data_7WDB
#
_model_server_result.job_id            0eMSI-OA1i2N39HZmE43-w 
_model_server_result.datetime_utc      '2024-10-31 12:16:46' 
_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          7wdb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":904}' 
#
_entry.id    7WDB 
#
_exptl.entry_id    7WDB 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CALCIUM ION' 
_entity.pdbx_number_of_molecules    4 
_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            7WDB 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7WDB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA 
_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    ? 
_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
? 5 H N N 
? 5 O N N 
? 5 V N N 
? 5 CA 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
disulf ? disulf1 A SG CYS 553 A CYS 553 1_555 A SG CYS 558 A CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 B SG CYS 553 B CYS 553 1_555 B SG CYS 558 B CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf3 C SG CYS 553 C CYS 553 1_555 C SG CYS 558 C CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf4 D SG CYS 553 D CYS 553 1_555 D SG CYS 558 D CYS 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
metalc ? metalc1 A ND1 HIS 172 A HIS 172 1_555 G ZN ZN . A ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc2 A SG CYS 176 A CYS 176 1_555 G ZN ZN . A ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc3 A SG CYS 178 A CYS 178 1_555 G ZN ZN . A ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc4 A SG CYS 181 A CYS 181 1_555 G ZN ZN . A ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc5 A OE1 GLU 418 A GLU 418 1_555 H CA CA . A CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
metalc ? metalc6 A OD1 ASN 436 A ASN 436 1_555 H CA CA . A CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? 
metalc ? metalc7 A OD2 ASP 439 A ASP 439 1_555 H CA CA . A CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? 
metalc ? metalc8 B ND1 HIS 172 B HIS 172 1_555 N ZN ZN . B ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc9 B SG CYS 176 B CYS 176 1_555 N ZN ZN . B ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc10 B SG CYS 178 B CYS 178 1_555 N ZN ZN . B ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc11 B SG CYS 181 B CYS 181 1_555 N ZN ZN . B ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc12 B OE1 GLU 418 B GLU 418 1_555 O CA CA . B CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
metalc ? metalc13 B OD1 ASN 436 B ASN 436 1_555 O CA CA . B CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? 
metalc ? metalc14 B OD2 ASP 439 B ASP 439 1_555 O CA CA . B CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? 
metalc ? metalc15 C ND1 HIS 172 C HIS 172 1_555 U ZN ZN . C ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc16 C SG CYS 176 C CYS 176 1_555 U ZN ZN . C ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc17 C SG CYS 178 C CYS 178 1_555 U ZN ZN . C ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc18 C SG CYS 181 C CYS 181 1_555 U ZN ZN . C ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc19 C OE1 GLU 418 C GLU 418 1_555 V CA CA . C CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
metalc ? metalc20 C OD1 ASN 436 C ASN 436 1_555 V CA CA . C CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? 
metalc ? metalc21 C OD2 ASP 439 C ASP 439 1_555 V CA CA . C CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? 
metalc ? metalc22 D ND1 HIS 172 D HIS 172 1_555 BA ZN ZN . D ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? 
metalc ? metalc23 D SG CYS 176 D CYS 176 1_555 BA ZN ZN . D ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc24 D SG CYS 178 D CYS 178 1_555 BA ZN ZN . D ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc25 D SG CYS 181 D CYS 181 1_555 BA ZN ZN . D ZN 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc26 D OE1 GLU 418 D GLU 418 1_555 CA CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
metalc ? metalc27 D OD1 ASN 436 D ASN 436 1_555 CA CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? 
metalc ? metalc28 D OD2 ASP 439 D ASP 439 1_555 CA CA CA . D CA 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? 
#
_chem_comp.formula           'Ca 2' 
_chem_comp.formula_weight    40.078 
_chem_comp.id                CA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'CALCIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     7WDB 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
E 2 POV A 1 901 901 POV POV . 
F 3 Y01 A 1 902 1001 Y01 Y01 . 
G 4 ZN A 1 903 1101 ZN ZN . 
H 5 CA A 1 904 1201 CA CA . 
I 6 657 A 1 905 1401 657 LIG . 
J 7 PTY A 1 906 1501 PTY PTY . 
K 8 7OC A 1 907 1601 7OC DAX . 
L 2 POV B 1 901 901 POV POV . 
M 3 Y01 B 1 902 1001 Y01 Y01 . 
N 4 ZN B 1 903 1101 ZN ZN . 
O 5 CA B 1 904 1201 CA CA . 
P 6 657 B 1 905 1401 657 LIG . 
Q 7 PTY B 1 906 1501 PTY PTY . 
R 8 7OC B 1 907 1601 7OC DAX . 
S 2 POV C 1 901 901 POV POV . 
T 3 Y01 C 1 902 1001 Y01 Y01 . 
U 4 ZN C 1 903 1101 ZN ZN . 
V 5 CA C 1 904 1201 CA CA . 
W 6 657 C 1 905 1401 657 LIG . 
X 7 PTY C 1 906 1501 PTY PTY . 
Y 8 7OC C 1 907 1601 7OC DAX . 
Z 2 POV D 1 901 901 POV POV . 
AA 3 Y01 D 1 902 1001 Y01 Y01 . 
BA 4 ZN D 1 903 1101 ZN ZN . 
CA 5 CA D 1 904 1201 CA CA . 
DA 6 657 D 1 905 1401 657 LIG . 
EA 7 PTY D 1 906 1501 PTY PTY . 
FA 8 7OC D 1 907 1601 7OC DAX . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           CA 
_atom_site.label_atom_id         CA 
_atom_site.label_comp_id         CA 
_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       5 
_atom_site.Cartn_x               160.234 
_atom_site.Cartn_y               181.236 
_atom_site.Cartn_z               154.132 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        83.36 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           904 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    34 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#