data_2PYB
#
_model_server_result.job_id            PIirJYAjYQPdk1bB15sp-Q 
_model_server_result.datetime_utc      '2024-11-09 02:20:32' 
_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          2pyb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":505}' 
#
_entry.id    2PYB 
#
_exptl.entry_id    2PYB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              55.845 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'FE (III) 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          90 
_cell.angle_gamma         120 
_cell.entry_id            2PYB 
_cell.length_a            93.078 
_cell.length_b            93.078 
_cell.length_c            227.5 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2PYB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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    1,2,3 
#
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_655 -y+1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 93.078 0 0 
3 'crystal symmetry operation' 3_665 -x+y+1,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 46.539 80.607913 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L 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 NE2 HIS 28 A HIS 38 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? 
metalc ? metalc2 A OD1 ASP 55 A ASP 65 1_555 F FE FE . A FE 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc3 A OD2 ASP 55 A ASP 65 1_555 F FE FE . A FE 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? 
metalc ? metalc4 A OE2 GLU 59 A GLU 69 1_555 F FE FE . A FE 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc5 E FE FE . A FE 502 1_555 N O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? 
metalc ? metalc6 F FE FE . A FE 503 1_555 B NE2 HIS 28 B HIS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.544 ? 
metalc ? metalc7 G FE FE . A FE 504 1_555 N O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.799 ? 
metalc ? metalc8 B OD1 ASP 55 B ASP 65 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? 
metalc ? metalc9 B OD2 ASP 55 B ASP 65 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc10 B OE2 GLU 59 B GLU 69 1_555 H FE FE . B FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc11 H FE FE . B FE 501 1_555 N O HOH . B HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc12 C NE2 HIS 28 C HIS 38 1_555 L FE FE . D FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc13 C NE2 HIS 40 C HIS 50 1_555 I FE FE . C FE 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? 
metalc ? metalc14 C OD1 ASP 55 C ASP 65 1_555 J FE FE . C FE 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? 
metalc ? metalc15 C OD2 ASP 55 C ASP 65 1_555 J FE FE . C FE 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc16 C OE2 GLU 59 C GLU 69 1_555 J FE FE . C FE 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? 
metalc ? metalc17 I FE FE . C FE 506 1_555 O O HOH . C HOH 510 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc18 I FE FE . C FE 506 1_555 O O HOH . C HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc19 J FE FE . C FE 507 1_555 D NE2 HIS 28 D HIS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc20 J FE FE . C FE 507 1_555 P O HOH . D HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc21 K FE FE . C FE 508 1_555 O O HOH . C HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc22 K FE FE . C FE 508 1_555 P O HOH . D HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc23 O O HOH . C HOH 510 1_555 L FE FE . D FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? 
metalc ? metalc24 D OD1 ASP 55 D ASP 65 1_555 L FE FE . D FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? 
metalc ? metalc25 D OD2 ASP 55 D ASP 65 1_555 L FE FE . D FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc26 D OE2 GLU 59 D GLU 69 1_555 L FE FE . D FE 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? 
#
_chem_comp.formula           'Fe 3' 
_chem_comp.formula_weight    55.845 
_chem_comp.id                FE 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'FE (III) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     2PYB 
_atom_sites.fract_transf_matrix[1][1]    0.010744 
_atom_sites.fract_transf_matrix[1][2]    0.006203 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012406 
_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]    0.004396 
_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 FE A 1 502 2 FE FE . 
F 2 FE A 1 503 3 FE FE . 
G 2 FE A 1 504 4 FE FE . 
H 2 FE B 1 501 1 FE FE . 
I 2 FE C 1 506 6 FE FE . 
J 2 FE C 1 507 7 FE FE . 
K 2 FE C 1 508 8 FE FE . 
L 2 FE D 1 505 5 FE FE . 
M 3 HOH A 1 505 6 HOH HOH . 
M 3 HOH A 2 506 7 HOH HOH . 
M 3 HOH A 3 507 18 HOH HOH . 
M 3 HOH A 4 508 21 HOH HOH . 
M 3 HOH A 5 509 23 HOH HOH . 
N 3 HOH B 1 502 1 HOH HOH . 
N 3 HOH B 2 503 2 HOH HOH . 
N 3 HOH B 3 504 3 HOH HOH . 
N 3 HOH B 4 505 5 HOH HOH . 
N 3 HOH B 5 506 12 HOH HOH . 
N 3 HOH B 6 507 13 HOH HOH . 
N 3 HOH B 7 508 19 HOH HOH . 
N 3 HOH B 8 509 27 HOH HOH . 
N 3 HOH B 9 510 30 HOH HOH . 
O 3 HOH C 1 509 4 HOH HOH . 
O 3 HOH C 2 510 28 HOH HOH . 
O 3 HOH C 3 511 31 HOH HOH . 
O 3 HOH C 4 512 32 HOH HOH . 
P 3 HOH D 1 506 9 HOH HOH . 
P 3 HOH D 2 507 11 HOH HOH . 
P 3 HOH D 3 508 16 HOH HOH . 
P 3 HOH D 4 509 22 HOH HOH . 
P 3 HOH D 5 510 24 HOH HOH . 
P 3 HOH D 6 511 29 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           FE 
_atom_site.label_atom_id         FE 
_atom_site.label_comp_id         FE 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         L 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               38.052 
_atom_site.Cartn_y               12.145 
_atom_site.Cartn_z               18.023 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        36.65 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          FE 
_atom_site.auth_comp_id          FE 
_atom_site.auth_seq_id           505 
_atom_site.auth_asym_id          D 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#