data_1VZ4
#
_model_server_result.job_id            sf6St0uOpQfB_DK_9B3S9g 
_model_server_result.datetime_utc      '2025-02-26 21:39:00' 
_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          1vz4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":1302}' 
#
_entry.id    1VZ4 
#
_exptl.entry_id    1VZ4 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.088 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'SUCCINIC 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            1VZ4 
_cell.length_a            71.845 
_cell.length_b            141 
_cell.length_c            160.149 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
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_symmetry.entry_id                 1VZ4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        24 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 21 21 21' 
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_pdbx_struct_assembly.method_details        PQS 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_565 x,-y+1,-z+1/2 1 0 0 0 -1 0 0 0 -1 0 141 80.0745 
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loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 D N N 
? 3 F 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 A NE2 HIS 108 A HIS 108 1_555 C FE FE2 . A FE2 1299 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? 
metalc ? metalc2 A OD1 ASP 110 A ASP 110 1_555 C FE FE2 . A FE2 1299 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
metalc ? metalc3 A OH TYR 168 A TYR 168 1_555 C FE FE2 . A FE2 1299 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc4 A NE2 HIS 264 A HIS 264 1_555 C FE FE2 . A FE2 1299 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? 
metalc ? metalc5 C FE FE2 . A FE2 1299 1_555 D O1 SIN . A SIN 1300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? 
metalc ? metalc6 B NE2 HIS 108 D HIS 108 1_555 E FE FE2 . D FE2 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc7 B OD1 ASP 110 D ASP 110 1_555 E FE FE2 . D FE2 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc8 B OH TYR 168 D TYR 168 1_555 E FE FE2 . D FE2 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc9 B NE2 HIS 264 D HIS 264 1_555 E FE FE2 . D FE2 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc10 E FE FE2 . D FE2 1301 1_555 F O1 SIN . D SIN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
metalc ? metalc11 E FE FE2 . D FE2 1301 1_555 F O2 SIN . D SIN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? 
#
_chem_comp.formula           'C4 H6 O4' 
_chem_comp.formula_weight    118.088 
_chem_comp.id                SIN 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'SUCCINIC 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 O1 SIN doub 277 n n 
C1 O2 SIN sing 278 n n 
C1 C2 SIN sing 279 n n 
O2 HO2 SIN sing 280 n n 
C2 C3 SIN sing 281 n n 
C2 H21 SIN sing 282 n n 
C2 H22 SIN sing 283 n n 
C3 C4 SIN sing 284 n n 
C3 H31 SIN sing 285 n n 
C3 H32 SIN sing 286 n n 
C4 O3 SIN doub 287 n n 
C4 O4 SIN sing 288 n n 
O4 HO4 SIN sing 289 n n 
#
_atom_sites.entry_id                     1VZ4 
_atom_sites.fract_transf_matrix[1][1]    0.013919 
_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]    0.007092 
_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]    0.006244 
_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
C 2 FE2 A 1 1299 1299 FE2 FE2 . 
D 3 SIN A 1 1300 1300 SIN SIN . 
E 2 FE2 D 1 1301 1301 FE2 FE2 . 
F 3 SIN D 1 1302 1302 SIN SIN . 
G 4 HOH A 1 2001 2001 HOH HOH . 
G 4 HOH A 2 2002 2002 HOH HOH . 
G 4 HOH A 3 2003 2003 HOH HOH . 
G 4 HOH A 4 2004 2004 HOH HOH . 
G 4 HOH A 5 2005 2005 HOH HOH . 
G 4 HOH A 6 2006 2006 HOH HOH . 
G 4 HOH A 7 2007 2007 HOH HOH . 
G 4 HOH A 8 2008 2008 HOH HOH . 
G 4 HOH A 9 2009 2009 HOH HOH . 
G 4 HOH A 10 2010 2010 HOH HOH . 
G 4 HOH A 11 2011 2011 HOH HOH . 
G 4 HOH A 12 2012 2012 HOH HOH . 
G 4 HOH A 13 2013 2013 HOH HOH . 
G 4 HOH A 14 2014 2014 HOH HOH . 
G 4 HOH A 15 2015 2015 HOH HOH . 
G 4 HOH A 16 2016 2016 HOH HOH . 
G 4 HOH A 17 2017 2017 HOH HOH . 
G 4 HOH A 18 2018 2018 HOH HOH . 
G 4 HOH A 19 2019 2019 HOH HOH . 
G 4 HOH A 20 2020 2020 HOH HOH . 
H 4 HOH D 1 2001 2001 HOH HOH . 
H 4 HOH D 2 2002 2002 HOH HOH . 
H 4 HOH D 3 2003 2003 HOH HOH . 
H 4 HOH D 4 2004 2004 HOH HOH . 
H 4 HOH D 5 2005 2005 HOH HOH . 
H 4 HOH D 6 2006 2006 HOH HOH . 
H 4 HOH D 7 2007 2007 HOH HOH . 
H 4 HOH D 8 2008 2008 HOH HOH . 
H 4 HOH D 9 2009 2009 HOH HOH . 
H 4 HOH D 10 2010 2010 HOH HOH . 
H 4 HOH D 11 2011 2011 HOH HOH . 
H 4 HOH D 12 2012 2012 HOH HOH . 
H 4 HOH D 13 2013 2013 HOH HOH . 
H 4 HOH D 14 2014 2014 HOH HOH . 
H 4 HOH D 15 2015 2015 HOH HOH . 
H 4 HOH D 16 2016 2016 HOH HOH . 
H 4 HOH D 17 2017 2017 HOH HOH . 
H 4 HOH D 18 2018 2018 HOH HOH . 
H 4 HOH D 19 2019 2019 HOH HOH . 
H 4 HOH D 20 2020 2020 HOH HOH . 
H 4 HOH D 21 2021 2021 HOH HOH . 
H 4 HOH D 22 2022 2022 HOH HOH . 
H 4 HOH D 23 2023 2023 HOH HOH . 
H 4 HOH D 24 2024 2024 HOH HOH . 
H 4 HOH D 25 2025 2025 HOH HOH . 
H 4 HOH D 26 2026 2026 HOH HOH . 
H 4 HOH D 27 2027 2027 HOH HOH . 
H 4 HOH D 28 2028 2028 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 SIN . . . F 3 48.514 44.86 29.985 1 53.94 ? C1 SIN 1302 D 1 
HETATM 2 O O1 SIN . . . F 3 48.219 45.76 30.845 1 43.72 ? O1 SIN 1302 D 1 
HETATM 3 O O2 SIN . . . F 3 49.441 44.095 30.34 1 55.19 ? O2 SIN 1302 D 1 
HETATM 4 C C2 SIN . . . F 3 47.903 44.665 28.564 1 51.23 ? C2 SIN 1302 D 1 
HETATM 5 C C3 SIN . . . F 3 46.632 45.486 28.471 1 54.58 ? C3 SIN 1302 D 1 
HETATM 6 C C4 SIN . . . F 3 45.733 45.095 27.338 1 52.61 ? C4 SIN 1302 D 1 
HETATM 7 O O3 SIN . . . F 3 45.767 45.625 26.189 1 47.79 ? O3 SIN 1302 D 1 
HETATM 8 O O4 SIN . . . F 3 44.891 44.228 27.586 1 49.14 ? O4 SIN 1302 D 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           239 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           8 
#