data_2YDE
#
_model_server_result.job_id            EkOydueqKbUvsGVhHxFUuQ 
_model_server_result.datetime_utc      '2024-11-14 13:40:26' 
_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          2yde 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    2YDE 
#
_exptl.entry_id    2YDE 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              148.114 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2S)-2-HYDROXYPENTANEDIOIC 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            2YDE 
_cell.length_a            86.727 
_cell.length_b            86.727 
_cell.length_c            146.053 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YDE 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 C N N 
? 3 D 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 202 A HIS 199 1_555 B FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? 
metalc ? metalc2 A OD2 ASP 204 A ASP 201 1_555 B FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.173 ? 
metalc ? metalc3 A NE2 HIS 282 A HIS 279 1_555 B FE FE . A FE 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? 
metalc ? metalc4 B FE FE . A FE 501 1_555 C O2 S2G . A S2G 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc5 B FE FE . A FE 501 1_555 C O3 S2G . A S2G 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc6 B FE FE . A FE 501 1_555 F O3 GOL . A GOL 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? 
#
_chem_comp.formula           'C5 H8 O5' 
_chem_comp.formula_weight    148.114 
_chem_comp.id                S2G 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2S)-2-HYDROXYPENTANEDIOIC 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 O2 S2G sing 290 n n 
C1 O1 S2G doub 291 n n 
C1 C2 S2G sing 292 n n 
C3 C4 S2G sing 293 n n 
C3 C2 S2G sing 294 n n 
C4 C5 S2G sing 295 n n 
C5 O5 S2G sing 296 n n 
C5 O4 S2G doub 297 n n 
O3 C2 S2G sing 298 n n 
C2 H2 S2G sing 299 n n 
C3 H3 S2G sing 300 n n 
C3 H3A S2G sing 301 n n 
C4 H4 S2G sing 302 n n 
C4 H4A S2G sing 303 n n 
O5 H5 S2G sing 304 n n 
O3 HO3 S2G sing 305 n n 
O2 HO2 S2G sing 306 n n 
#
_atom_sites.entry_id                     2YDE 
_atom_sites.fract_transf_matrix[1][1]    0.01153 
_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]    0.01153 
_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]    0.006847 
_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
B 2 FE A 1 501 501 FE FE . 
C 3 S2G A 1 601 601 S2G S2G . 
D 3 S2G A 1 602 602 S2G S2G . 
E 4 GOL A 1 603 603 GOL GOL . 
F 4 GOL A 1 604 604 GOL GOL . 
G 5 SO4 A 1 901 901 SO4 SO4 . 
H 5 SO4 A 1 902 902 SO4 SO4 . 
I 5 SO4 A 1 903 903 SO4 SO4 . 
J 5 SO4 A 1 905 905 SO4 SO4 . 
K 6 HOH A 1 2001 2001 HOH HOH . 
K 6 HOH A 2 2002 2002 HOH HOH . 
K 6 HOH A 3 2003 2003 HOH HOH . 
K 6 HOH A 4 2004 2004 HOH HOH . 
K 6 HOH A 5 2005 2005 HOH HOH . 
K 6 HOH A 6 2006 2006 HOH HOH . 
K 6 HOH A 7 2007 2007 HOH HOH . 
K 6 HOH A 8 2008 2008 HOH HOH . 
K 6 HOH A 9 2009 2009 HOH HOH . 
K 6 HOH A 10 2010 2010 HOH HOH . 
K 6 HOH A 11 2011 2011 HOH HOH . 
K 6 HOH A 12 2012 2012 HOH HOH . 
K 6 HOH A 13 2013 2013 HOH HOH . 
K 6 HOH A 14 2014 2014 HOH HOH . 
K 6 HOH A 15 2015 2015 HOH HOH . 
K 6 HOH A 16 2016 2016 HOH HOH . 
K 6 HOH A 17 2017 2017 HOH HOH . 
K 6 HOH A 18 2018 2018 HOH HOH . 
K 6 HOH A 19 2019 2019 HOH HOH . 
K 6 HOH A 20 2020 2020 HOH HOH . 
K 6 HOH A 21 2021 2021 HOH HOH . 
K 6 HOH A 22 2022 2022 HOH HOH . 
K 6 HOH A 23 2023 2023 HOH HOH . 
K 6 HOH A 24 2024 2024 HOH HOH . 
K 6 HOH A 25 2025 2025 HOH HOH . 
K 6 HOH A 26 2026 2026 HOH HOH . 
K 6 HOH A 27 2027 2027 HOH HOH . 
K 6 HOH A 28 2028 2028 HOH HOH . 
K 6 HOH A 29 2029 2029 HOH HOH . 
K 6 HOH A 30 2030 2030 HOH HOH . 
K 6 HOH A 31 2031 2031 HOH HOH . 
K 6 HOH A 32 2032 2032 HOH HOH . 
K 6 HOH A 33 2033 2033 HOH HOH . 
K 6 HOH A 34 2034 2034 HOH HOH . 
K 6 HOH A 35 2035 2035 HOH HOH . 
K 6 HOH A 36 2036 2036 HOH HOH . 
K 6 HOH A 37 2037 2037 HOH HOH . 
K 6 HOH A 38 2038 2038 HOH HOH . 
K 6 HOH A 39 2039 2039 HOH HOH . 
K 6 HOH A 40 2040 2040 HOH HOH . 
K 6 HOH A 41 2041 2041 HOH HOH . 
K 6 HOH A 42 2042 2042 HOH HOH . 
K 6 HOH A 43 2043 2043 HOH HOH . 
K 6 HOH A 44 2044 2044 HOH HOH . 
K 6 HOH A 45 2045 2045 HOH HOH . 
K 6 HOH A 46 2046 2046 HOH HOH . 
K 6 HOH A 47 2047 2047 HOH HOH . 
K 6 HOH A 48 2048 2048 HOH HOH . 
K 6 HOH A 49 2049 2049 HOH HOH . 
K 6 HOH A 50 2050 2050 HOH HOH . 
K 6 HOH A 51 2051 2051 HOH HOH . 
K 6 HOH A 52 2052 2052 HOH HOH . 
K 6 HOH A 53 2053 2053 HOH HOH . 
K 6 HOH A 54 2054 2054 HOH HOH . 
K 6 HOH A 55 2055 2055 HOH HOH . 
K 6 HOH A 56 2056 2056 HOH HOH . 
K 6 HOH A 57 2057 2057 HOH HOH . 
K 6 HOH A 58 2058 2058 HOH HOH . 
K 6 HOH A 59 2059 2059 HOH HOH . 
K 6 HOH A 60 2060 2060 HOH HOH . 
K 6 HOH A 61 2061 2061 HOH HOH . 
K 6 HOH A 62 2062 2062 HOH HOH . 
K 6 HOH A 63 2063 2063 HOH HOH . 
K 6 HOH A 64 2064 2064 HOH HOH . 
K 6 HOH A 65 2065 2065 HOH HOH . 
K 6 HOH A 66 2066 2066 HOH HOH . 
K 6 HOH A 67 2067 2067 HOH HOH . 
K 6 HOH A 68 2068 2068 HOH HOH . 
K 6 HOH A 69 2069 2069 HOH HOH . 
K 6 HOH A 70 2070 2070 HOH HOH . 
K 6 HOH A 71 2071 2071 HOH HOH . 
K 6 HOH A 72 2072 2072 HOH HOH . 
K 6 HOH A 73 2073 2073 HOH HOH . 
K 6 HOH A 74 2074 2074 HOH HOH . 
K 6 HOH A 75 2075 2075 HOH HOH . 
K 6 HOH A 76 2076 2076 HOH HOH . 
K 6 HOH A 77 2077 2077 HOH HOH . 
K 6 HOH A 78 2078 2078 HOH HOH . 
K 6 HOH A 79 2079 2079 HOH HOH . 
K 6 HOH A 80 2080 2080 HOH HOH . 
K 6 HOH A 81 2081 2081 HOH HOH . 
K 6 HOH A 82 2082 2082 HOH HOH . 
K 6 HOH A 83 2083 2083 HOH HOH . 
K 6 HOH A 84 2084 2084 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 S2G . . . D 3 -29.248 14.877 0.444 1 100.38 ? C1 S2G 602 A 1 
HETATM 2 C C3 S2G . . . D 3 -29.104 16.719 2.109 1 99.54 ? C3 S2G 602 A 1 
HETATM 3 C C4 S2G . . . D 3 -28.251 17.4 3.179 1 99.35 ? C4 S2G 602 A 1 
HETATM 4 C C5 S2G . . . D 3 -29.046 18.523 3.847 1 99.73 ? C5 S2G 602 A 1 
HETATM 5 O O2 S2G . . . D 3 -30.3 15.481 0.138 1 99.69 ? O2 S2G 602 A 1 
HETATM 6 O O1 S2G . . . D 3 -28.869 13.782 -0.021 1 100.04 ? O1 S2G 602 A 1 
HETATM 7 O O3 S2G . . . D 3 -27.146 15.994 0.888 1 100.23 ? O3 S2G 602 A 1 
HETATM 8 O O5 S2G . . . D 3 -30.052 18.189 4.507 1 99.89 ? O5 S2G 602 A 1 
HETATM 9 C C2 S2G . . . D 3 -28.355 15.534 1.496 1 100.1 ? C2 S2G 602 A 1 
HETATM 10 O O4 S2G . . . D 3 -28.629 19.689 3.68 1 99.12 ? O4 S2G 602 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           303 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           10 
#