data_2YD7
#
_model_server_result.job_id            DYNKN-RiGe_ATif4rt07iQ 
_model_server_result.datetime_utc      '2024-12-27 00:20:20' 
_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          2yd7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1221}' 
#
_entry.id    2YD7 
#
_exptl.entry_id    2YD7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              94.971 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PHOSPHATE 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          111.97 
_cell.angle_gamma         90 
_cell.entry_id            2YD7 
_cell.length_a            161.157 
_cell.length_b            31.724 
_cell.length_c            92.323 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YD7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 software_defined_assembly 1 
PISA monomeric 1 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,C,F 1 1 
B,D,E,G 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
? 2 C N N 
? 2 D N N 
? 2 E 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
disulf ? disulf1 A SG CYS 28 A CYS 45 1_555 A SG CYS 81 A CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
disulf ? disulf2 A SG CYS 130 A CYS 147 1_555 A SG CYS 184 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.991 ? 
disulf ? disulf3 B SG CYS 28 B CYS 45 1_555 B SG CYS 81 B CYS 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
disulf ? disulf4 B SG CYS 130 B CYS 147 1_555 B SG CYS 184 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? 
#
_chem_comp.formula           'O4 P -3' 
_chem_comp.formula_weight    94.971 
_chem_comp.id                PO4 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PHOSPHATE 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
P O1 PO4 doub 260 n n 
P O2 PO4 sing 261 n n 
P O3 PO4 sing 262 n n 
P O4 PO4 sing 263 n n 
#
_atom_sites.entry_id                     2YD7 
_atom_sites.fract_transf_matrix[1][1]    0.006205 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002503 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.031522 
_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]    0.01168 
_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 PO4 A 1 1221 1221 PO4 PO4 . 
D 2 PO4 B 1 1221 1221 PO4 PO4 . 
E 2 PO4 B 1 1222 1222 PO4 PO4 . 
F 3 HOH A 1 2001 2001 HOH HOH . 
F 3 HOH A 2 2002 2002 HOH HOH . 
F 3 HOH A 3 2003 2003 HOH HOH . 
F 3 HOH A 4 2004 2004 HOH HOH . 
F 3 HOH A 5 2005 2005 HOH HOH . 
F 3 HOH A 6 2006 2006 HOH HOH . 
F 3 HOH A 7 2007 2007 HOH HOH . 
F 3 HOH A 8 2008 2008 HOH HOH . 
F 3 HOH A 9 2009 2009 HOH HOH . 
F 3 HOH A 10 2010 2010 HOH HOH . 
F 3 HOH A 11 2011 2011 HOH HOH . 
F 3 HOH A 12 2012 2012 HOH HOH . 
F 3 HOH A 13 2013 2013 HOH HOH . 
F 3 HOH A 14 2014 2014 HOH HOH . 
F 3 HOH A 15 2015 2015 HOH HOH . 
F 3 HOH A 16 2016 2016 HOH HOH . 
F 3 HOH A 17 2017 2017 HOH HOH . 
F 3 HOH A 18 2018 2018 HOH HOH . 
F 3 HOH A 19 2019 2019 HOH HOH . 
F 3 HOH A 20 2020 2020 HOH HOH . 
F 3 HOH A 21 2021 2021 HOH HOH . 
F 3 HOH A 22 2022 2022 HOH HOH . 
F 3 HOH A 23 2023 2023 HOH HOH . 
F 3 HOH A 24 2024 2024 HOH HOH . 
F 3 HOH A 25 2025 2025 HOH HOH . 
F 3 HOH A 26 2026 2026 HOH HOH . 
F 3 HOH A 27 2027 2027 HOH HOH . 
F 3 HOH A 28 2028 2028 HOH HOH . 
F 3 HOH A 29 2029 2029 HOH HOH . 
F 3 HOH A 30 2030 2030 HOH HOH . 
F 3 HOH A 31 2031 2031 HOH HOH . 
F 3 HOH A 32 2032 2032 HOH HOH . 
F 3 HOH A 33 2033 2033 HOH HOH . 
F 3 HOH A 34 2034 2034 HOH HOH . 
F 3 HOH A 35 2035 2035 HOH HOH . 
F 3 HOH A 36 2036 2036 HOH HOH . 
F 3 HOH A 37 2037 2037 HOH HOH . 
F 3 HOH A 38 2038 2038 HOH HOH . 
F 3 HOH A 39 2039 2039 HOH HOH . 
F 3 HOH A 40 2040 2040 HOH HOH . 
F 3 HOH A 41 2041 2041 HOH HOH . 
F 3 HOH A 42 2042 2042 HOH HOH . 
F 3 HOH A 43 2043 2043 HOH HOH . 
F 3 HOH A 44 2044 2044 HOH HOH . 
F 3 HOH A 45 2045 2045 HOH HOH . 
F 3 HOH A 46 2046 2046 HOH HOH . 
F 3 HOH A 47 2047 2047 HOH HOH . 
F 3 HOH A 48 2048 2048 HOH HOH . 
F 3 HOH A 49 2049 2049 HOH HOH . 
F 3 HOH A 50 2050 2050 HOH HOH . 
F 3 HOH A 51 2051 2051 HOH HOH . 
F 3 HOH A 52 2052 2052 HOH HOH . 
F 3 HOH A 53 2053 2053 HOH HOH . 
F 3 HOH A 54 2054 2054 HOH HOH . 
F 3 HOH A 55 2055 2055 HOH HOH . 
F 3 HOH A 56 2056 2056 HOH HOH . 
F 3 HOH A 57 2057 2057 HOH HOH . 
F 3 HOH A 58 2058 2058 HOH HOH . 
F 3 HOH A 59 2059 2059 HOH HOH . 
F 3 HOH A 60 2060 2060 HOH HOH . 
F 3 HOH A 61 2061 2061 HOH HOH . 
F 3 HOH A 62 2062 2062 HOH HOH . 
F 3 HOH A 63 2063 2063 HOH HOH . 
F 3 HOH A 64 2064 2064 HOH HOH . 
F 3 HOH A 65 2065 2065 HOH HOH . 
F 3 HOH A 66 2066 2066 HOH HOH . 
F 3 HOH A 67 2067 2067 HOH HOH . 
F 3 HOH A 68 2068 2068 HOH HOH . 
F 3 HOH A 69 2069 2069 HOH HOH . 
F 3 HOH A 70 2070 2070 HOH HOH . 
F 3 HOH A 71 2071 2071 HOH HOH . 
F 3 HOH A 72 2072 2072 HOH HOH . 
F 3 HOH A 73 2073 2073 HOH HOH . 
F 3 HOH A 74 2074 2074 HOH HOH . 
F 3 HOH A 75 2075 2075 HOH HOH . 
F 3 HOH A 76 2076 2076 HOH HOH . 
G 3 HOH B 1 2001 2001 HOH HOH . 
G 3 HOH B 2 2002 2002 HOH HOH . 
G 3 HOH B 3 2003 2003 HOH HOH . 
G 3 HOH B 4 2004 2004 HOH HOH . 
G 3 HOH B 5 2005 2005 HOH HOH . 
G 3 HOH B 6 2006 2006 HOH HOH . 
G 3 HOH B 7 2007 2007 HOH HOH . 
G 3 HOH B 8 2008 2008 HOH HOH . 
G 3 HOH B 9 2009 2009 HOH HOH . 
G 3 HOH B 10 2010 2010 HOH HOH . 
G 3 HOH B 11 2011 2011 HOH HOH . 
G 3 HOH B 12 2012 2012 HOH HOH . 
G 3 HOH B 13 2013 2013 HOH HOH . 
G 3 HOH B 14 2014 2014 HOH HOH . 
G 3 HOH B 15 2015 2015 HOH HOH . 
G 3 HOH B 16 2016 2016 HOH HOH . 
G 3 HOH B 17 2017 2017 HOH HOH . 
G 3 HOH B 18 2018 2018 HOH HOH . 
G 3 HOH B 19 2019 2019 HOH HOH . 
G 3 HOH B 20 2020 2020 HOH HOH . 
G 3 HOH B 21 2021 2021 HOH HOH . 
G 3 HOH B 22 2022 2022 HOH HOH . 
G 3 HOH B 23 2023 2023 HOH HOH . 
G 3 HOH B 24 2024 2024 HOH HOH . 
G 3 HOH B 25 2025 2025 HOH HOH . 
G 3 HOH B 26 2026 2026 HOH HOH . 
G 3 HOH B 27 2027 2027 HOH HOH . 
G 3 HOH B 28 2028 2028 HOH HOH . 
G 3 HOH B 29 2029 2029 HOH HOH . 
G 3 HOH B 30 2030 2030 HOH HOH . 
G 3 HOH B 31 2031 2031 HOH HOH . 
G 3 HOH B 32 2032 2032 HOH HOH . 
G 3 HOH B 33 2033 2033 HOH HOH . 
G 3 HOH B 34 2034 2034 HOH HOH . 
G 3 HOH B 35 2035 2035 HOH HOH . 
G 3 HOH B 36 2036 2036 HOH HOH . 
G 3 HOH B 37 2037 2037 HOH HOH . 
G 3 HOH B 38 2038 2038 HOH HOH . 
G 3 HOH B 39 2039 2039 HOH HOH . 
G 3 HOH B 40 2040 2040 HOH HOH . 
G 3 HOH B 41 2041 2041 HOH HOH . 
G 3 HOH B 42 2042 2042 HOH HOH . 
G 3 HOH B 43 2043 2043 HOH HOH . 
G 3 HOH B 44 2044 2044 HOH HOH . 
G 3 HOH B 45 2045 2045 HOH HOH . 
G 3 HOH B 46 2046 2046 HOH HOH . 
G 3 HOH B 47 2047 2047 HOH HOH . 
G 3 HOH B 48 2048 2048 HOH HOH . 
G 3 HOH B 49 2049 2049 HOH HOH . 
G 3 HOH B 50 2050 2050 HOH HOH . 
G 3 HOH B 51 2051 2051 HOH HOH . 
G 3 HOH B 52 2052 2052 HOH HOH . 
G 3 HOH B 53 2053 2053 HOH HOH . 
G 3 HOH B 54 2054 2054 HOH HOH . 
G 3 HOH B 55 2055 2055 HOH HOH . 
G 3 HOH B 56 2056 2056 HOH HOH . 
G 3 HOH B 57 2057 2057 HOH HOH . 
G 3 HOH B 58 2058 2058 HOH HOH . 
G 3 HOH B 59 2059 2059 HOH HOH . 
G 3 HOH B 60 2060 2060 HOH HOH . 
G 3 HOH B 61 2061 2061 HOH HOH . 
G 3 HOH B 62 2062 2062 HOH HOH . 
G 3 HOH B 63 2063 2063 HOH HOH . 
G 3 HOH B 64 2064 2064 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 P P PO4 . . . D 2 114.216 17.074 30.306 1 60.69 ? P PO4 1221 B 1 
HETATM 2 O O1 PO4 . . . D 2 113.384 16.878 31.558 1 57.72 ? O1 PO4 1221 B 1 
HETATM 3 O O2 PO4 . . . D 2 115.691 17.036 30.648 1 56.65 ? O2 PO4 1221 B 1 
HETATM 4 O O3 PO4 . . . D 2 113.894 18.406 29.669 1 55.1 ? O3 PO4 1221 B 1 
HETATM 5 O O4 PO4 . . . D 2 113.887 15.992 29.306 1 55.79 ? O4 PO4 1221 B 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           255 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           5 
#