data_2Z5Q
#
_model_server_result.job_id            72Vp2_fXUi0jESaZzkJjiQ 
_model_server_result.datetime_utc      '2024-12-12 04:38:14' 
_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          2z5q 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":202}' 
#
_entry.id    2Z5Q 
#
_exptl.entry_id    2Z5Q 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              106.42 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PALLADIUM ION' 
_entity.pdbx_number_of_molecules    9 
_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            2Z5Q 
_cell.length_a            180.57 
_cell.length_b            180.57 
_cell.length_c            180.57 
_cell.Z_PDB               96 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Z5Q 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        209 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'F 4 3 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    24-meric 
_pdbx_struct_assembly.oligomeric_count      24 
_pdbx_struct_assembly.details               author_and_software_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,L,M,N 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24 
#
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 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
5 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
6 'crystal symmetry operation' 6_555 z,-x,-y 0 0 1 -1 0 0 0 -1 0 0 0 0 
7 'crystal symmetry operation' 7_555 -z,-x,y 0 0 -1 -1 0 0 0 1 0 0 0 0 
8 'crystal symmetry operation' 8_555 -z,x,-y 0 0 -1 1 0 0 0 -1 0 0 0 0 
9 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
10 'crystal symmetry operation' 10_555 -y,z,-x 0 -1 0 0 0 1 -1 0 0 0 0 0 
11 'crystal symmetry operation' 11_555 y,-z,-x 0 1 0 0 0 -1 -1 0 0 0 0 0 
12 'crystal symmetry operation' 12_555 -y,-z,x 0 -1 0 0 0 -1 1 0 0 0 0 0 
13 'crystal symmetry operation' 13_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
14 'crystal symmetry operation' 14_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 
15 'crystal symmetry operation' 15_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 
16 'crystal symmetry operation' 16_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
17 'crystal symmetry operation' 17_555 x,z,-y 1 0 0 0 0 1 0 -1 0 0 0 0 
18 'crystal symmetry operation' 18_555 -x,z,y -1 0 0 0 0 1 0 1 0 0 0 0 
19 'crystal symmetry operation' 19_555 -x,-z,-y -1 0 0 0 0 -1 0 -1 0 0 0 0 
20 'crystal symmetry operation' 20_555 x,-z,y 1 0 0 0 0 -1 0 1 0 0 0 0 
21 'crystal symmetry operation' 21_555 z,y,-x 0 0 1 0 1 0 -1 0 0 0 0 0 
22 'crystal symmetry operation' 22_555 z,-y,x 0 0 1 0 -1 0 1 0 0 0 0 0 
23 'crystal symmetry operation' 23_555 -z,y,x 0 0 -1 0 1 0 1 0 0 0 0 0 
24 'crystal symmetry operation' 24_555 -z,-y,-x 0 0 -1 0 -1 0 -1 0 0 0 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 B N N 
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J 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 N SER 2 A SER 2 1_555 G PD PD . A PD 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.255 ? 
metalc ? metalc2 A NH2 ARG 52 A ARG 52 1_555 D PD PD . A PD 203 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.286 ? 
metalc ? metalc3 A OD1 ASP 80 A ASP 80 1_555 K CD CD . A CD 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.412 ? 
metalc ? metalc4 A OD2 ASP 80 A ASP 80 1_555 K CD CD . A CD 210 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc5 A NE2 HIS 114 A HIS 114 1_555 E PD PD . A PD 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.333 ? 
#
_chem_comp.formula           'Pd 2' 
_chem_comp.formula_weight    106.42 
_chem_comp.id                PD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PALLADIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     2Z5Q 
_atom_sites.fract_transf_matrix[1][1]    0.005538 
_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]    0.005538 
_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]    0.005538 
_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 PD A 1 201 201 PD PD . 
C 2 PD A 1 202 202 PD PD . 
D 2 PD A 1 203 203 PD PD . 
E 2 PD A 1 204 204 PD PD . 
F 2 PD A 1 205 205 PD PD . 
G 2 PD A 1 206 206 PD PD . 
H 2 PD A 1 207 207 PD PD . 
I 2 PD A 1 208 208 PD PD . 
J 2 PD A 1 209 209 PD PD . 
K 3 CD A 1 210 210 CD CD . 
L 4 GOL A 1 301 301 GOL GOL . 
M 4 GOL A 1 302 302 GOL GOL . 
N 5 HOH A 1 1001 1001 HOH HOH . 
N 5 HOH A 2 1002 1002 HOH HOH . 
N 5 HOH A 3 1003 1003 HOH HOH . 
N 5 HOH A 4 1004 1004 HOH HOH . 
N 5 HOH A 5 1005 1005 HOH HOH . 
N 5 HOH A 6 1006 1006 HOH HOH . 
N 5 HOH A 7 1007 1007 HOH HOH . 
N 5 HOH A 8 1008 1008 HOH HOH . 
N 5 HOH A 9 1009 1009 HOH HOH . 
N 5 HOH A 10 1010 1010 HOH HOH . 
N 5 HOH A 11 1011 1011 HOH HOH . 
N 5 HOH A 12 1012 1012 HOH HOH . 
N 5 HOH A 13 1013 1013 HOH HOH . 
N 5 HOH A 14 1014 1014 HOH HOH . 
N 5 HOH A 15 1015 1015 HOH HOH . 
N 5 HOH A 16 1016 1016 HOH HOH . 
N 5 HOH A 17 1017 1017 HOH HOH . 
N 5 HOH A 18 1018 1018 HOH HOH . 
N 5 HOH A 19 1019 1019 HOH HOH . 
N 5 HOH A 20 1020 1020 HOH HOH . 
N 5 HOH A 21 1021 1021 HOH HOH . 
N 5 HOH A 22 1022 1022 HOH HOH . 
N 5 HOH A 23 1023 1023 HOH HOH . 
N 5 HOH A 24 1024 1024 HOH HOH . 
N 5 HOH A 25 1025 1025 HOH HOH . 
N 5 HOH A 26 1026 1026 HOH HOH . 
N 5 HOH A 27 1027 1027 HOH HOH . 
N 5 HOH A 28 1028 1028 HOH HOH . 
N 5 HOH A 29 1029 1029 HOH HOH . 
N 5 HOH A 30 1030 1030 HOH HOH . 
N 5 HOH A 31 1031 1031 HOH HOH . 
N 5 HOH A 32 1032 1032 HOH HOH . 
N 5 HOH A 33 1033 1033 HOH HOH . 
N 5 HOH A 34 1034 1034 HOH HOH . 
N 5 HOH A 35 1035 1035 HOH HOH . 
N 5 HOH A 36 1036 1036 HOH HOH . 
N 5 HOH A 37 1037 1037 HOH HOH . 
N 5 HOH A 38 1038 1038 HOH HOH . 
N 5 HOH A 39 1039 1039 HOH HOH . 
N 5 HOH A 40 1040 1040 HOH HOH . 
N 5 HOH A 41 1041 1041 HOH HOH . 
N 5 HOH A 42 1042 1042 HOH HOH . 
N 5 HOH A 43 1043 1043 HOH HOH . 
N 5 HOH A 44 1044 1044 HOH HOH . 
N 5 HOH A 45 1045 1045 HOH HOH . 
N 5 HOH A 46 1046 1046 HOH HOH . 
N 5 HOH A 47 1047 1047 HOH HOH . 
N 5 HOH A 48 1048 1048 HOH HOH . 
N 5 HOH A 49 1049 1049 HOH HOH . 
N 5 HOH A 50 1050 1050 HOH HOH . 
N 5 HOH A 51 1051 1051 HOH HOH . 
N 5 HOH A 52 1052 1052 HOH HOH . 
N 5 HOH A 53 1053 1053 HOH HOH . 
N 5 HOH A 54 1054 1054 HOH HOH . 
N 5 HOH A 55 1055 1055 HOH HOH . 
N 5 HOH A 56 1056 1056 HOH HOH . 
N 5 HOH A 57 1057 1057 HOH HOH . 
N 5 HOH A 58 1058 1058 HOH HOH . 
N 5 HOH A 59 1059 1059 HOH HOH . 
N 5 HOH A 60 1060 1060 HOH HOH . 
N 5 HOH A 61 1061 1061 HOH HOH . 
N 5 HOH A 62 1062 1062 HOH HOH . 
N 5 HOH A 63 1063 1063 HOH HOH . 
N 5 HOH A 64 1064 1064 HOH HOH . 
N 5 HOH A 65 1065 1065 HOH HOH . 
N 5 HOH A 66 1066 1066 HOH HOH . 
N 5 HOH A 67 1067 1067 HOH HOH . 
N 5 HOH A 68 1068 1068 HOH HOH . 
N 5 HOH A 69 1069 1069 HOH HOH . 
N 5 HOH A 70 1070 1070 HOH HOH . 
N 5 HOH A 71 1071 1071 HOH HOH . 
N 5 HOH A 72 1072 1072 HOH HOH . 
N 5 HOH A 73 1073 1073 HOH HOH . 
N 5 HOH A 74 1074 1074 HOH HOH . 
N 5 HOH A 75 1075 1075 HOH HOH . 
N 5 HOH A 76 1076 1076 HOH HOH . 
N 5 HOH A 77 1077 1077 HOH HOH . 
N 5 HOH A 78 1078 1078 HOH HOH . 
N 5 HOH A 79 1079 1079 HOH HOH . 
N 5 HOH A 80 1080 1080 HOH HOH . 
N 5 HOH A 81 1081 1081 HOH HOH . 
N 5 HOH A 82 1082 1082 HOH HOH . 
N 5 HOH A 83 1083 1083 HOH HOH . 
N 5 HOH A 84 1084 1084 HOH HOH . 
N 5 HOH A 85 1085 1085 HOH HOH . 
N 5 HOH A 86 1086 1086 HOH HOH . 
N 5 HOH A 87 1087 1087 HOH HOH . 
N 5 HOH A 88 1088 1088 HOH HOH . 
N 5 HOH A 89 1089 1089 HOH HOH . 
N 5 HOH A 90 1090 1090 HOH HOH . 
N 5 HOH A 91 1091 1091 HOH HOH . 
N 5 HOH A 92 1092 1092 HOH HOH . 
N 5 HOH A 93 1093 1093 HOH HOH . 
N 5 HOH A 94 1094 1094 HOH HOH . 
N 5 HOH A 95 1095 1095 HOH HOH . 
N 5 HOH A 96 1096 1096 HOH HOH . 
N 5 HOH A 97 1097 1097 HOH HOH . 
N 5 HOH A 98 1098 1098 HOH HOH . 
N 5 HOH A 99 1099 1099 HOH HOH . 
N 5 HOH A 100 1100 1100 HOH HOH . 
N 5 HOH A 101 1101 1101 HOH HOH . 
N 5 HOH A 102 1102 1102 HOH HOH . 
N 5 HOH A 103 1103 1103 HOH HOH . 
N 5 HOH A 104 1104 1104 HOH HOH . 
N 5 HOH A 105 1105 1105 HOH HOH . 
N 5 HOH A 106 1106 1106 HOH HOH . 
N 5 HOH A 107 1107 1107 HOH HOH . 
N 5 HOH A 108 1108 1108 HOH HOH . 
N 5 HOH A 109 1109 1109 HOH HOH . 
N 5 HOH A 110 1110 1110 HOH HOH . 
N 5 HOH A 111 1111 1111 HOH HOH . 
N 5 HOH A 112 1112 1112 HOH HOH . 
N 5 HOH A 113 1113 1113 HOH HOH . 
N 5 HOH A 114 1114 1114 HOH HOH . 
N 5 HOH A 115 1115 1115 HOH HOH . 
N 5 HOH A 116 1116 1116 HOH HOH . 
N 5 HOH A 117 1117 1117 HOH HOH . 
N 5 HOH A 118 1118 1118 HOH HOH . 
N 5 HOH A 119 1119 1119 HOH HOH . 
N 5 HOH A 120 1120 1120 HOH HOH . 
N 5 HOH A 121 1121 1121 HOH HOH . 
N 5 HOH A 122 1122 1122 HOH HOH . 
N 5 HOH A 123 1123 1123 HOH HOH . 
N 5 HOH A 124 1124 1124 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           PD 
_atom_site.label_atom_id         PD 
_atom_site.label_comp_id         PD 
_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               -19.182 
_atom_site.Cartn_y               -38.951 
_atom_site.Cartn_z               6.823 
_atom_site.occupancy             0.7 
_atom_site.B_iso_or_equiv        58.05 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          PD 
_atom_site.auth_comp_id          PD 
_atom_site.auth_seq_id           202 
_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    15 
_model_server_stats.query_time_ms           256 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           1 
#