data_4YTP
#
_model_server_result.job_id            mv48uJwGoxkxl1Pnw4Iwmw 
_model_server_result.datetime_utc      '2024-11-06 03:02:42' 
_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          4ytp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":701}' 
#
_entry.id    4YTP 
#
_exptl.entry_id    4YTP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              785.55 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'FLAVIN-ADENINE DINUCLEOTIDE' 
_entity.pdbx_number_of_molecules    1 
_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            4YTP 
_cell.length_a            71.429 
_cell.length_b            84.008 
_cell.length_c            294.817 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YTP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 B SG CYS 93 B CYS 65 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc2 B SG CYS 98 B CYS 70 1_555 F FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? 
metalc ? metalc3 B SG CYS 101 B CYS 73 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc4 B SG CYS 113 B CYS 85 1_555 F FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc5 B SG CYS 186 B CYS 158 1_555 G FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc6 B SG CYS 189 B CYS 161 1_555 G FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc7 B SG CYS 192 B CYS 164 1_555 G FE1 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc8 B SG CYS 196 B CYS 168 1_555 H FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.829 ? 
metalc ? metalc9 B SG CYS 243 B CYS 215 1_555 H FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? 
metalc ? metalc10 B SG CYS 249 B CYS 221 1_555 H FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? 
metalc ? metalc11 B SG CYS 253 B CYS 225 1_555 G FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? 
metalc ? metalc12 C NE2 HIS 127 C HIS 101 1_555 I FE HEM . C HEM 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc13 I FE HEM . C HEM 301 1_555 D NE2 HIS 102 D HIS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? 
#
_chem_comp.formula           'C27 H33 N9 O15 P2' 
_chem_comp.formula_weight    785.55 
_chem_comp.id                FAD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'FLAVIN-ADENINE DINUCLEOTIDE' 
_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
PA O1A FAD doub 137 n n 
PA O2A FAD sing 138 n n 
PA O5B FAD sing 139 n n 
PA O3P FAD sing 140 n n 
O2A HOA2 FAD sing 141 n n 
O5B C5B FAD sing 142 n n 
C5B C4B FAD sing 143 n n 
C5B H51A FAD sing 144 n n 
C5B H52A FAD sing 145 n n 
C4B O4B FAD sing 146 n n 
C4B C3B FAD sing 147 n n 
C4B H4B FAD sing 148 n n 
O4B C1B FAD sing 149 n n 
C3B O3B FAD sing 150 n n 
C3B C2B FAD sing 151 n n 
C3B H3B FAD sing 152 n n 
O3B HO3A FAD sing 153 n n 
C2B O2B FAD sing 154 n n 
C2B C1B FAD sing 155 n n 
C2B H2B FAD sing 156 n n 
O2B HO2A FAD sing 157 n n 
C1B N9A FAD sing 158 n n 
C1B H1B FAD sing 159 n n 
N9A C8A FAD sing 160 n y 
N9A C4A FAD sing 161 n y 
C8A N7A FAD doub 162 n y 
C8A H8A FAD sing 163 n n 
N7A C5A FAD sing 164 n y 
C5A C6A FAD sing 165 n y 
C5A C4A FAD doub 166 n y 
C6A N6A FAD sing 167 n n 
C6A N1A FAD doub 168 n y 
N6A H61A FAD sing 169 n n 
N6A H62A FAD sing 170 n n 
N1A C2A FAD sing 171 n y 
C2A N3A FAD doub 172 n y 
C2A H2A FAD sing 173 n n 
N3A C4A FAD sing 174 n y 
N1 C2 FAD sing 175 n n 
N1 C10 FAD doub 176 n n 
C2 O2 FAD doub 177 n n 
C2 N3 FAD sing 178 n n 
N3 C4 FAD sing 179 n n 
N3 HN3 FAD sing 180 n n 
C4 O4 FAD doub 181 n n 
C4 C4X FAD sing 182 n n 
C4X N5 FAD doub 183 n n 
C4X C10 FAD sing 184 n n 
N5 C5X FAD sing 185 n n 
C5X C6 FAD doub 186 n y 
C5X C9A FAD sing 187 n y 
C6 C7 FAD sing 188 n y 
C6 H6 FAD sing 189 n n 
C7 C7M FAD sing 190 n n 
C7 C8 FAD doub 191 n y 
C7M HM71 FAD sing 192 n n 
C7M HM72 FAD sing 193 n n 
C7M HM73 FAD sing 194 n n 
C8 C8M FAD sing 195 n n 
C8 C9 FAD sing 196 n y 
C8M HM81 FAD sing 197 n n 
C8M HM82 FAD sing 198 n n 
C8M HM83 FAD sing 199 n n 
C9 C9A FAD doub 200 n y 
C9 H9 FAD sing 201 n n 
C9A N10 FAD sing 202 n n 
N10 C10 FAD sing 203 n n 
N10 C1' FAD sing 204 n n 
C1' C2' FAD sing 205 n n 
C1' "H1'1" FAD sing 206 n n 
C1' "H1'2" FAD sing 207 n n 
C2' O2' FAD sing 208 n n 
C2' C3' FAD sing 209 n n 
C2' H2' FAD sing 210 n n 
O2' HO2' FAD sing 211 n n 
C3' O3' FAD sing 212 n n 
C3' C4' FAD sing 213 n n 
C3' H3' FAD sing 214 n n 
O3' HO3' FAD sing 215 n n 
C4' O4' FAD sing 216 n n 
C4' C5' FAD sing 217 n n 
C4' H4' FAD sing 218 n n 
O4' HO4' FAD sing 219 n n 
C5' O5' FAD sing 220 n n 
C5' "H5'1" FAD sing 221 n n 
C5' "H5'2" FAD sing 222 n n 
O5' P FAD sing 223 n n 
P O1P FAD doub 224 n n 
P O2P FAD sing 225 n n 
P O3P FAD sing 226 n n 
O2P HOP2 FAD sing 227 n n 
#
_atom_sites.entry_id                     4YTP 
_atom_sites.fract_transf_matrix[1][1]    0.014 
_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]    0.011904 
_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]    0.003392 
_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 5 FAD A 1 701 702 FAD FAD . 
F 6 FES B 1 301 302 FES FES . 
G 7 SF4 B 1 302 303 SF4 SF4 . 
H 8 F3S B 1 303 304 F3S F3S . 
I 9 HEM C 1 301 301 HEM HEM . 
J 10 E23 C 1 302 302 E23 n23 . 
K 11 HOH A 1 801 9 HOH HOH . 
K 11 HOH A 2 802 12 HOH HOH . 
K 11 HOH A 3 803 6 HOH HOH . 
K 11 HOH A 4 804 19 HOH HOH . 
K 11 HOH A 5 805 10 HOH HOH . 
K 11 HOH A 6 806 7 HOH HOH . 
K 11 HOH A 7 807 15 HOH HOH . 
K 11 HOH A 8 808 1 HOH HOH . 
K 11 HOH A 9 809 11 HOH HOH . 
L 11 HOH B 1 401 18 HOH HOH . 
L 11 HOH B 2 402 17 HOH HOH . 
L 11 HOH B 3 403 22 HOH HOH . 
L 11 HOH B 4 404 14 HOH HOH . 
L 11 HOH B 5 405 16 HOH HOH . 
L 11 HOH B 6 406 21 HOH HOH . 
M 11 HOH C 1 401 13 HOH HOH . 
M 11 HOH C 2 402 8 HOH HOH . 
M 11 HOH C 3 403 2 HOH HOH . 
M 11 HOH C 4 404 4 HOH HOH . 
M 11 HOH C 5 405 20 HOH HOH . 
N 11 HOH D 1 201 5 HOH HOH . 
N 11 HOH D 2 202 3 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 P PA FAD . . . E 5 -12.983 -16.299 22.551 1 49.05 ? PA FAD 701 A 1 
HETATM 2 O O1A FAD . . . E 5 -14.433 -16.139 22.902 1 50.18 ? O1A FAD 701 A 1 
HETATM 3 O O2A FAD . . . E 5 -11.996 -15.261 23.02 1 48.7 ? O2A FAD 701 A 1 
HETATM 4 O O5B FAD . . . E 5 -12.494 -17.73 23.118 1 53.03 ? O5B FAD 701 A 1 
HETATM 5 C C5B FAD . . . E 5 -11.221 -18.284 22.787 1 54.38 ? C5B FAD 701 A 1 
HETATM 6 C C4B FAD . . . E 5 -11.103 -19.734 23.256 1 55.44 ? C4B FAD 701 A 1 
HETATM 7 O O4B FAD . . . E 5 -9.877 -20.309 22.776 1 58.42 ? O4B FAD 701 A 1 
HETATM 8 C C3B FAD . . . E 5 -11.051 -19.885 24.766 1 56.16 ? C3B FAD 701 A 1 
HETATM 9 O O3B FAD . . . E 5 -11.857 -21.004 25.147 1 56.03 ? O3B FAD 701 A 1 
HETATM 10 C C2B FAD . . . E 5 -9.591 -20.138 25.093 1 56.01 ? C2B FAD 701 A 1 
HETATM 11 O O2B FAD . . . E 5 -9.412 -20.94 26.262 1 54.94 ? O2B FAD 701 A 1 
HETATM 12 C C1B FAD . . . E 5 -9.096 -20.857 23.85 1 56.27 ? C1B FAD 701 A 1 
HETATM 13 N N9A FAD . . . E 5 -7.608 -20.739 23.682 1 53.85 ? N9A FAD 701 A 1 
HETATM 14 C C8A FAD . . . E 5 -6.849 -19.63 23.541 1 52.33 ? C8A FAD 701 A 1 
HETATM 15 N N7A FAD . . . E 5 -5.536 -19.961 23.42 1 50.76 ? N7A FAD 701 A 1 
HETATM 16 C C5A FAD . . . E 5 -5.441 -21.3 23.489 1 50.95 ? C5A FAD 701 A 1 
HETATM 17 C C6A FAD . . . E 5 -4.375 -22.334 23.444 1 51.52 ? C6A FAD 701 A 1 
HETATM 18 N N6A FAD . . . E 5 -3.065 -22.025 23.296 1 51.75 ? N6A FAD 701 A 1 
HETATM 19 N N1A FAD . . . E 5 -4.748 -23.633 23.55 1 50.61 ? N1A FAD 701 A 1 
HETATM 20 C C2A FAD . . . E 5 -6.026 -24.018 23.702 1 48.55 ? C2A FAD 701 A 1 
HETATM 21 N N3A FAD . . . E 5 -7.028 -23.135 23.757 1 49.78 ? N3A FAD 701 A 1 
HETATM 22 C C4A FAD . . . E 5 -6.808 -21.8 23.661 1 51.51 ? C4A FAD 701 A 1 
HETATM 23 N N1 FAD . . . E 5 -19.099 -9.105 19.652 1 75.24 ? N1 FAD 701 A 1 
HETATM 24 C C2 FAD . . . E 5 -20.407 -8.937 19.337 1 76.56 ? C2 FAD 701 A 1 
HETATM 25 O O2 FAD . . . E 5 -20.814 -9.449 18.261 1 73.91 ? O2 FAD 701 A 1 
HETATM 26 N N3 FAD . . . E 5 -21.254 -8.261 20.151 1 76.32 ? N3 FAD 701 A 1 
HETATM 27 C C4 FAD . . . E 5 -20.849 -7.708 21.306 1 73.96 ? C4 FAD 701 A 1 
HETATM 28 O O4 FAD . . . E 5 -21.65 -7.085 22.044 1 75.64 ? O4 FAD 701 A 1 
HETATM 29 C C4X FAD . . . E 5 -19.426 -7.846 21.692 1 69.37 ? C4X FAD 701 A 1 
HETATM 30 N N5 FAD . . . E 5 -18.936 -7.327 22.83 1 70.69 ? N5 FAD 701 A 1 
HETATM 31 C C5X FAD . . . E 5 -17.637 -7.479 23.165 1 65.37 ? C5X FAD 701 A 1 
HETATM 32 C C6 FAD . . . E 5 -17.19 -6.925 24.353 1 65.43 ? C6 FAD 701 A 1 
HETATM 33 C C7 FAD . . . E 5 -15.86 -7.063 24.728 1 65.83 ? C7 FAD 701 A 1 
HETATM 34 C C7M FAD . . . E 5 -15.371 -6.453 26.021 1 66.75 ? C7M FAD 701 A 1 
HETATM 35 C C8 FAD . . . E 5 -14.936 -7.806 23.835 1 61.24 ? C8 FAD 701 A 1 
HETATM 36 C C8M FAD . . . E 5 -13.515 -7.942 24.215 1 59.74 ? C8M FAD 701 A 1 
HETATM 37 C C9 FAD . . . E 5 -15.367 -8.359 22.652 1 59.24 ? C9 FAD 701 A 1 
HETATM 38 C C9A FAD . . . E 5 -16.696 -8.219 22.283 1 61.55 ? C9A FAD 701 A 1 
HETATM 39 N N10 FAD . . . E 5 -17.193 -8.759 21.088 1 64.19 ? N10 FAD 701 A 1 
HETATM 40 C C10 FAD . . . E 5 -18.556 -8.601 20.782 1 67.89 ? C10 FAD 701 A 1 
HETATM 41 C C1' FAD . . . E 5 -16.342 -9.531 20.176 1 62.94 ? C1' FAD 701 A 1 
HETATM 42 C C2' FAD . . . E 5 -16.514 -10.982 20.608 1 61 ? C2' FAD 701 A 1 
HETATM 43 O O2' FAD . . . E 5 -16.678 -11.09 22.034 1 60.93 ? O2' FAD 701 A 1 
HETATM 44 C C3' FAD . . . E 5 -15.327 -11.836 20.218 1 58.32 ? C3' FAD 701 A 1 
HETATM 45 O O3' FAD . . . E 5 -15.059 -11.616 18.84 1 59.91 ? O3' FAD 701 A 1 
HETATM 46 C C4' FAD . . . E 5 -15.673 -13.292 20.512 1 55.46 ? C4' FAD 701 A 1 
HETATM 47 O O4' FAD . . . E 5 -15.855 -13.409 21.932 1 55.47 ? O4' FAD 701 A 1 
HETATM 48 C C5' FAD . . . E 5 -14.61 -14.274 20.024 1 51.56 ? C5' FAD 701 A 1 
HETATM 49 O O5' FAD . . . E 5 -15.065 -15.601 20.262 1 48.38 ? O5' FAD 701 A 1 
HETATM 50 P P FAD . . . E 5 -14.099 -16.853 19.989 1 49.24 ? P FAD 701 A 1 
HETATM 51 O O1P FAD . . . E 5 -14.762 -18.129 20.467 1 47.5 ? O1P FAD 701 A 1 
HETATM 52 O O2P FAD . . . E 5 -13.588 -16.775 18.556 1 46.59 ? O2P FAD 701 A 1 
HETATM 53 O O3P FAD . . . E 5 -12.861 -16.483 20.959 1 49.17 ? O3P FAD 701 A 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           257 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           53 
#