWbNItHmebLMHMLKg 
_model_server_result.datetime_utc      '2025-04-03 15:49:29' 
_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          1d39 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":15}' 
#
_entry.id    1D39 
#
_exptl.entry_id    1D39 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              63.546 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'COPPER (II) ION' 
_entity.pdbx_number_of_molecules    6 
_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            1D39 
_cell.length_a            18.01 
_cell.length_b            31.03 
_cell.length_c            44.8 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1D39 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K 
_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 
#
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 
? 2 G N N 
? 2 H 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 N7 DG 2 A DG 2 1_555 C CU CU . A CU 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? 
metalc ? metalc2 A N7 DG 4 A DG 4 1_555 D CU CU . A CU 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc3 A N7 DG 6 A DG 6 1_555 E CU CU . A CU 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc4 C CU CU . A CU 7 1_555 J O HOH . A HOH 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc5 C CU CU . A CU 7 1_555 J O HOH . A HOH 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc6 D CU CU . A CU 8 1_555 J O HOH . A HOH 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? 
metalc ? metalc7 E CU CU . A CU 9 1_555 J O HOH . A HOH 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc8 E CU CU . A CU 9 1_555 J O HOH . A HOH 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc9 E CU CU . A CU 9 1_555 J O HOH . A HOH 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? 
metalc ? metalc10 E CU CU . A CU 9 1_555 J O HOH . A HOH 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc11 E CU CU . A CU 9 1_555 J O HOH . A HOH 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc12 B N7 DG 2 B DG 8 1_555 F CU CU . B CU 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.31 ? 
metalc ? metalc13 B N7 DG 4 B DG 10 1_555 G CU CU . B CU 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? 
metalc ? metalc14 B N7 DG 6 B DG 12 1_555 H CU CU . B CU 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? 
metalc ? metalc15 F CU CU . B CU 13 1_555 K O HOH . B HOH 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
metalc ? metalc16 F CU CU . B CU 13 1_555 K O HOH . B HOH 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.994 ? 
metalc ? metalc17 F CU CU . B CU 13 1_555 K O HOH . B HOH 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? 
metalc ? metalc18 G CU CU . B CU 14 1_555 H CU CU . B CU 15 4_566 ? ? ? ? ? ? ? ? ? ? ? ? 1.551 ? 
metalc ? metalc19 G CU CU . B CU 14 4_466 H CU CU . B CU 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.551 ? 
metalc ? metalc20 G CU CU . B CU 14 1_555 K O HOH . B HOH 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc21 G CU CU . B CU 14 1_555 K O HOH . B HOH 78 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc22 G CU CU . B CU 14 1_555 K O HOH . B HOH 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.834 ? 
metalc ? metalc23 H CU CU . B CU 15 1_555 K O HOH . B HOH 27 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
metalc ? metalc24 H CU CU . B CU 15 1_555 K O HOH . B HOH 76 4_466 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? 
metalc ? metalc25 H CU CU . B CU 15 1_555 K O HOH . B HOH 77 4_466 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
metalc ? metalc26 I NA NA . B NA 16 1_555 K O HOH . B HOH 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.551 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'Cu 2' 
_chem_comp.formula_weight    63.546 
_chem_comp.id                CU 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'COPPER (II) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     1D39 
_atom_sites.fract_transf_matrix[1][1]    0.055525 
_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]    0.032227 
_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]    0.022321 
_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 CU A 1 7 2 CU G . 
D 2 CU A 1 8 4 CU G . 
E 2 CU A 1 9 6 CU G . 
F 2 CU B 1 13 8 CU G . 
G 2 CU B 1 14 10 CU G . 
H 2 CU B 1 15 12 CU G . 
I 3 NA B 1 16 13 NA NA . 
J 4 HOH A 1 14 14 HOH HOH . 
J 4 HOH A 2 15 15 HOH HOH . 
J 4 HOH A 3 16 16 HOH HOH . 
J 4 HOH A 4 17 17 HOH HOH . 
J 4 HOH A 5 18 18 HOH HOH . 
J 4 HOH A 6 19 19 HOH HOH . 
J 4 HOH A 7 20 20 HOH HOH . 
J 4 HOH A 8 21 21 HOH HOH . 
J 4 HOH A 9 30 30 HOH HOH . 
J 4 HOH A 10 32 32 HOH HOH . 
J 4 HOH A 11 33 33 HOH HOH . 
J 4 HOH A 12 35 35 HOH HOH . 
J 4 HOH A 13 36 36 HOH HOH . 
J 4 HOH A 14 39 39 HOH HOH . 
J 4 HOH A 15 40 40 HOH HOH . 
J 4 HOH A 16 41 41 HOH HOH . 
J 4 HOH A 17 42 42 HOH HOH . 
J 4 HOH A 18 43 43 HOH HOH . 
J 4 HOH A 19 45 45 HOH HOH . 
J 4 HOH A 20 46 46 HOH HOH . 
J 4 HOH A 21 47 47 HOH HOH . 
J 4 HOH A 22 48 48 HOH HOH . 
J 4 HOH A 23 49 49 HOH HOH . 
J 4 HOH A 24 50 50 HOH HOH . 
J 4 HOH A 25 51 51 HOH HOH . 
J 4 HOH A 26 54 54 HOH HOH . 
J 4 HOH A 27 57 57 HOH HOH . 
J 4 HOH A 28 58 58 HOH HOH . 
J 4 HOH A 29 61 61 HOH HOH . 
J 4 HOH A 30 62 62 HOH HOH . 
J 4 HOH A 31 64 64 HOH HOH . 
J 4 HOH A 32 65 65 HOH HOH . 
J 4 HOH A 33 67 67 HOH HOH . 
J 4 HOH A 34 70 70 HOH HOH . 
J 4 HOH A 35 71 71 HOH HOH . 
J 4 HOH A 36 72 72 HOH HOH . 
J 4 HOH A 37 74 74 HOH HOH . 
J 4 HOH A 38 75 75 HOH HOH . 
K 4 HOH B 1 22 22 HOH HOH . 
K 4 HOH B 2 23 23 HOH HOH . 
K 4 HOH B 3 24 24 HOH HOH . 
K 4 HOH B 4 25 25 HOH HOH . 
K 4 HOH B 5 26 26 HOH HOH . 
K 4 HOH B 6 27 27 HOH HOH . 
K 4 HOH B 7 28 28 HOH HOH . 
K 4 HOH B 8 29 29 HOH HOH . 
K 4 HOH B 9 31 31 HOH HOH . 
K 4 HOH B 10 34 34 HOH HOH . 
K 4 HOH B 11 37 37 HOH HOH . 
K 4 HOH B 12 38 38 HOH HOH . 
K 4 HOH B 13 44 44 HOH HOH . 
K 4 HOH B 14 52 52 HOH HOH . 
K 4 HOH B 15 53 53 HOH HOH . 
K 4 HOH B 16 55 55 HOH HOH . 
K 4 HOH B 17 56 56 HOH HOH . 
K 4 HOH B 18 59 59 HOH HOH . 
K 4 HOH B 19 60 60 HOH HOH . 
K 4 HOH B 20 63 63 HOH HOH . 
K 4 HOH B 21 66 66 HOH HOH . 
K 4 HOH B 22 68 68 HOH HOH . 
K 4 HOH B 23 69 69 HOH HOH . 
K 4 HOH B 24 73 73 HOH HOH . 
K 4 HOH B 25 76 76 HOH HOH . 
K 4 HOH B 26 77 77 HOH HOH . 
K 4 HOH B 27 78 78 HOH HOH . 
K 4 HOH B 28 79 79 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           CU 
_atom_site.label_atom_id         CU 
_atom_site.label_comp_id         CU 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         H 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               7.24 
_atom_site.Cartn_y               21.516 
_atom_site.Cartn_z               18.276 
_atom_site.occupancy             0.39 
_atom_site.B_iso_or_equiv        38.1 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CU 
_atom_site.auth_comp_id          CU 
_atom_site.auth_seq_id           15 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           248 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           1 
#