data_4Y9P
#
_model_server_result.job_id            iaZ_Sq5lBpnnnutBqxDzMQ 
_model_server_result.datetime_utc      '2024-11-28 13:43:50' 
_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          4y9p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":303}' 
#
_entry.id    4Y9P 
#
_exptl.entry_id    4Y9P 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              40.078 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'CALCIUM 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          115.03 
_cell.angle_gamma         90 
_cell.entry_id            4Y9P 
_cell.length_a            112.23 
_cell.length_b            59.4 
_cell.length_c            92.78 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4Y9P 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,K 1 1 
B,G,H,I,J,L 2 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 G N N 
? 2 H N N 
? 2 I 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 OE2 GLU 39 A GLU 39 1_555 E CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc2 A OD1 ASN 98 A ASN 98 1_555 E CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
metalc ? metalc3 A OE1 GLU 130 A GLU 130 1_555 E CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? 
metalc ? metalc4 A OE1 GLU 135 A GLU 135 1_555 C CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.16 ? 
metalc ? metalc5 A OD1 ASP 160 A ASP 160 1_555 E CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? 
metalc ? metalc6 A OD2 ASP 160 A ASP 160 1_555 E CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? 
metalc ? metalc7 A OD1 ASP 161 A ASP 161 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? 
metalc ? metalc8 A OD1 ASP 183 A ASP 183 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.066 ? 
metalc ? metalc9 A OE1 GLU 217 A GLU 217 1_555 D CA CA . A CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc10 C CA CA . A CA 301 1_555 K O HOH . A HOH 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc11 D CA CA . A CA 302 1_555 F O1P C2E . A C2E 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? 
metalc ? metalc12 E CA CA . A CA 303 1_555 F O2P C2E . A C2E 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? 
metalc ? metalc13 E CA CA . A CA 303 1_555 K O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? 
metalc ? metalc14 B OE2 GLU 39 B GLU 39 1_555 H CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc15 B OD1 ASN 98 B ASN 98 1_555 H CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc16 B O ILE 99 B ILE 99 1_555 G CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? 
metalc ? metalc17 B OE1 GLU 130 B GLU 130 1_555 H CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc18 B OE1 GLU 135 B GLU 135 1_555 G CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? 
metalc ? metalc19 B OE2 GLU 135 B GLU 135 1_555 G CA CA . B CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.029 ? 
metalc ? metalc20 B OD1 ASP 160 B ASP 160 1_555 H CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.135 ? 
metalc ? metalc21 B OD2 ASP 160 B ASP 160 1_555 H CA CA . B CA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? 
metalc ? metalc22 B OD1 ASP 160 B ASP 160 1_555 I CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? 
metalc ? metalc23 B OD1 ASP 161 B ASP 161 1_555 I CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc24 B OE1 GLU 217 B GLU 217 1_555 I CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc25 B OE2 GLU 217 B GLU 217 1_555 I CA CA . B CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? 
metalc ? metalc26 G CA CA . B CA 301 1_555 L O HOH . B HOH 421 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? 
metalc ? metalc27 H CA CA . B CA 302 1_555 J O21 C2E . B C2E 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc28 H CA CA . B CA 302 1_555 L O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? 
metalc ? metalc29 I CA CA . B CA 303 1_555 J O11 C2E . B C2E 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? 
metalc ? metalc30 I CA CA . B CA 303 1_555 L O HOH . B HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? 
#
_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                     4Y9P 
_atom_sites.fract_transf_matrix[1][1]    0.00891 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004161 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.016835 
_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]    0.011895 
_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 CA A 1 301 1 CA CA . 
D 2 CA A 1 302 5 CA CA . 
E 2 CA A 1 303 7 CA CA . 
F 3 C2E A 1 304 3 C2E C2E . 
G 2 CA B 1 301 2 CA CA . 
H 2 CA B 1 302 8 CA CA . 
I 2 CA B 1 303 9 CA CA . 
J 3 C2E B 1 304 2 C2E C2E . 
K 4 HOH A 1 401 100 HOH HOH . 
K 4 HOH A 2 402 33 HOH HOH . 
K 4 HOH A 3 403 132 HOH HOH . 
K 4 HOH A 4 404 77 HOH HOH . 
K 4 HOH A 5 405 138 HOH HOH . 
K 4 HOH A 6 406 388 HOH HOH . 
K 4 HOH A 7 407 193 HOH HOH . 
K 4 HOH A 8 408 18 HOH HOH . 
K 4 HOH A 9 409 183 HOH HOH . 
K 4 HOH A 10 410 3 HOH HOH . 
K 4 HOH A 11 411 49 HOH HOH . 
K 4 HOH A 12 412 38 HOH HOH . 
K 4 HOH A 13 413 1 HOH HOH . 
K 4 HOH A 14 414 385 HOH HOH . 
K 4 HOH A 15 415 165 HOH HOH . 
K 4 HOH A 16 416 107 HOH HOH . 
K 4 HOH A 17 417 220 HOH HOH . 
K 4 HOH A 18 418 155 HOH HOH . 
K 4 HOH A 19 419 355 HOH HOH . 
K 4 HOH A 20 420 27 HOH HOH . 
K 4 HOH A 21 421 270 HOH HOH . 
K 4 HOH A 22 422 6 HOH HOH . 
K 4 HOH A 23 423 13 HOH HOH . 
K 4 HOH A 24 424 205 HOH HOH . 
K 4 HOH A 25 425 47 HOH HOH . 
K 4 HOH A 26 426 146 HOH HOH . 
K 4 HOH A 27 427 290 HOH HOH . 
K 4 HOH A 28 428 274 HOH HOH . 
K 4 HOH A 29 429 140 HOH HOH . 
L 4 HOH B 1 401 87 HOH HOH . 
L 4 HOH B 2 402 72 HOH HOH . 
L 4 HOH B 3 403 26 HOH HOH . 
L 4 HOH B 4 404 111 HOH HOH . 
L 4 HOH B 5 405 56 HOH HOH . 
L 4 HOH B 6 406 2 HOH HOH . 
L 4 HOH B 7 407 376 HOH HOH . 
L 4 HOH B 8 408 149 HOH HOH . 
L 4 HOH B 9 409 22 HOH HOH . 
L 4 HOH B 10 410 162 HOH HOH . 
L 4 HOH B 11 411 169 HOH HOH . 
L 4 HOH B 12 412 85 HOH HOH . 
L 4 HOH B 13 413 30 HOH HOH . 
L 4 HOH B 14 414 80 HOH HOH . 
L 4 HOH B 15 415 338 HOH HOH . 
L 4 HOH B 16 416 39 HOH HOH . 
L 4 HOH B 17 417 211 HOH HOH . 
L 4 HOH B 18 418 374 HOH HOH . 
L 4 HOH B 19 419 187 HOH HOH . 
L 4 HOH B 20 420 185 HOH HOH . 
L 4 HOH B 21 421 31 HOH HOH . 
L 4 HOH B 22 422 14 HOH HOH . 
L 4 HOH B 23 423 96 HOH HOH . 
L 4 HOH B 24 424 24 HOH HOH . 
L 4 HOH B 25 425 35 HOH HOH . 
L 4 HOH B 26 426 203 HOH HOH . 
L 4 HOH B 27 427 119 HOH HOH . 
#
_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         E 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               -2.212 
_atom_site.Cartn_y               -1.972 
_atom_site.Cartn_z               -18.46 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        53.62 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          CA 
_atom_site.auth_comp_id          CA 
_atom_site.auth_seq_id           303 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           36 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           357 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           1 
#