data_3P4R
#
_model_server_result.job_id            4C-niAoXHk6-6ad58WYrkw 
_model_server_result.datetime_utc      '2025-03-26 19:19:18' 
_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          3p4r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":577}' 
#
_entry.id    3P4R 
#
_exptl.entry_id    3P4R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              132.115 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'GLUTARIC ACID' 
_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            3P4R 
_cell.length_a            96.678 
_cell.length_b            138.016 
_cell.length_c            269.558 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3P4R 
_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 1 1 
E,F,G,H,N,O,P,Q,R 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
? 6 J N N 
? 6 N 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
metalc ? metalc1 B SG CYS 57 B CYS 57 1_555 K FE2 FES . B FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc2 B SG CYS 62 B CYS 62 1_555 K FE2 FES . B FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc3 B SG CYS 65 B CYS 65 1_555 K FE1 FES . B FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.148 ? 
metalc ? metalc4 B SG CYS 77 B CYS 77 1_555 K FE1 FES . B FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? 
metalc ? metalc5 B SG CYS 148 B CYS 148 1_555 M FE2 SF4 . B SF4 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc6 B SG CYS 154 B CYS 154 1_555 M FE3 SF4 . B SF4 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? 
metalc ? metalc7 B SG CYS 158 B CYS 158 1_555 L FE4 F3S . B F3S 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? 
metalc ? metalc8 B SG CYS 214 B CYS 214 1_555 M FE4 SF4 . B SF4 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc9 F SG CYS 57 N CYS 57 1_555 P FE2 FES . N FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc10 F SG CYS 62 N CYS 62 1_555 P FE2 FES . N FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc11 F SG CYS 65 N CYS 65 1_555 P FE1 FES . N FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc12 F SG CYS 77 N CYS 77 1_555 P FE1 FES . N FES 244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? 
metalc ? metalc13 F SG CYS 148 N CYS 148 1_555 R FE2 SF4 . N SF4 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? 
metalc ? metalc14 F SG CYS 151 N CYS 151 1_555 R FE1 SF4 . N SF4 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.645 ? 
metalc ? metalc15 F SG CYS 154 N CYS 154 1_555 R FE3 SF4 . N SF4 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? 
metalc ? metalc16 F SG CYS 158 N CYS 158 1_555 Q FE4 F3S . N F3S 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? 
metalc ? metalc17 F SG CYS 204 N CYS 204 1_555 Q FE1 F3S . N F3S 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
metalc ? metalc18 F SG CYS 210 N CYS 210 1_555 Q FE3 F3S . N F3S 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
#
_chem_comp.formula           'C5 H8 O4' 
_chem_comp.formula_weight    132.115 
_chem_comp.id                GUA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'GLUTARIC ACID' 
_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 GUA sing 233 n n 
C1 O1 GUA doub 234 n n 
C1 O2 GUA sing 235 n n 
C2 C3 GUA sing 236 n n 
C2 H21 GUA sing 237 n n 
C2 H22 GUA sing 238 n n 
C3 C4 GUA sing 239 n n 
C3 H31 GUA sing 240 n n 
C3 H32 GUA sing 241 n n 
C4 C5 GUA sing 242 n n 
C4 H41 GUA sing 243 n n 
C4 H42 GUA sing 244 n n 
C5 O3 GUA doub 245 n n 
C5 O4 GUA sing 246 n n 
O2 HO2 GUA sing 247 n n 
O4 HO4 GUA sing 248 n n 
#
_atom_sites.entry_id                     3P4R 
_atom_sites.fract_transf_matrix[1][1]    0.010344 
_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]    0.007246 
_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]    0.00371 
_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 FAD A 1 601 601 FAD FAD . 
J 6 GUA A 1 577 1 GUA GUA . 
K 7 FES B 1 244 244 FES FES . 
L 8 F3S B 1 245 245 F3S F3S . 
M 9 SF4 B 1 246 246 SF4 SF4 . 
N 6 GUA M 1 577 1 GUA GUA . 
O 5 FAD M 1 601 601 FAD FAD . 
P 7 FES N 1 244 244 FES FES . 
Q 8 F3S N 1 245 245 F3S F3S . 
R 9 SF4 N 1 246 246 SF4 SF4 . 
#
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 GUA . . . N 6 11.431 -52.017 -27.411 1 87.25 ? C1 GUA 577 M 1 
HETATM 2 C C2 GUA . . . N 6 11.578 -53.507 -27.671 1 87.15 ? C2 GUA 577 M 1 
HETATM 3 C C3 GUA . . . N 6 12.228 -53.805 -29.022 1 87.19 ? C3 GUA 577 M 1 
HETATM 4 C C4 GUA . . . N 6 12.886 -52.573 -29.645 1 87.55 ? C4 GUA 577 M 1 
HETATM 5 C C5 GUA . . . N 6 14.278 -52.911 -30.112 1 88.08 ? C5 GUA 577 M 1 
HETATM 6 O O1 GUA . . . N 6 10.753 -51.313 -28.214 1 87.79 ? O1 GUA 577 M 1 
HETATM 7 O O2 GUA . . . N 6 12.001 -51.539 -26.389 1 86.38 ? O2 GUA 577 M 1 
HETATM 8 O O3 GUA . . . N 6 14.414 -53.425 -31.246 1 87.46 ? O3 GUA 577 M 1 
HETATM 9 O O4 GUA . . . N 6 15.229 -52.664 -29.333 1 88.44 ? O4 GUA 577 M 1 
#
_model_server_stats.io_time_ms              39 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           284 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           9 
#