data_3VRA
#
_model_server_result.job_id            cMM7tJQFUJ9HWmACjQuI-A 
_model_server_result.datetime_utc      '2024-11-28 07:21:06' 
_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          3vra 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"W","auth_seq_id":202}' 
#
_entry.id    3VRA 
#
_exptl.entry_id    3VRA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              366.237 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE 
_entity.pdbx_number_of_molecules    2 
_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            3VRA 
_cell.length_a            122.823 
_cell.length_b            132.25 
_cell.length_c            220.577 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VRA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 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,B,C,D,I,J,K,L,M,N,O,P 1 1 
E,F,G,H,Q,R,S,T,U,V,W,X 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
? 11 O N N 
? 11 W 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 NE2 HIS 79 A HIS 79 1_555 J C8M FAD . A FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.666 ? 
covale ? covale2 E NE2 HIS 79 E HIS 79 1_555 R C8M FAD . E FAD 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.886 ? 
metalc ? metalc1 B SG CYS 89 B CYS 89 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? 
metalc ? metalc2 B SG CYS 94 B CYS 94 1_555 K FE2 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc3 B SG CYS 97 B CYS 97 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc4 B SG CYS 109 B CYS 109 1_555 K FE1 FES . B FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.301 ? 
metalc ? metalc5 B SG CYS 182 B CYS 182 1_555 L FE3 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? 
metalc ? metalc6 B SG CYS 188 B CYS 188 1_555 L FE4 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc7 B SG CYS 192 B CYS 192 1_555 M FE4 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? 
metalc ? metalc8 B SG CYS 239 B CYS 239 1_555 M FE1 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
metalc ? metalc9 B SG CYS 245 B CYS 245 1_555 M FE3 F3S . B F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? 
metalc ? metalc10 B SG CYS 249 B CYS 249 1_555 L FE2 SF4 . B SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc11 C NE2 HIS 131 C HIS 131 1_555 N FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc12 N FE HEM . C HEM 201 1_555 D NE2 HIS 95 D HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc13 F SG CYS 94 F CYS 94 1_555 S FE2 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
metalc ? metalc14 F SG CYS 97 F CYS 97 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc15 F SG CYS 109 F CYS 109 1_555 S FE1 FES . F FES 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? 
metalc ? metalc16 F SG CYS 182 F CYS 182 1_555 T FE3 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? 
metalc ? metalc17 F SG CYS 185 F CYS 185 1_555 T FE1 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc18 F SG CYS 188 F CYS 188 1_555 T FE4 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? 
metalc ? metalc19 F SG CYS 192 F CYS 192 1_555 U FE4 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.55 ? 
metalc ? metalc20 F SG CYS 239 F CYS 239 1_555 U FE1 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc21 F SG CYS 245 F CYS 245 1_555 U FE3 F3S . F F3S 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? 
metalc ? metalc22 F SG CYS 249 F CYS 249 1_555 T FE2 SF4 . F SF4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? 
metalc ? metalc23 G NE2 HIS 131 G HIS 131 1_555 V FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? 
metalc ? metalc24 V FE HEM . G HEM 201 1_555 H NE2 HIS 95 H HIS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
#
_chem_comp.formula           'C15 H21 Cl2 N O5' 
_chem_comp.formula_weight    366.237 
_chem_comp.id                AT5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              3-[(2S,4S,5R)-5,6-DICHLORO-2,4-DIMETHYL-1-OXOHEXYL]-4-HYDROXY-5,6-DIMETHOXY-2(1H)-PYRIDINONE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'ATPENIN A5;AA5' 
#
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
O5 C7 AT5 doub 70 n n 
C7 C8 AT5 sing 71 n n 
C7 C6 AT5 sing 72 n n 
C8 C11 AT5 sing 73 n n 
C8 C10 AT5 sing 74 n n 
C8 H8 AT5 sing 75 n n 
C11 C12 AT5 sing 76 n n 
C11 H111 AT5 sing 77 n n 
C11 H112 AT5 sing 78 n n 
C12 C17 AT5 sing 79 n n 
C12 C13 AT5 sing 80 n n 
C12 H12 AT5 sing 81 n n 
C17 H171 AT5 sing 82 n n 
C17 H172 AT5 sing 83 n n 
C17 H173 AT5 sing 84 n n 
C13 CL12 AT5 sing 85 n n 
C13 C14 AT5 sing 86 n n 
C13 H13 AT5 sing 87 n n 
C14 CL16 AT5 sing 88 n n 
C14 H141 AT5 sing 89 n n 
C14 H142 AT5 sing 90 n n 
C10 H101 AT5 sing 91 n n 
C10 H102 AT5 sing 92 n n 
C10 H103 AT5 sing 93 n n 
C6 C5 AT5 sing 94 n y 
C6 C1 AT5 doub 95 n y 
C5 N4 AT5 sing 96 n y 
C5 O4 AT5 doub 97 n n 
N4 C3 AT5 sing 98 n y 
N4 HN4 AT5 sing 99 n n 
C3 C2 AT5 doub 100 n y 
C3 O3 AT5 sing 101 n n 
C2 C1 AT5 sing 102 n y 
C2 O2 AT5 sing 103 n n 
C1 O1 AT5 sing 104 n n 
O1 HO1 AT5 sing 105 n n 
O2 CM2 AT5 sing 106 n n 
CM2 HM21 AT5 sing 107 n n 
CM2 HM22 AT5 sing 108 n n 
CM2 HM23 AT5 sing 109 n n 
O3 CM3 AT5 sing 110 n n 
CM3 HM31 AT5 sing 111 n n 
CM3 HM32 AT5 sing 112 n n 
CM3 HM33 AT5 sing 113 n n 
#
_atom_sites.entry_id                     3VRA 
_atom_sites.fract_transf_matrix[1][1]    0.008142 
_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]    0.007561 
_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]    0.004534 
_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
I 5 MLI A 1 701 300 MLI MLI . 
J 6 FAD A 1 702 301 FAD FAD . 
K 7 FES B 1 301 302 FES FES . 
L 8 SF4 B 1 302 303 SF4 FS4 . 
M 9 F3S B 1 303 304 F3S F3S . 
N 10 HEM C 1 201 305 HEM HEM . 
O 11 AT5 C 1 202 811 AT5 AT5 . 
P 12 EPH D 1 201 306 EPH EPH . 
Q 5 MLI E 1 701 300 MLI MLI . 
R 6 FAD E 1 702 301 FAD FAD . 
S 7 FES F 1 301 302 FES FES . 
T 8 SF4 F 1 302 303 SF4 FS4 . 
U 9 F3S F 1 303 304 F3S F3S . 
V 10 HEM G 1 201 305 HEM HEM . 
W 11 AT5 G 1 202 811 AT5 AT5 . 
X 12 EPH H 1 201 306 EPH EPH . 
#
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 O O5 AT5 . . . W 11 58.016 -14.537 -92.674 1 124.83 ? O5 AT5 202 G 1 
HETATM 2 C C7 AT5 . . . W 11 59.102 -14.637 -92.102 1 124.11 ? C7 AT5 202 G 1 
HETATM 3 C C8 AT5 . . . W 11 60.191 -15.454 -92.779 1 125.79 ? C8 AT5 202 G 1 
HETATM 4 C C11 AT5 . . . W 11 60.543 -16.515 -91.765 1 128.4 ? C11 AT5 202 G 1 
HETATM 5 C C12 AT5 . . . W 11 60.591 -17.877 -92.371 1 130.93 ? C12 AT5 202 G 1 
HETATM 6 C C17 AT5 . . . W 11 59.966 -18.845 -91.377 1 130.79 ? C17 AT5 202 G 1 
HETATM 7 C C13 AT5 . . . W 11 62.068 -18.164 -92.538 1 134.9 ? C13 AT5 202 G 1 
HETATM 8 CL CL12 AT5 . . . W 11 63.031 -17.063 -91.478 1 133.11 ? CL12 AT5 202 G 1 
HETATM 9 C C14 AT5 . . . W 11 62.416 -19.666 -92.385 1 139.9 ? C14 AT5 202 G 1 
HETATM 10 CL CL16 AT5 . . . W 11 62.529 -20.524 -93.978 1 148.56 ? CL16 AT5 202 G 1 
HETATM 11 C C10 AT5 . . . W 11 61.4 -14.572 -93.129 1 125.42 ? C10 AT5 202 G 1 
HETATM 12 C C6 AT5 . . . W 11 59.299 -14.094 -90.653 1 121.72 ? C6 AT5 202 G 1 
HETATM 13 C C5 AT5 . . . W 11 59.931 -12.878 -90.372 1 119.57 ? C5 AT5 202 G 1 
HETATM 14 N N4 AT5 . . . W 11 60.077 -12.454 -89.113 1 118.37 ? N4 AT5 202 G 1 
HETATM 15 C C3 AT5 . . . W 11 59.624 -13.177 -88.083 1 117.92 ? C3 AT5 202 G 1 
HETATM 16 C C2 AT5 . . . W 11 58.981 -14.39 -88.273 1 118.46 ? C2 AT5 202 G 1 
HETATM 17 C C1 AT5 . . . W 11 58.821 -14.864 -89.583 1 121.13 ? C1 AT5 202 G 1 
HETATM 18 O O1 AT5 . . . W 11 58.198 -16.069 -89.839 1 122.8 ? O1 AT5 202 G 1 
HETATM 19 O O2 AT5 . . . W 11 58.562 -15.102 -87.184 1 116.32 ? O2 AT5 202 G 1 
HETATM 20 C CM2 AT5 . . . W 11 57.225 -14.872 -86.772 1 115.52 ? CM2 AT5 202 G 1 
HETATM 21 O O3 AT5 . . . W 11 59.804 -12.717 -86.834 1 118.04 ? O3 AT5 202 G 1 
HETATM 22 C CM3 AT5 . . . W 11 58.66 -12.014 -86.422 1 118.55 ? CM3 AT5 202 G 1 
HETATM 23 O O4 AT5 . . . W 11 60.406 -12.094 -91.356 1 119.35 ? O4 AT5 202 G 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    38 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           23 
#