data_5D0B
#
_model_server_result.job_id            1a3XkY7BwqY0G3KDlUG8aQ 
_model_server_result.datetime_utc      '2024-11-15 06:35:21' 
_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          5d0b 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":502}' 
#
_entry.id    5D0B 
#
_exptl.entry_id    5D0B 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              351.64 
_entity.id                          3 
_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          95.16 
_cell.angle_gamma         90 
_cell.entry_id            5D0B 
_cell.length_a            45.644 
_cell.length_b            110.754 
_cell.length_c            99.223 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5D0B 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 dimeric 2 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,G,H,M,O 1 1 
B,I,J,K,L,N 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
? 3 D N N 
? 3 E N N 
? 3 I N N 
? 3 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 O3' U 7 F U 33 1_555 C P 56B 8 F 56B 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? 
covale ? covale2 C O3' 56B 8 F 56B 34 1_555 C P U 9 F U 35 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? 
metalc ? metalc1 A SG CYS 216 A CYS 188 1_555 D FE4 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc2 A SG CYS 219 A CYS 191 1_555 D FE2 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc3 A SG CYS 222 A CYS 194 1_555 D FE1 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc4 A SG CYS 226 A CYS 198 1_555 E FE1 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc5 A SG CYS 242 A CYS 214 1_555 E FE4 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc6 A SG CYS 268 A CYS 240 1_555 E FE3 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? 
metalc ? metalc7 A SG CYS 271 A CYS 243 1_555 E FE2 SF4 . A SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc8 A SG CYS 275 A CYS 247 1_555 D FE3 SF4 . A SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc9 B SG CYS 216 B CYS 188 1_555 I FE4 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc10 B SG CYS 219 B CYS 191 1_555 I FE2 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc11 B SG CYS 222 B CYS 194 1_555 I FE1 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? 
metalc ? metalc12 B SG CYS 226 B CYS 198 1_555 J FE1 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? 
metalc ? metalc13 B SG CYS 242 B CYS 214 1_555 J FE4 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? 
metalc ? metalc14 B SG CYS 268 B CYS 240 1_555 J FE3 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc15 B SG CYS 271 B CYS 243 1_555 J FE2 SF4 . B SF4 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc16 B SG CYS 275 B CYS 247 1_555 I FE3 SF4 . B SF4 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? 
hydrog WATSON-CRICK hydrog1 C N1 G 1 F G 27 1_555 C N3 C 17 F C 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 C N2 G 1 F G 27 1_555 C O2 C 17 F C 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 C O6 G 1 F G 27 1_555 C N4 C 17 F C 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 C N3 C 2 F C 28 1_555 C N1 G 16 F G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 C N4 C 2 F C 28 1_555 C O6 G 16 F G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 C O2 C 2 F C 28 1_555 C N2 G 16 F G 42 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 C N1 A 3 F A 29 1_555 C N3 U 15 F U 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 C N6 A 3 F A 29 1_555 C O4 U 15 F U 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 C N1 G 4 F G 30 1_555 C N3 C 14 F C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 C N2 G 4 F G 30 1_555 C O2 C 14 F C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 C O6 G 4 F G 30 1_555 C N4 C 14 F C 40 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 C N1 A 5 F A 31 1_555 C N3 U 13 F U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 C N6 A 5 F A 31 1_555 C O4 U 13 F U 39 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog 'C-A MISPAIR' hydrog14 C N3 C 6 F C 32 1_555 C N6 A 12 F A 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 C N3 U 7 F U 33 1_555 C N1 A 11 F A 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 C O4 U 7 F U 33 1_555 C N6 A 11 F A 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 672 n n 
FE1 S3 SF4 sing 673 n n 
FE1 S4 SF4 sing 674 n n 
FE2 S1 SF4 sing 675 n n 
FE2 S3 SF4 sing 676 n n 
FE2 S4 SF4 sing 677 n n 
FE3 S1 SF4 sing 678 n n 
FE3 S2 SF4 sing 679 n n 
FE3 S4 SF4 sing 680 n n 
FE4 S1 SF4 sing 681 n n 
FE4 S2 SF4 sing 682 n n 
FE4 S3 SF4 sing 683 n n 
#
_atom_sites.entry_id                     5D0B 
_atom_sites.fract_transf_matrix[1][1]    0.021909 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001978 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009029 
_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]    0.010119 
_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 3 SF4 A 1 501 500 SF4 SF4 . 
E 3 SF4 A 1 502 501 SF4 SF4 . 
F 4 B12 A 1 503 600 B12 B12 . 
G 5 PO4 A 1 504 1 PO4 PO4 . 
H 6 GOL A 1 505 1 GOL GOL . 
I 3 SF4 B 1 501 500 SF4 SF4 . 
J 3 SF4 B 1 502 501 SF4 SF4 . 
K 4 B12 B 1 503 600 B12 B12 . 
L 5 PO4 B 1 504 2 PO4 PO4 . 
M 7 HOH A 1 601 11 HOH HOH . 
M 7 HOH A 2 602 61 HOH HOH . 
M 7 HOH A 3 603 3 HOH HOH . 
M 7 HOH A 4 604 2 HOH HOH . 
M 7 HOH A 5 605 53 HOH HOH . 
M 7 HOH A 6 606 22 HOH HOH . 
M 7 HOH A 7 607 62 HOH HOH . 
M 7 HOH A 8 608 37 HOH HOH . 
M 7 HOH A 9 609 27 HOH HOH . 
M 7 HOH A 10 610 45 HOH HOH . 
M 7 HOH A 11 611 15 HOH HOH . 
M 7 HOH A 12 612 5 HOH HOH . 
M 7 HOH A 13 613 9 HOH HOH . 
M 7 HOH A 14 614 57 HOH HOH . 
M 7 HOH A 15 615 34 HOH HOH . 
M 7 HOH A 16 616 38 HOH HOH . 
M 7 HOH A 17 617 59 HOH HOH . 
M 7 HOH A 18 618 50 HOH HOH . 
M 7 HOH A 19 619 49 HOH HOH . 
M 7 HOH A 20 620 58 HOH HOH . 
M 7 HOH A 21 621 13 HOH HOH . 
M 7 HOH A 22 622 31 HOH HOH . 
M 7 HOH A 23 623 20 HOH HOH . 
M 7 HOH A 24 624 35 HOH HOH . 
M 7 HOH A 25 625 23 HOH HOH . 
M 7 HOH A 26 626 56 HOH HOH . 
M 7 HOH A 27 627 29 HOH HOH . 
M 7 HOH A 28 628 14 HOH HOH . 
M 7 HOH A 29 629 19 HOH HOH . 
M 7 HOH A 30 630 47 HOH HOH . 
M 7 HOH A 31 631 12 HOH HOH . 
M 7 HOH A 32 632 40 HOH HOH . 
M 7 HOH A 33 633 25 HOH HOH . 
M 7 HOH A 34 634 42 HOH HOH . 
M 7 HOH A 35 635 43 HOH HOH . 
N 7 HOH B 1 601 10 HOH HOH . 
N 7 HOH B 2 602 28 HOH HOH . 
N 7 HOH B 3 603 21 HOH HOH . 
N 7 HOH B 4 604 32 HOH HOH . 
N 7 HOH B 5 605 46 HOH HOH . 
N 7 HOH B 6 606 51 HOH HOH . 
N 7 HOH B 7 607 7 HOH HOH . 
N 7 HOH B 8 608 63 HOH HOH . 
N 7 HOH B 9 609 4 HOH HOH . 
N 7 HOH B 10 610 54 HOH HOH . 
N 7 HOH B 11 611 6 HOH HOH . 
N 7 HOH B 12 612 64 HOH HOH . 
N 7 HOH B 13 613 17 HOH HOH . 
N 7 HOH B 14 614 1 HOH HOH . 
N 7 HOH B 15 615 52 HOH HOH . 
N 7 HOH B 16 616 48 HOH HOH . 
N 7 HOH B 17 617 41 HOH HOH . 
N 7 HOH B 18 618 60 HOH HOH . 
N 7 HOH B 19 619 44 HOH HOH . 
N 7 HOH B 20 620 8 HOH HOH . 
N 7 HOH B 21 621 16 HOH HOH . 
N 7 HOH B 22 622 24 HOH HOH . 
N 7 HOH B 23 623 55 HOH HOH . 
N 7 HOH B 24 624 39 HOH HOH . 
N 7 HOH B 25 625 30 HOH HOH . 
N 7 HOH B 26 626 26 HOH HOH . 
N 7 HOH B 27 627 33 HOH HOH . 
O 7 HOH F 1 101 65 HOH HOH . 
O 7 HOH F 2 102 36 HOH HOH . 
O 7 HOH F 3 103 70 HOH HOH . 
O 7 HOH F 4 104 68 HOH HOH . 
O 7 HOH F 5 105 66 HOH HOH . 
O 7 HOH F 6 106 69 HOH HOH . 
O 7 HOH F 7 107 18 HOH HOH . 
O 7 HOH F 8 108 67 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 . . . E 3 -4.751 -8.307 -30.476 1 20.94 ? FE1 SF4 502 A 1 
HETATM 2 FE FE2 SF4 . . . E 3 -4.941 -10.864 -31.397 1 21.65 ? FE2 SF4 502 A 1 
HETATM 3 FE FE3 SF4 . . . E 3 -5.448 -8.778 -33.069 1 24.09 ? FE3 SF4 502 A 1 
HETATM 4 FE FE4 SF4 . . . E 3 -7.197 -9.356 -31.062 1 19.66 ? FE4 SF4 502 A 1 
HETATM 5 S S1 SF4 . . . E 3 -6.687 -10.667 -32.842 1 22.96 ? S1 SF4 502 A 1 
HETATM 6 S S2 SF4 . . . E 3 -6.425 -7.302 -31.643 1 26.47 ? S2 SF4 502 A 1 
HETATM 7 S S3 SF4 . . . E 3 -5.762 -10.056 -29.434 1 20.73 ? S3 SF4 502 A 1 
HETATM 8 S S4 SF4 . . . E 3 -3.464 -9.275 -32.076 1 22.56 ? S4 SF4 502 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           351 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           8 
#