data_3N4R
#
_model_server_result.job_id            XGaHHz-6pqI8xTx08YT8AQ 
_model_server_result.datetime_utc      '2025-09-08 23:46:05' 
_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          3n4r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":2}' 
#
_entry.id    3N4R 
#
_exptl.entry_id    3N4R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              102.046 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'MALONATE ION' 
_entity.pdbx_number_of_molecules    3 
_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            3N4R 
_cell.length_a            72.47 
_cell.length_b            72.47 
_cell.length_c            267.388 
_cell.Z_PDB               36 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3N4R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        146 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,E,F,G,H,L,M 1 1 
C,D,I,J,K,N,O 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 F N N 
? 3 H 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 A C ILE 50 A ILE 115 1_555 A N MSE 51 A MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C MSE 51 A MSE 116 1_555 A N ASP 52 A ASP 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 A C TYR 91 A TYR 156 1_555 A N MSE 92 A MSE 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale4 A C MSE 92 A MSE 157 1_555 A N PHE 93 A PHE 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale5 B C ILE 50 B ILE 115 1_555 B N MSE 51 B MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale6 B C MSE 51 B MSE 116 1_555 B N ASP 52 B ASP 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale7 B C TYR 91 B TYR 156 1_555 B N MSE 92 B MSE 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale8 B C MSE 92 B MSE 157 1_555 B N PHE 93 B PHE 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale9 C C ILE 50 C ILE 115 1_555 C N MSE 51 C MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale10 C C MSE 51 C MSE 116 1_555 C N ASP 52 C ASP 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale11 C C TYR 91 C TYR 156 1_555 C N MSE 92 C MSE 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? 
covale ? covale12 C C MSE 92 C MSE 157 1_555 C N PHE 93 C PHE 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale13 D C ILE 50 D ILE 115 1_555 D N MSE 51 D MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale14 D C MSE 51 D MSE 116 1_555 D N ASP 52 D ASP 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale15 D C TYR 91 D TYR 156 1_555 D N MSE 92 D MSE 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale16 D C MSE 92 D MSE 157 1_555 D N PHE 93 D PHE 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
#
_chem_comp.formula           'C3 H2 O4 -2' 
_chem_comp.formula_weight    102.046 
_chem_comp.id                MLI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'MALONATE ION' 
_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
C1 C2 MLI sing 255 n n 
C1 C3 MLI sing 256 n n 
C1 H11 MLI sing 257 n n 
C1 H12 MLI sing 258 n n 
C2 O6 MLI doub 259 n n 
C2 O7 MLI sing 260 n n 
C3 O8 MLI doub 261 n n 
C3 O9 MLI sing 262 n n 
#
_atom_sites.entry_id                     3N4R 
_atom_sites.fract_transf_matrix[1][1]    0.013799 
_atom_sites.fract_transf_matrix[1][2]    0.007967 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015933 
_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]    0.00374 
_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 1PE A 1 4 4 1PE 1PE . 
F 3 MLI A 1 2 2 MLI MLI . 
G 2 1PE B 1 1 1 1PE 1PE . 
H 3 MLI B 1 3 3 MLI MLI . 
I 2 1PE C 1 3 3 1PE 1PE . 
J 3 MLI C 1 1 1 MLI MLI . 
K 2 1PE D 1 2 2 1PE 1PE . 
L 4 HOH A 1 28 28 HOH HOH . 
L 4 HOH A 2 35 35 HOH HOH . 
L 4 HOH A 3 42 42 HOH HOH . 
L 4 HOH A 4 44 44 HOH HOH . 
L 4 HOH A 5 48 48 HOH HOH . 
L 4 HOH A 6 57 57 HOH HOH . 
L 4 HOH A 7 58 58 HOH HOH . 
L 4 HOH A 8 182 73 HOH HOH . 
L 4 HOH A 9 183 74 HOH HOH . 
L 4 HOH A 10 184 75 HOH HOH . 
L 4 HOH A 11 185 76 HOH HOH . 
L 4 HOH A 12 186 77 HOH HOH . 
M 4 HOH B 1 2 2 HOH HOH . 
M 4 HOH B 2 9 9 HOH HOH . 
M 4 HOH B 3 10 10 HOH HOH . 
M 4 HOH B 4 11 11 HOH HOH . 
M 4 HOH B 5 12 12 HOH HOH . 
M 4 HOH B 6 14 14 HOH HOH . 
M 4 HOH B 7 15 15 HOH HOH . 
M 4 HOH B 8 17 17 HOH HOH . 
M 4 HOH B 9 18 18 HOH HOH . 
M 4 HOH B 10 21 21 HOH HOH . 
M 4 HOH B 11 26 26 HOH HOH . 
M 4 HOH B 12 29 29 HOH HOH . 
M 4 HOH B 13 37 37 HOH HOH . 
M 4 HOH B 14 39 39 HOH HOH . 
M 4 HOH B 15 50 50 HOH HOH . 
M 4 HOH B 16 51 51 HOH HOH . 
M 4 HOH B 17 54 54 HOH HOH . 
M 4 HOH B 18 55 55 HOH HOH . 
M 4 HOH B 19 56 56 HOH HOH . 
M 4 HOH B 20 61 61 HOH HOH . 
M 4 HOH B 21 63 63 HOH HOH . 
M 4 HOH B 22 182 1 HOH HOH . 
M 4 HOH B 23 183 66 HOH HOH . 
M 4 HOH B 24 184 67 HOH HOH . 
M 4 HOH B 25 185 68 HOH HOH . 
M 4 HOH B 26 186 71 HOH HOH . 
M 4 HOH B 27 187 72 HOH HOH . 
N 4 HOH C 1 4 4 HOH HOH . 
N 4 HOH C 2 6 6 HOH HOH . 
N 4 HOH C 3 16 16 HOH HOH . 
N 4 HOH C 4 20 20 HOH HOH . 
N 4 HOH C 5 24 24 HOH HOH . 
N 4 HOH C 6 27 27 HOH HOH . 
N 4 HOH C 7 30 30 HOH HOH . 
N 4 HOH C 8 31 31 HOH HOH . 
N 4 HOH C 9 32 32 HOH HOH . 
N 4 HOH C 10 34 34 HOH HOH . 
N 4 HOH C 11 36 36 HOH HOH . 
N 4 HOH C 12 40 40 HOH HOH . 
N 4 HOH C 13 41 41 HOH HOH . 
N 4 HOH C 14 43 43 HOH HOH . 
N 4 HOH C 15 49 49 HOH HOH . 
N 4 HOH C 16 52 52 HOH HOH . 
N 4 HOH C 17 53 53 HOH HOH . 
N 4 HOH C 18 59 59 HOH HOH . 
N 4 HOH C 19 60 60 HOH HOH . 
N 4 HOH C 20 62 62 HOH HOH . 
N 4 HOH C 21 182 3 HOH HOH . 
N 4 HOH C 22 183 69 HOH HOH . 
N 4 HOH C 23 184 70 HOH HOH . 
N 4 HOH C 24 185 78 HOH HOH . 
O 4 HOH D 1 5 5 HOH HOH . 
O 4 HOH D 2 7 7 HOH HOH . 
O 4 HOH D 3 8 8 HOH HOH . 
O 4 HOH D 4 13 13 HOH HOH . 
O 4 HOH D 5 19 19 HOH HOH . 
O 4 HOH D 6 22 22 HOH HOH . 
O 4 HOH D 7 23 23 HOH HOH . 
O 4 HOH D 8 25 25 HOH HOH . 
O 4 HOH D 9 33 33 HOH HOH . 
O 4 HOH D 10 38 38 HOH HOH . 
O 4 HOH D 11 45 45 HOH HOH . 
O 4 HOH D 12 46 46 HOH HOH . 
O 4 HOH D 13 47 47 HOH HOH . 
O 4 HOH D 14 64 64 HOH HOH . 
O 4 HOH D 15 65 65 HOH HOH . 
O 4 HOH D 16 182 79 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 C C1 MLI . . . F 3 10.753 -34.491 -33.964 1 100.6 ? C1 MLI 2 A 1 
HETATM 2 C C2 MLI . . . F 3 10.367 -35.889 -34.395 1 100.35 ? C2 MLI 2 A 1 
HETATM 3 C C3 MLI . . . F 3 10.309 -34.15 -32.557 1 103.58 ? C3 MLI 2 A 1 
HETATM 4 O O6 MLI . . . F 3 9.639 -36.574 -33.645 1 100.26 ? O6 MLI 2 A 1 
HETATM 5 O O7 MLI . . . F 3 10.79 -36.303 -35.5 1 97.86 ? O7 MLI 2 A 1 
HETATM 6 O O8 MLI . . . F 3 10.122 -35.068 -31.726 1 103.53 ? O8 MLI 2 A 1 
HETATM 7 O O9 MLI . . . F 3 10.163 -32.939 -32.272 1 106.23 ? O9 MLI 2 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           25 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           518 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           7 
#