data_5AMJ
#
_model_server_result.job_id            l23p5BSJVKMCuNms1O1kjg 
_model_server_result.datetime_utc      '2024-12-02 08:05:03' 
_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          5amj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":151}' 
#
_entry.id    5AMJ 
#
_exptl.entry_id    5AMJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              258.229 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            S-Thalidomide 
_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            5AMJ 
_cell.length_a            57.35 
_cell.length_b            59.43 
_cell.length_c            86.04 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5AMJ 
_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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,M 1 1 
B,H,I,J,K,N 2 1 
C,L,O 3 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 E N N 
? 3 I 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 SG CYS 25 A CYS 24 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc2 A SG CYS 28 A CYS 27 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc3 A SG CYS 91 A CYS 90 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc4 A SG CYS 94 A CYS 93 1_555 D ZN ZN . A ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc5 B SG CYS 25 B CYS 24 1_555 H ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc6 B SG CYS 28 B CYS 27 1_555 H ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? 
metalc ? metalc7 B SG CYS 91 B CYS 90 1_555 H ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc8 B SG CYS 94 B CYS 93 1_555 H ZN ZN . B ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
metalc ? metalc9 C SG CYS 25 C CYS 24 1_555 L ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? 
metalc ? metalc10 C SG CYS 28 C CYS 27 1_555 L ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc11 C SG CYS 91 C CYS 90 1_555 L ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc12 C SG CYS 94 C CYS 93 1_555 L ZN ZN . C ZN 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? 
#
_chem_comp.formula           'C13 H10 N2 O4' 
_chem_comp.formula_weight    258.229 
_chem_comp.id                EF2 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              S-Thalidomide 
_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
O01 C02 EF2 doub 83 n n 
C02 N03 EF2 sing 84 n n 
C02 C08 EF2 sing 85 n n 
N03 C04 EF2 sing 86 n n 
C04 O05 EF2 doub 87 n n 
C04 C06 EF2 sing 88 n n 
C06 C07 EF2 sing 89 n n 
C07 C08 EF2 sing 90 n n 
C08 N09 EF2 sing 91 n n 
N09 C3 EF2 sing 92 n n 
N09 C4 EF2 sing 93 n n 
C11 C12 EF2 sing 94 n y 
C11 C20 EF2 doub 95 n y 
C12 C13 EF2 doub 96 n y 
C13 C14 EF2 sing 97 n y 
C13 C4 EF2 sing 98 n n 
C14 C19 EF2 doub 99 n y 
C14 C3 EF2 sing 100 n n 
O16 C4 EF2 doub 101 n n 
O18 C3 EF2 doub 102 n n 
C19 C20 EF2 sing 103 n y 
N03 H03 EF2 sing 104 n n 
C08 H08 EF2 sing 105 n n 
C06 H061 EF2 sing 106 n n 
C06 H062 EF2 sing 107 n n 
C07 H071 EF2 sing 108 n n 
C07 H072 EF2 sing 109 n n 
C11 H11 EF2 sing 110 n n 
C12 H12 EF2 sing 111 n n 
C20 H20 EF2 sing 112 n n 
C19 H19 EF2 sing 113 n n 
#
_atom_sites.entry_id                     5AMJ 
_atom_sites.fract_transf_matrix[1][1]    0.017437 
_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]    0.016827 
_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]    0.011623 
_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
D 2 ZN A 1 150 150 ZN ZN . 
E 3 EF2 A 1 151 151 EF2 EF2 . 
F 4 PO4 A 1 1127 1127 PO4 PO4 . 
G 4 PO4 A 1 1128 1128 PO4 PO4 . 
H 2 ZN B 1 150 150 ZN ZN . 
I 3 EF2 B 1 151 151 EF2 EF2 . 
J 4 PO4 B 1 1126 1126 PO4 PO4 . 
K 4 PO4 B 1 1127 1127 PO4 PO4 . 
L 2 ZN C 1 150 150 ZN ZN . 
M 5 HOH A 1 2001 2001 HOH HOH . 
M 5 HOH A 2 2002 2002 HOH HOH . 
M 5 HOH A 3 2003 2003 HOH HOH . 
M 5 HOH A 4 2004 2004 HOH HOH . 
M 5 HOH A 5 2005 2005 HOH HOH . 
M 5 HOH A 6 2006 2006 HOH HOH . 
M 5 HOH A 7 2007 2007 HOH HOH . 
M 5 HOH A 8 2008 2008 HOH HOH . 
M 5 HOH A 9 2009 2009 HOH HOH . 
M 5 HOH A 10 2010 2010 HOH HOH . 
M 5 HOH A 11 2011 2011 HOH HOH . 
M 5 HOH A 12 2012 2012 HOH HOH . 
M 5 HOH A 13 2013 2013 HOH HOH . 
M 5 HOH A 14 2014 2014 HOH HOH . 
M 5 HOH A 15 2015 2015 HOH HOH . 
M 5 HOH A 16 2016 2016 HOH HOH . 
M 5 HOH A 17 2017 2017 HOH HOH . 
M 5 HOH A 18 2018 2018 HOH HOH . 
M 5 HOH A 19 2019 2019 HOH HOH . 
M 5 HOH A 20 2020 2020 HOH HOH . 
M 5 HOH A 21 2021 2021 HOH HOH . 
M 5 HOH A 22 2022 2022 HOH HOH . 
M 5 HOH A 23 2023 2023 HOH HOH . 
M 5 HOH A 24 2024 2024 HOH HOH . 
M 5 HOH A 25 2025 2025 HOH HOH . 
M 5 HOH A 26 2026 2026 HOH HOH . 
M 5 HOH A 27 2027 2027 HOH HOH . 
M 5 HOH A 28 2028 2028 HOH HOH . 
M 5 HOH A 29 2029 2029 HOH HOH . 
M 5 HOH A 30 2030 2030 HOH HOH . 
M 5 HOH A 31 2031 2031 HOH HOH . 
M 5 HOH A 32 2032 2032 HOH HOH . 
M 5 HOH A 33 2033 2033 HOH HOH . 
M 5 HOH A 34 2034 2034 HOH HOH . 
M 5 HOH A 35 2035 2035 HOH HOH . 
M 5 HOH A 36 2036 2036 HOH HOH . 
M 5 HOH A 37 2037 2037 HOH HOH . 
M 5 HOH A 38 2038 2038 HOH HOH . 
M 5 HOH A 39 2039 2039 HOH HOH . 
M 5 HOH A 40 2040 2040 HOH HOH . 
M 5 HOH A 41 2041 2041 HOH HOH . 
M 5 HOH A 42 2042 2042 HOH HOH . 
M 5 HOH A 43 2043 2043 HOH HOH . 
M 5 HOH A 44 2044 2044 HOH HOH . 
M 5 HOH A 45 2045 2045 HOH HOH . 
M 5 HOH A 46 2046 2046 HOH HOH . 
M 5 HOH A 47 2047 2047 HOH HOH . 
M 5 HOH A 48 2048 2048 HOH HOH . 
M 5 HOH A 49 2049 2049 HOH HOH . 
M 5 HOH A 50 2050 2050 HOH HOH . 
M 5 HOH A 51 2051 2051 HOH HOH . 
M 5 HOH A 52 2052 2052 HOH HOH . 
N 5 HOH B 1 2001 2001 HOH HOH . 
N 5 HOH B 2 2002 2002 HOH HOH . 
N 5 HOH B 3 2003 2003 HOH HOH . 
N 5 HOH B 4 2004 2004 HOH HOH . 
N 5 HOH B 5 2005 2005 HOH HOH . 
N 5 HOH B 6 2006 2006 HOH HOH . 
N 5 HOH B 7 2007 2007 HOH HOH . 
N 5 HOH B 8 2008 2008 HOH HOH . 
N 5 HOH B 9 2009 2009 HOH HOH . 
N 5 HOH B 10 2010 2010 HOH HOH . 
N 5 HOH B 11 2011 2011 HOH HOH . 
N 5 HOH B 12 2012 2012 HOH HOH . 
N 5 HOH B 13 2013 2013 HOH HOH . 
N 5 HOH B 14 2014 2014 HOH HOH . 
N 5 HOH B 15 2015 2015 HOH HOH . 
N 5 HOH B 16 2016 2016 HOH HOH . 
N 5 HOH B 17 2017 2017 HOH HOH . 
N 5 HOH B 18 2018 2018 HOH HOH . 
N 5 HOH B 19 2019 2019 HOH HOH . 
N 5 HOH B 20 2020 2020 HOH HOH . 
N 5 HOH B 21 2021 2021 HOH HOH . 
N 5 HOH B 22 2022 2022 HOH HOH . 
N 5 HOH B 23 2023 2023 HOH HOH . 
N 5 HOH B 24 2024 2024 HOH HOH . 
N 5 HOH B 25 2025 2025 HOH HOH . 
N 5 HOH B 26 2026 2026 HOH HOH . 
N 5 HOH B 27 2027 2027 HOH HOH . 
N 5 HOH B 28 2028 2028 HOH HOH . 
N 5 HOH B 29 2029 2029 HOH HOH . 
N 5 HOH B 30 2030 2030 HOH HOH . 
N 5 HOH B 31 2031 2031 HOH HOH . 
N 5 HOH B 32 2032 2032 HOH HOH . 
N 5 HOH B 33 2033 2033 HOH HOH . 
N 5 HOH B 34 2034 2034 HOH HOH . 
N 5 HOH B 35 2035 2035 HOH HOH . 
N 5 HOH B 36 2036 2036 HOH HOH . 
N 5 HOH B 37 2037 2037 HOH HOH . 
N 5 HOH B 38 2038 2038 HOH HOH . 
N 5 HOH B 39 2039 2039 HOH HOH . 
N 5 HOH B 40 2040 2040 HOH HOH . 
N 5 HOH B 41 2041 2041 HOH HOH . 
O 5 HOH C 1 2001 2001 HOH HOH . 
O 5 HOH C 2 2002 2002 HOH HOH . 
O 5 HOH C 3 2003 2003 HOH HOH . 
O 5 HOH C 4 2004 2004 HOH HOH . 
O 5 HOH C 5 2005 2005 HOH HOH . 
O 5 HOH C 6 2006 2006 HOH HOH . 
O 5 HOH C 7 2007 2007 HOH HOH . 
O 5 HOH C 8 2008 2008 HOH HOH . 
O 5 HOH C 9 2009 2009 HOH HOH . 
O 5 HOH C 10 2010 2010 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 O O01 EF2 . . . E 3 26.877 15.391 -8.48 1 24.76 ? O01 EF2 151 A 1 
HETATM 2 C C02 EF2 . . . E 3 25.905 15.913 -7.979 1 22 ? C02 EF2 151 A 1 
HETATM 3 N N03 EF2 . . . E 3 24.649 15.239 -8.055 1 21.79 ? N03 EF2 151 A 1 
HETATM 4 C C04 EF2 . . . E 3 23.45 15.767 -7.455 1 20.44 ? C04 EF2 151 A 1 
HETATM 5 O O05 EF2 . . . E 3 22.439 15.109 -7.489 1 21.79 ? O05 EF2 151 A 1 
HETATM 6 C C06 EF2 . . . E 3 23.561 17.094 -6.797 1 19.77 ? C06 EF2 151 A 1 
HETATM 7 C C07 EF2 . . . E 3 24.642 17.969 -7.374 1 20.66 ? C07 EF2 151 A 1 
HETATM 8 C C08 EF2 . . . E 3 25.961 17.264 -7.283 1 21.44 ? C08 EF2 151 A 1 
HETATM 9 N N09 EF2 . . . E 3 27.074 17.887 -7.862 1 23.14 ? N09 EF2 151 A 1 
HETATM 10 C C11 EF2 . . . E 3 31.066 20.056 -9.107 1 32.07 ? C11 EF2 151 A 1 
HETATM 11 C C12 EF2 . . . E 3 30.441 19.616 -7.947 1 29.08 ? C12 EF2 151 A 1 
HETATM 12 C C13 EF2 . . . E 3 29.157 19.003 -8.115 1 27.38 ? C13 EF2 151 A 1 
HETATM 13 C C14 EF2 . . . E 3 28.578 18.889 -9.343 1 28.26 ? C14 EF2 151 A 1 
HETATM 14 O O16 EF2 . . . E 3 28.278 18.169 -5.858 1 23.19 ? O16 EF2 151 A 1 
HETATM 15 O O18 EF2 . . . E 3 26.387 17.863 -10.135 1 26.44 ? O18 EF2 151 A 1 
HETATM 16 C C19 EF2 . . . E 3 29.177 19.345 -10.5 1 32.25 ? C19 EF2 151 A 1 
HETATM 17 C C20 EF2 . . . E 3 30.446 19.956 -10.322 1 33.13 ? C20 EF2 151 A 1 
HETATM 18 C C3 EF2 . . . E 3 27.237 18.312 -9.216 1 26.03 ? C3 EF2 151 A 1 
HETATM 19 C C4 EF2 . . . E 3 28.214 18.456 -7.177 1 23.95 ? C4 EF2 151 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           325 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           19 
#