data_4Q9X
#
_model_server_result.job_id            gkmCyjfOI65POXOA0M5bzA 
_model_server_result.datetime_utc      '2024-10-18 23:31:16' 
_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          4q9x 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":907}' 
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_entry.id    4Q9X 
#
_exptl.entry_id    4Q9X 
_exptl.method      'X-RAY DIFFRACTION' 
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_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    8 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          112.01 
_cell.angle_gamma         90 
_cell.entry_id            4Q9X 
_cell.length_a            34.47 
_cell.length_b            83.63 
_cell.length_c            37.82 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Q9X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,O,P 
_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 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 O 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
covale ? covale1 A C PHE 61 A PHE 61 1_555 A N1 PIA 62 A PIA 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.277 ? 
covale ? covale2 A C3 PIA 62 A PIA 62 1_555 A N ASN 63 A ASN 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.275 ? 
metalc ? metalc1 A OD2 ASP 7 A ASP 7 1_555 C PD PD . A PD 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? 
metalc ? metalc2 A NZ LYS 32 A LYS 32 1_555 C PD PD . A PD 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? 
metalc ? metalc3 A OE1 GLU 43 A GLU 43 1_555 D PD PD . A PD 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? 
metalc ? metalc4 A NZ LYS 100 A LYS 102 1_555 B PD PD . A PD 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? 
metalc ? metalc5 A OE1 GLU 115 A GLU 117 1_555 H PD PD . A PD 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
metalc ? metalc6 A OE1 GLU 121 A GLU 123 1_555 B PD PD . A PD 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
metalc ? metalc7 A OD1 ASP 148 A ASP 150 1_555 G PD PD . A PD 907 1_554 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc8 A OE1 GLU 162 A GLU 164 1_555 E PD PD . A PD 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? 
metalc ? metalc9 B PD PD . A PD 901 1_555 P O HOH . A HOH 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
metalc ? metalc10 C PD PD . A PD 902 1_555 P O HOH . A HOH 1050 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.499 ? 
metalc ? metalc11 C PD PD . A PD 902 1_555 P O HOH . A HOH 1052 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc12 F PD PD . A PD 906 1_555 P O HOH . A HOH 1046 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.114 ? 
#
_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                     4Q9X 
_atom_sites.fract_transf_matrix[1][1]    0.029011 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.011727 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011957 
_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]    0.02852 
_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 1 901 901 PD PD . 
C 2 PD A 1 902 902 PD PD . 
D 2 PD A 1 903 903 PD PD . 
E 2 PD A 1 904 904 PD PD . 
F 2 PD A 1 906 909 PD PD . 
G 2 PD A 1 907 912 PD PD . 
H 2 PD A 1 905 908 PD PD . 
I 3 CL A 1 909 914 CL CL . 
J 3 CL A 1 910 915 CL CL . 
K 3 CL A 1 911 916 CL CL . 
L 4 CO3 A 1 912 918 CO3 CO3 . 
M 3 CL A 1 908 913 CL CL . 
N 3 CL A 1 913 1 CL CL . 
O 2 PD A 1 914 1 PD PD . 
P 5 HOH A 1 1001 3 HOH HOH . 
P 5 HOH A 2 1002 4 HOH HOH . 
P 5 HOH A 3 1003 6 HOH HOH . 
P 5 HOH A 4 1004 7 HOH HOH . 
P 5 HOH A 5 1005 8 HOH HOH . 
P 5 HOH A 6 1006 10 HOH HOH . 
P 5 HOH A 7 1007 12 HOH HOH . 
P 5 HOH A 8 1008 13 HOH HOH . 
P 5 HOH A 9 1009 14 HOH HOH . 
P 5 HOH A 10 1010 16 HOH HOH . 
P 5 HOH A 11 1011 18 HOH HOH . 
P 5 HOH A 12 1012 19 HOH HOH . 
P 5 HOH A 13 1013 21 HOH HOH . 
P 5 HOH A 14 1014 22 HOH HOH . 
P 5 HOH A 15 1015 23 HOH HOH . 
P 5 HOH A 16 1016 24 HOH HOH . 
P 5 HOH A 17 1017 28 HOH HOH . 
P 5 HOH A 18 1018 29 HOH HOH . 
P 5 HOH A 19 1019 30 HOH HOH . 
P 5 HOH A 20 1020 31 HOH HOH . 
P 5 HOH A 21 1021 32 HOH HOH . 
P 5 HOH A 22 1022 33 HOH HOH . 
P 5 HOH A 23 1023 34 HOH HOH . 
P 5 HOH A 24 1024 37 HOH HOH . 
P 5 HOH A 25 1025 38 HOH HOH . 
P 5 HOH A 26 1026 39 HOH HOH . 
P 5 HOH A 27 1027 40 HOH HOH . 
P 5 HOH A 28 1028 41 HOH HOH . 
P 5 HOH A 29 1029 42 HOH HOH . 
P 5 HOH A 30 1030 43 HOH HOH . 
P 5 HOH A 31 1031 44 HOH HOH . 
P 5 HOH A 32 1032 45 HOH HOH . 
P 5 HOH A 33 1033 47 HOH HOH . 
P 5 HOH A 34 1034 48 HOH HOH . 
P 5 HOH A 35 1035 50 HOH HOH . 
P 5 HOH A 36 1036 52 HOH HOH . 
P 5 HOH A 37 1037 53 HOH HOH . 
P 5 HOH A 38 1038 54 HOH HOH . 
P 5 HOH A 39 1039 56 HOH HOH . 
P 5 HOH A 40 1040 57 HOH HOH . 
P 5 HOH A 41 1041 58 HOH HOH . 
P 5 HOH A 42 1042 59 HOH HOH . 
P 5 HOH A 43 1043 60 HOH HOH . 
P 5 HOH A 44 1044 61 HOH HOH . 
P 5 HOH A 45 1045 63 HOH HOH . 
P 5 HOH A 46 1046 64 HOH HOH . 
P 5 HOH A 47 1047 67 HOH HOH . 
P 5 HOH A 48 1048 68 HOH HOH . 
P 5 HOH A 49 1049 69 HOH HOH . 
P 5 HOH A 50 1050 70 HOH HOH . 
P 5 HOH A 51 1051 72 HOH HOH . 
P 5 HOH A 52 1052 73 HOH HOH . 
P 5 HOH A 53 1053 75 HOH HOH . 
P 5 HOH A 54 1054 76 HOH HOH . 
P 5 HOH A 55 1055 78 HOH HOH . 
P 5 HOH A 56 1056 79 HOH HOH . 
P 5 HOH A 57 1057 80 HOH HOH . 
P 5 HOH A 58 1058 81 HOH HOH . 
P 5 HOH A 59 1059 82 HOH HOH . 
P 5 HOH A 60 1060 83 HOH HOH . 
P 5 HOH A 61 1061 84 HOH HOH . 
P 5 HOH A 62 1062 85 HOH HOH . 
P 5 HOH A 63 1063 88 HOH HOH . 
P 5 HOH A 64 1064 89 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         G 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               35.998 
_atom_site.Cartn_y               -12.968 
_atom_site.Cartn_z               65.88 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        93.69 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          PD 
_atom_site.auth_comp_id          PD 
_atom_site.auth_seq_id           907 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           1 
#