data_3RDH
#
_model_server_result.job_id            kkU5NQS5jHAfh3G3PAETmg 
_model_server_result.datetime_utc      '2025-03-04 23:22:26' 
_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          3rdh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":246}' 
#
_entry.id    3RDH 
#
_exptl.entry_id    3RDH 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              395.261 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '4-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]benzoic acid' 
_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         120 
_cell.entry_id            3RDH 
_cell.length_a            94.745 
_cell.length_b            94.745 
_cell.length_c            237.862 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RDH 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 65' 
#
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 dimeric 2 author_and_software_defined_assembly 2 
PISA tetrameric 4 software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,K,L,M,P 1 1 
B,C,G,H,I,J,N,O 2 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 3 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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K 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 A NZ LYS 123 A LYS 120 1_555 E N3 3RD . A 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.204 doub 
covale ? covale2 B NZ LYS 123 B LYS 120 1_555 G N3 3RD . B 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.2 doub 
covale ? covale3 C NZ LYS 123 C LYS 120 1_555 I N3 3RD . C 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.211 doub 
covale ? covale4 D NZ LYS 123 D LYS 120 1_555 K N3 3RD . D 3RD 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.207 doub 
metalc ? metalc1 A N GLY 1 A GLY -2 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.898 ? 
metalc ? metalc2 A N SER 2 A SER -1 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.81 ? 
metalc ? metalc3 A ND1 HIS 3 A HIS 0 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc4 A N HIS 3 A HIS 0 1_555 F NI NI . A NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc5 B N GLY 1 B GLY -2 1_555 H NI NI . B NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.901 ? 
metalc ? metalc6 B N HIS 3 B HIS 0 1_555 H NI NI . B NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc7 B ND1 HIS 3 B HIS 0 1_555 H NI NI . B NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? 
metalc ? metalc8 C N GLY 1 C GLY -2 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.751 ? 
metalc ? metalc9 C N SER 2 C SER -1 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? 
metalc ? metalc10 C ND1 HIS 3 C HIS 0 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.859 ? 
metalc ? metalc11 C N HIS 3 C HIS 0 1_555 J NI NI . C NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
metalc ? metalc12 D N GLY 1 D GLY -2 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.941 ? 
metalc ? metalc13 D N SER 2 D SER -1 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.894 ? 
metalc ? metalc14 D ND1 HIS 3 D HIS 0 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? 
metalc ? metalc15 D N HIS 3 D HIS 0 1_555 L NI NI . D NI 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
#
_chem_comp.formula           'C15 H14 N3 O8 P' 
_chem_comp.formula_weight    395.261 
_chem_comp.id                3RD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '4-[(E)-{4-formyl-5-hydroxy-6-methyl-3-[(phosphonooxy)methyl]pyridin-2-yl}diazenyl]benzoic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     FOBISIN101 
#
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
N1 N3 3RD doub 1 n n 
C1 C2 3RD doub 2 n y 
C1 O2 3RD sing 3 n n 
C2 C7 3RD sing 4 n n 
N2 C2 3RD sing 5 n y 
C3 N2 3RD doub 6 n y 
C4 C3 3RD sing 7 n y 
C4 C5 3RD doub 8 n y 
C5 C1 3RD sing 9 n y 
C6 C5 3RD sing 10 n n 
C6 O1 3RD doub 11 n n 
C6 H1 3RD sing 12 n n 
O2 H2 3RD sing 13 n n 
C7 H3 3RD sing 14 n n 
C7 H4 3RD sing 15 n n 
C7 H5 3RD sing 16 n n 
C8 C4 3RD sing 17 n n 
C8 O3 3RD sing 18 n n 
C8 H6 3RD sing 19 n n 
C8 H7 3RD sing 20 n n 
P1 O3 3RD sing 21 n n 
P1 O6 3RD sing 22 n n 
O4 P1 3RD doub 23 n n 
O5 P1 3RD sing 24 n n 
O5 H8 3RD sing 25 n n 
O6 H9 3RD sing 26 n n 
N3 C3 3RD sing 27 n n 
N1 C9 3RD sing 28 n n 
C9 C10 3RD doub 29 n y 
C9 C14 3RD sing 30 n y 
C10 C11 3RD sing 31 n y 
C11 C12 3RD doub 32 n y 
C12 C13 3RD sing 33 n y 
C13 C14 3RD doub 34 n y 
C12 C15 3RD sing 35 n n 
C15 O7 3RD sing 36 n n 
C15 O8 3RD doub 37 n n 
C10 H10 3RD sing 38 n n 
C11 H11 3RD sing 39 n n 
C13 H12 3RD sing 40 n n 
C14 H13 3RD sing 41 n n 
O7 H14 3RD sing 42 n n 
#
_atom_sites.entry_id                     3RDH 
_atom_sites.fract_transf_matrix[1][1]    0.010555 
_atom_sites.fract_transf_matrix[1][2]    0.006094 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012187 
_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]    0.004204 
_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 3RD A 1 246 231 3RD 3RD . 
F 3 NI A 1 247 1 NI NI . 
G 2 3RD B 1 246 231 3RD 3RD . 
H 3 NI B 1 247 2 NI NI . 
I 2 3RD C 1 246 231 3RD 3RD . 
J 3 NI C 1 247 3 NI NI . 
K 2 3RD D 1 246 231 3RD 3RD . 
L 3 NI D 1 247 4 NI NI . 
M 4 HOH A 1 248 4 HOH TIP . 
M 4 HOH A 2 249 5 HOH TIP . 
M 4 HOH A 3 250 6 HOH TIP . 
M 4 HOH A 4 251 11 HOH TIP . 
M 4 HOH A 5 252 12 HOH TIP . 
M 4 HOH A 6 253 13 HOH TIP . 
M 4 HOH A 7 254 14 HOH TIP . 
M 4 HOH A 8 255 23 HOH TIP . 
M 4 HOH A 9 256 24 HOH TIP . 
M 4 HOH A 10 257 25 HOH TIP . 
M 4 HOH A 11 258 26 HOH TIP . 
M 4 HOH A 12 259 51 HOH TIP . 
M 4 HOH A 13 260 53 HOH TIP . 
M 4 HOH A 14 261 54 HOH TIP . 
M 4 HOH A 15 262 62 HOH TIP . 
M 4 HOH A 16 263 63 HOH TIP . 
M 4 HOH A 17 264 64 HOH TIP . 
M 4 HOH A 18 265 77 HOH TIP . 
M 4 HOH A 19 266 78 HOH TIP . 
M 4 HOH A 20 267 79 HOH TIP . 
M 4 HOH A 21 268 80 HOH TIP . 
N 4 HOH B 1 248 3 HOH TIP . 
N 4 HOH B 2 249 10 HOH TIP . 
N 4 HOH B 3 250 21 HOH TIP . 
N 4 HOH B 4 251 22 HOH TIP . 
N 4 HOH B 5 252 33 HOH TIP . 
N 4 HOH B 6 253 34 HOH TIP . 
N 4 HOH B 7 254 35 HOH TIP . 
N 4 HOH B 8 255 38 HOH TIP . 
N 4 HOH B 9 256 39 HOH TIP . 
N 4 HOH B 10 257 40 HOH TIP . 
N 4 HOH B 11 258 41 HOH TIP . 
N 4 HOH B 12 259 42 HOH TIP . 
N 4 HOH B 13 260 43 HOH TIP . 
N 4 HOH B 14 261 44 HOH TIP . 
N 4 HOH B 15 262 45 HOH TIP . 
N 4 HOH B 16 263 48 HOH TIP . 
N 4 HOH B 17 264 49 HOH TIP . 
N 4 HOH B 18 265 50 HOH TIP . 
N 4 HOH B 19 266 66 HOH TIP . 
N 4 HOH B 20 267 68 HOH TIP . 
N 4 HOH B 21 268 70 HOH TIP . 
N 4 HOH B 22 269 71 HOH TIP . 
N 4 HOH B 23 270 74 HOH TIP . 
N 4 HOH B 24 271 76 HOH TIP . 
O 4 HOH C 1 248 7 HOH TIP . 
O 4 HOH C 2 249 8 HOH TIP . 
O 4 HOH C 3 250 9 HOH TIP . 
O 4 HOH C 4 251 27 HOH TIP . 
O 4 HOH C 5 252 28 HOH TIP . 
O 4 HOH C 6 253 29 HOH TIP . 
O 4 HOH C 7 254 30 HOH TIP . 
O 4 HOH C 8 255 31 HOH TIP . 
O 4 HOH C 9 256 32 HOH TIP . 
O 4 HOH C 10 257 52 HOH TIP . 
O 4 HOH C 11 258 61 HOH TIP . 
O 4 HOH C 12 259 65 HOH TIP . 
O 4 HOH C 13 260 67 HOH TIP . 
O 4 HOH C 14 261 69 HOH TIP . 
O 4 HOH C 15 262 72 HOH TIP . 
O 4 HOH C 16 263 73 HOH TIP . 
O 4 HOH C 17 264 81 HOH TIP . 
O 4 HOH C 18 265 82 HOH TIP . 
O 4 HOH C 19 266 83 HOH TIP . 
O 4 HOH C 20 267 84 HOH TIP . 
O 4 HOH C 21 268 85 HOH TIP . 
P 4 HOH D 1 248 1 HOH TIP . 
P 4 HOH D 2 249 2 HOH TIP . 
P 4 HOH D 3 250 15 HOH TIP . 
P 4 HOH D 4 251 16 HOH TIP . 
P 4 HOH D 5 252 17 HOH TIP . 
P 4 HOH D 6 253 18 HOH TIP . 
P 4 HOH D 7 254 19 HOH TIP . 
P 4 HOH D 8 255 20 HOH TIP . 
P 4 HOH D 9 256 36 HOH TIP . 
P 4 HOH D 10 257 37 HOH TIP . 
P 4 HOH D 11 258 46 HOH TIP . 
P 4 HOH D 12 259 47 HOH TIP . 
P 4 HOH D 13 260 55 HOH TIP . 
P 4 HOH D 14 261 56 HOH TIP . 
P 4 HOH D 15 262 57 HOH TIP . 
P 4 HOH D 16 263 58 HOH TIP . 
P 4 HOH D 17 264 59 HOH TIP . 
P 4 HOH D 18 265 60 HOH TIP . 
P 4 HOH D 19 266 75 HOH TIP . 
P 4 HOH D 20 267 86 HOH TIP . 
#
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 C C1 3RD . . . G 2 -45.357 13.018 11.087 1 66.43 ? C1 3RD 246 B 1 
HETATM 2 C C2 3RD . . . G 2 -44.193 13.79 11.392 1 65.57 ? C2 3RD 246 B 1 
HETATM 3 N N2 3RD . . . G 2 -43.816 14.809 10.572 1 66.82 ? N2 3RD 246 B 1 
HETATM 4 C C3 3RD . . . G 2 -44.503 15.156 9.436 1 66.57 ? C3 3RD 246 B 1 
HETATM 5 C C4 3RD . . . G 2 -45.695 14.443 9.034 1 67.62 ? C4 3RD 246 B 1 
HETATM 6 C C5 3RD . . . G 2 -46.111 13.353 9.897 1 66.02 ? C5 3RD 246 B 1 
HETATM 7 C C6 3RD . . . G 2 -47.38 12.502 9.577 1 65.3 ? C6 3RD 246 B 1 
HETATM 8 O O1 3RD . . . G 2 -48.26 12.385 10.445 1 62.7 ? O1 3RD 246 B 1 
HETATM 9 O O2 3RD . . . G 2 -45.737 11.99 11.914 1 69.5 ? O2 3RD 246 B 1 
HETATM 10 C C7 3RD . . . G 2 -43.34 13.503 12.634 1 63.91 ? C7 3RD 246 B 1 
HETATM 11 C C8 3RD . . . G 2 -46.49 14.82 7.752 1 69.56 ? C8 3RD 246 B 1 
HETATM 12 O O3 3RD . . . G 2 -47.338 15.828 8.36 1 74.28 ? O3 3RD 246 B 1 
HETATM 13 P P1 3RD . . . G 2 -48.506 16.787 7.784 1 74.83 ? P1 3RD 246 B 1 
HETATM 14 O O4 3RD . . . G 2 -48.795 16.496 6.353 1 73.26 ? O4 3RD 246 B 1 
HETATM 15 O O5 3RD . . . G 2 -47.859 18.263 7.916 1 73.79 ? O5 3RD 246 B 1 
HETATM 16 O O6 3RD . . . G 2 -49.796 16.705 8.724 1 72.48 ? O6 3RD 246 B 1 
HETATM 17 N N3 3RD . . . G 2 -43.917 16.185 8.821 1 65.15 ? N3 3RD 246 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    21 
_model_server_stats.query_time_ms           270 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           17 
#