data_1Y5N
#
_model_server_result.job_id            DVNAd-4Ghx-fmSSvIe0fTA 
_model_server_result.datetime_utc      '2024-11-12 21:27:18' 
_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          1y5n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1803}' 
#
_entry.id    1Y5N 
#
_exptl.entry_id    1Y5N 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              351.64 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'IRON/SULFUR CLUSTER' 
_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            1Y5N 
_cell.length_a            154.258 
_cell.length_b            241.957 
_cell.length_c            140.121 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y5N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA hexameric 6 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,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 2 1,2 
#
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' 3_354 -x-2,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -308.516 0 -70.0605 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 6 G N N 
? 6 H N N 
? 6 I N N 
? 6 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
covale ? covale1 C C FME 1 C FME 1 1_555 C N GLN 2 C GLN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
metalc ? metalc1 A ND1 HIS 49 A HIS 49 1_555 G FE3 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc2 A SG CYS 53 A CYS 53 1_555 G FE4 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc3 A SG CYS 57 A CYS 57 1_555 G FE1 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc4 A SG CYS 92 A CYS 92 1_555 G FE2 SF4 . A SF4 1801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc5 A OD1 ASP 222 A ASP 222 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? 
metalc ? metalc6 D S12 MD1 . A MD1 1800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? 
metalc ? metalc7 D S13 MD1 . A MD1 1800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc8 E S12 MD1 . A MD1 2800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.462 ? 
metalc ? metalc9 E S13 MD1 . A MD1 2800 1_555 F MO 6MO . A 6MO 3800 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc10 B SG CYS 16 B CYS 16 1_555 H FE4 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? 
metalc ? metalc11 B SG CYS 19 B CYS 19 1_555 H FE3 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc12 B SG CYS 22 B CYS 22 1_555 H FE2 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc13 B SG CYS 26 B CYS 26 1_555 I FE4 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc14 B SG CYS 184 B CYS 184 1_555 J FE1 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc15 B SG CYS 187 B CYS 187 1_555 J FE2 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc16 B SG CYS 192 B CYS 192 1_555 J FE3 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc17 B SG CYS 196 B CYS 196 1_555 K FE1 F3S . B F3S 1805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
metalc ? metalc18 B SG CYS 217 B CYS 217 1_555 K FE4 F3S . B F3S 1805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc19 B SG CYS 223 B CYS 223 1_555 K FE3 F3S . B F3S 1805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc20 B SG CYS 227 B CYS 227 1_555 J FE4 SF4 . B SF4 1804 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc21 B SG CYS 244 B CYS 244 1_555 I FE2 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? 
metalc ? metalc22 B SG CYS 247 B CYS 247 1_555 I FE1 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc23 B SG CYS 259 B CYS 259 1_555 I FE3 SF4 . B SF4 1803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc24 B SG CYS 263 B CYS 263 1_555 H FE1 SF4 . B SF4 1802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? 
metalc ? metalc25 C NE2 HIS 56 C HIS 56 1_555 M FE HEM . C HEM 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc26 C NE2 HIS 66 C HIS 66 1_555 N FE HEM . C HEM 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? 
metalc ? metalc27 C NE2 HIS 187 C HIS 187 1_555 N FE HEM . C HEM 807 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc28 C NE2 HIS 205 C HIS 205 1_555 M FE HEM . C HEM 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
#
_chem_comp.formula           'Fe4 S4' 
_chem_comp.formula_weight    351.64 
_chem_comp.id                SF4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'IRON/SULFUR CLUSTER' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
FE1 S2 SF4 sing 681 n n 
FE1 S3 SF4 sing 682 n n 
FE1 S4 SF4 sing 683 n n 
FE2 S1 SF4 sing 684 n n 
FE2 S3 SF4 sing 685 n n 
FE2 S4 SF4 sing 686 n n 
FE3 S1 SF4 sing 687 n n 
FE3 S2 SF4 sing 688 n n 
FE3 S4 SF4 sing 689 n n 
FE4 S1 SF4 sing 690 n n 
FE4 S2 SF4 sing 691 n n 
FE4 S3 SF4 sing 692 n n 
#
_atom_sites.entry_id                     1Y5N 
_atom_sites.fract_transf_matrix[1][1]    0.006483 
_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]    0.004133 
_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]    0.007137 
_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
D 4 MD1 A 1 1800 1800 MD1 MD1 . 
E 4 MD1 A 1 2800 2800 MD1 MD1 . 
F 5 6MO A 1 3800 3800 6MO 6MO . 
G 6 SF4 A 1 1801 1801 SF4 SF4 . 
H 6 SF4 B 1 1802 1802 SF4 SF4 . 
I 6 SF4 B 1 1803 1803 SF4 SF4 . 
J 6 SF4 B 1 1804 1804 SF4 SF4 . 
K 7 F3S B 1 1805 1805 F3S F3S . 
L 8 3PH B 1 1806 310 3PH 3PH . 
M 9 HEM C 1 806 806 HEM HEM . 
N 9 HEM C 1 807 807 HEM HEM . 
O 10 AGA C 1 309 309 AGA AGA . 
P 11 PCI C 1 808 808 PCI PCI . 
Q 12 HOH A 1 3801 1 HOH HOH . 
Q 12 HOH A 2 3802 2 HOH HOH . 
Q 12 HOH A 3 3803 4 HOH HOH . 
Q 12 HOH A 4 3804 8 HOH HOH . 
Q 12 HOH A 5 3805 12 HOH HOH . 
Q 12 HOH A 6 3806 15 HOH HOH . 
Q 12 HOH A 7 3807 16 HOH HOH . 
Q 12 HOH A 8 3808 17 HOH HOH . 
Q 12 HOH A 9 3809 20 HOH HOH . 
Q 12 HOH A 10 3810 24 HOH HOH . 
Q 12 HOH A 11 3811 28 HOH HOH . 
Q 12 HOH A 12 3812 29 HOH HOH . 
Q 12 HOH A 13 3813 31 HOH HOH . 
Q 12 HOH A 14 3814 37 HOH HOH . 
Q 12 HOH A 15 3815 41 HOH HOH . 
Q 12 HOH A 16 3816 42 HOH HOH . 
Q 12 HOH A 17 3817 43 HOH HOH . 
Q 12 HOH A 18 3818 44 HOH HOH . 
Q 12 HOH A 19 3819 46 HOH HOH . 
Q 12 HOH A 20 3820 49 HOH HOH . 
Q 12 HOH A 21 3821 50 HOH HOH . 
Q 12 HOH A 22 3822 52 HOH HOH . 
Q 12 HOH A 23 3823 54 HOH HOH . 
R 12 HOH B 1 1807 3 HOH HOH . 
R 12 HOH B 2 1808 5 HOH HOH . 
R 12 HOH B 3 1809 6 HOH HOH . 
R 12 HOH B 4 1810 7 HOH HOH . 
R 12 HOH B 5 1811 9 HOH HOH . 
R 12 HOH B 6 1812 10 HOH HOH . 
R 12 HOH B 7 1813 11 HOH HOH . 
R 12 HOH B 8 1814 13 HOH HOH . 
R 12 HOH B 9 1815 14 HOH HOH . 
R 12 HOH B 10 1816 18 HOH HOH . 
R 12 HOH B 11 1817 19 HOH HOH . 
R 12 HOH B 12 1818 21 HOH HOH . 
R 12 HOH B 13 1819 22 HOH HOH . 
R 12 HOH B 14 1820 25 HOH HOH . 
R 12 HOH B 15 1821 26 HOH HOH . 
R 12 HOH B 16 1822 27 HOH HOH . 
R 12 HOH B 17 1823 30 HOH HOH . 
R 12 HOH B 18 1824 32 HOH HOH . 
R 12 HOH B 19 1825 33 HOH HOH . 
R 12 HOH B 20 1826 34 HOH HOH . 
R 12 HOH B 21 1827 36 HOH HOH . 
R 12 HOH B 22 1828 38 HOH HOH . 
R 12 HOH B 23 1829 39 HOH HOH . 
R 12 HOH B 24 1830 40 HOH HOH . 
R 12 HOH B 25 1831 45 HOH HOH . 
R 12 HOH B 26 1832 47 HOH HOH . 
R 12 HOH B 27 1833 48 HOH HOH . 
R 12 HOH B 28 1834 51 HOH HOH . 
R 12 HOH B 29 1835 53 HOH HOH . 
S 12 HOH C 1 809 23 HOH HOH . 
S 12 HOH C 2 810 35 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 FE FE1 SF4 . . . I 6 -152.912 -46.398 -18.532 1 33.01 ? FE1 SF4 1803 B 1 
HETATM 2 FE FE2 SF4 . . . I 6 -152.734 -45.052 -16.2 1 29.01 ? FE2 SF4 1803 B 1 
HETATM 3 FE FE3 SF4 . . . I 6 -151.977 -47.613 -16.39 1 27.09 ? FE3 SF4 1803 B 1 
HETATM 4 FE FE4 SF4 . . . I 6 -150.564 -45.596 -17.51 1 27.38 ? FE4 SF4 1803 B 1 
HETATM 5 S S1 SF4 . . . I 6 -150.9 -45.931 -15.324 1 25.01 ? S1 SF4 1803 B 1 
HETATM 6 S S2 SF4 . . . I 6 -151.026 -47.621 -18.377 1 22.85 ? S2 SF4 1803 B 1 
HETATM 7 S S3 SF4 . . . I 6 -152.232 -44.245 -18.247 1 29.04 ? S3 SF4 1803 B 1 
HETATM 8 S S4 SF4 . . . I 6 -154.078 -46.838 -16.655 1 30.41 ? S4 SF4 1803 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           8 
#