data_2CDQ
#
_model_server_result.job_id            G3ngs0n1hC8gzBqxPtNrjA 
_model_server_result.datetime_utc      '2024-11-14 20:49:24' 
_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          2cdq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":601}' 
#
_entry.id    2CDQ 
#
_exptl.entry_id    2CDQ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              147.195 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            LYSINE 
_entity.pdbx_number_of_molecules    4 
_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            2CDQ 
_cell.length_a            117.342 
_cell.length_b            117.342 
_cell.length_c            255.283 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2CDQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        80 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 41' 
#
_pdbx_struct_assembly.method_details        PQS 
_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,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 G N N 
? 2 H N N 
#
_chem_comp.formula           'C6 H15 N2 O2 1' 
_chem_comp.formula_weight    147.195 
_chem_comp.id                LYS 
_chem_comp.mon_nstd_flag     y 
_chem_comp.name              LYSINE 
_chem_comp.type              'l-peptide linking' 
_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
N CA LYS sing 194 n n 
N H LYS sing 195 n n 
N H2 LYS sing 196 n n 
CA C LYS sing 197 n n 
CA CB LYS sing 198 n n 
CA HA LYS sing 199 n n 
C O LYS doub 200 n n 
C OXT LYS sing 201 n n 
CB CG LYS sing 202 n n 
CB HB2 LYS sing 203 n n 
CB HB3 LYS sing 204 n n 
CG CD LYS sing 205 n n 
CG HG2 LYS sing 206 n n 
CG HG3 LYS sing 207 n n 
CD CE LYS sing 208 n n 
CD HD2 LYS sing 209 n n 
CD HD3 LYS sing 210 n n 
CE NZ LYS sing 211 n n 
CE HE2 LYS sing 212 n n 
CE HE3 LYS sing 213 n n 
NZ HZ1 LYS sing 214 n n 
NZ HZ2 LYS sing 215 n n 
NZ HZ3 LYS sing 216 n n 
OXT HXT LYS sing 217 n n 
#
_atom_sites.entry_id                     2CDQ 
_atom_sites.fract_transf_matrix[1][1]    0.008522 
_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]    0.008522 
_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]    0.003917 
_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 LYS A 1 600 600 LYS LYS . 
D 2 LYS A 1 601 601 LYS LYS . 
E 3 TAR A 1 700 700 TAR TAR . 
F 4 SAM A 1 1500 1500 SAM SAM . 
G 2 LYS B 1 600 600 LYS LYS . 
H 2 LYS B 1 601 601 LYS LYS . 
I 3 TAR B 1 700 700 TAR TAR . 
J 4 SAM B 1 1500 1500 SAM SAM . 
K 5 HOH A 1 2001 2001 HOH HOH . 
K 5 HOH A 2 2002 2002 HOH HOH . 
K 5 HOH A 3 2003 2003 HOH HOH . 
K 5 HOH A 4 2004 2004 HOH HOH . 
K 5 HOH A 5 2005 2005 HOH HOH . 
K 5 HOH A 6 2006 2006 HOH HOH . 
K 5 HOH A 7 2007 2007 HOH HOH . 
K 5 HOH A 8 2008 2008 HOH HOH . 
K 5 HOH A 9 2009 2009 HOH HOH . 
K 5 HOH A 10 2010 2010 HOH HOH . 
K 5 HOH A 11 2011 2011 HOH HOH . 
K 5 HOH A 12 2012 2012 HOH HOH . 
K 5 HOH A 13 2013 2013 HOH HOH . 
K 5 HOH A 14 2014 2014 HOH HOH . 
K 5 HOH A 15 2015 2015 HOH HOH . 
K 5 HOH A 16 2016 2016 HOH HOH . 
K 5 HOH A 17 2017 2017 HOH HOH . 
K 5 HOH A 18 2018 2018 HOH HOH . 
K 5 HOH A 19 2019 2019 HOH HOH . 
K 5 HOH A 20 2020 2020 HOH HOH . 
K 5 HOH A 21 2021 2021 HOH HOH . 
K 5 HOH A 22 2022 2022 HOH HOH . 
K 5 HOH A 23 2023 2023 HOH HOH . 
K 5 HOH A 24 2024 2024 HOH HOH . 
K 5 HOH A 25 2025 2025 HOH HOH . 
K 5 HOH A 26 2026 2026 HOH HOH . 
K 5 HOH A 27 2027 2027 HOH HOH . 
K 5 HOH A 28 2028 2028 HOH HOH . 
K 5 HOH A 29 2029 2029 HOH HOH . 
K 5 HOH A 30 2030 2030 HOH HOH . 
K 5 HOH A 31 2031 2031 HOH HOH . 
K 5 HOH A 32 2032 2032 HOH HOH . 
K 5 HOH A 33 2033 2033 HOH HOH . 
K 5 HOH A 34 2034 2034 HOH HOH . 
K 5 HOH A 35 2035 2035 HOH HOH . 
K 5 HOH A 36 2036 2036 HOH HOH . 
K 5 HOH A 37 2037 2037 HOH HOH . 
K 5 HOH A 38 2038 2038 HOH HOH . 
K 5 HOH A 39 2039 2039 HOH HOH . 
K 5 HOH A 40 2040 2040 HOH HOH . 
K 5 HOH A 41 2041 2041 HOH HOH . 
K 5 HOH A 42 2042 2042 HOH HOH . 
K 5 HOH A 43 2043 2043 HOH HOH . 
K 5 HOH A 44 2044 2044 HOH HOH . 
K 5 HOH A 45 2045 2045 HOH HOH . 
K 5 HOH A 46 2046 2046 HOH HOH . 
K 5 HOH A 47 2047 2047 HOH HOH . 
K 5 HOH A 48 2048 2048 HOH HOH . 
K 5 HOH A 49 2049 2049 HOH HOH . 
K 5 HOH A 50 2050 2050 HOH HOH . 
K 5 HOH A 51 2051 2051 HOH HOH . 
K 5 HOH A 52 2052 2052 HOH HOH . 
K 5 HOH A 53 2053 2053 HOH HOH . 
K 5 HOH A 54 2054 2054 HOH HOH . 
K 5 HOH A 55 2055 2055 HOH HOH . 
K 5 HOH A 56 2056 2056 HOH HOH . 
K 5 HOH A 57 2057 2057 HOH HOH . 
K 5 HOH A 58 2058 2058 HOH HOH . 
K 5 HOH A 59 2059 2059 HOH HOH . 
K 5 HOH A 60 2060 2060 HOH HOH . 
K 5 HOH A 61 2061 2061 HOH HOH . 
K 5 HOH A 62 2062 2062 HOH HOH . 
K 5 HOH A 63 2063 2063 HOH HOH . 
K 5 HOH A 64 2064 2064 HOH HOH . 
K 5 HOH A 65 2065 2065 HOH HOH . 
K 5 HOH A 66 2066 2066 HOH HOH . 
K 5 HOH A 67 2067 2067 HOH HOH . 
K 5 HOH A 68 2068 2068 HOH HOH . 
K 5 HOH A 69 2069 2069 HOH HOH . 
K 5 HOH A 70 2070 2070 HOH HOH . 
K 5 HOH A 71 2071 2071 HOH HOH . 
K 5 HOH A 72 2072 2072 HOH HOH . 
K 5 HOH A 73 2073 2073 HOH HOH . 
K 5 HOH A 74 2074 2074 HOH HOH . 
K 5 HOH A 75 2075 2075 HOH HOH . 
K 5 HOH A 76 2076 2076 HOH HOH . 
K 5 HOH A 77 2077 2077 HOH HOH . 
K 5 HOH A 78 2078 2078 HOH HOH . 
K 5 HOH A 79 2079 2079 HOH HOH . 
K 5 HOH A 80 2080 2080 HOH HOH . 
K 5 HOH A 81 2081 2081 HOH HOH . 
K 5 HOH A 82 2082 2082 HOH HOH . 
K 5 HOH A 83 2083 2083 HOH HOH . 
K 5 HOH A 84 2084 2084 HOH HOH . 
K 5 HOH A 85 2085 2085 HOH HOH . 
K 5 HOH A 86 2086 2086 HOH HOH . 
K 5 HOH A 87 2087 2087 HOH HOH . 
K 5 HOH A 88 2088 2088 HOH HOH . 
K 5 HOH A 89 2089 2089 HOH HOH . 
K 5 HOH A 90 2090 2090 HOH HOH . 
K 5 HOH A 91 2091 2091 HOH HOH . 
K 5 HOH A 92 2092 2092 HOH HOH . 
K 5 HOH A 93 2093 2093 HOH HOH . 
K 5 HOH A 94 2094 2094 HOH HOH . 
K 5 HOH A 95 2095 2095 HOH HOH . 
K 5 HOH A 96 2096 2096 HOH HOH . 
L 5 HOH B 1 2001 2001 HOH HOH . 
L 5 HOH B 2 2002 2002 HOH HOH . 
L 5 HOH B 3 2003 2003 HOH HOH . 
L 5 HOH B 4 2004 2004 HOH HOH . 
L 5 HOH B 5 2005 2005 HOH HOH . 
L 5 HOH B 6 2006 2006 HOH HOH . 
L 5 HOH B 7 2007 2007 HOH HOH . 
L 5 HOH B 8 2008 2008 HOH HOH . 
L 5 HOH B 9 2009 2009 HOH HOH . 
L 5 HOH B 10 2010 2010 HOH HOH . 
L 5 HOH B 11 2011 2011 HOH HOH . 
L 5 HOH B 12 2012 2012 HOH HOH . 
L 5 HOH B 13 2013 2013 HOH HOH . 
L 5 HOH B 14 2014 2014 HOH HOH . 
L 5 HOH B 15 2015 2015 HOH HOH . 
L 5 HOH B 16 2016 2016 HOH HOH . 
L 5 HOH B 17 2017 2017 HOH HOH . 
L 5 HOH B 18 2018 2018 HOH HOH . 
L 5 HOH B 19 2019 2019 HOH HOH . 
L 5 HOH B 20 2020 2020 HOH HOH . 
L 5 HOH B 21 2021 2021 HOH HOH . 
L 5 HOH B 22 2022 2022 HOH HOH . 
L 5 HOH B 23 2023 2023 HOH HOH . 
L 5 HOH B 24 2024 2024 HOH HOH . 
L 5 HOH B 25 2025 2025 HOH HOH . 
L 5 HOH B 26 2026 2026 HOH HOH . 
L 5 HOH B 27 2027 2027 HOH HOH . 
L 5 HOH B 28 2028 2028 HOH HOH . 
L 5 HOH B 29 2029 2029 HOH HOH . 
L 5 HOH B 30 2030 2030 HOH HOH . 
L 5 HOH B 31 2031 2031 HOH HOH . 
L 5 HOH B 32 2032 2032 HOH HOH . 
L 5 HOH B 33 2033 2033 HOH HOH . 
L 5 HOH B 34 2034 2034 HOH HOH . 
L 5 HOH B 35 2035 2035 HOH HOH . 
L 5 HOH B 36 2036 2036 HOH HOH . 
L 5 HOH B 37 2037 2037 HOH HOH . 
L 5 HOH B 38 2038 2038 HOH HOH . 
L 5 HOH B 39 2039 2039 HOH HOH . 
L 5 HOH B 40 2040 2040 HOH HOH . 
L 5 HOH B 41 2041 2041 HOH HOH . 
L 5 HOH B 42 2042 2042 HOH HOH . 
L 5 HOH B 43 2043 2043 HOH HOH . 
L 5 HOH B 44 2044 2044 HOH HOH . 
L 5 HOH B 45 2045 2045 HOH HOH . 
L 5 HOH B 46 2046 2046 HOH HOH . 
L 5 HOH B 47 2047 2047 HOH HOH . 
L 5 HOH B 48 2048 2048 HOH HOH . 
L 5 HOH B 49 2049 2049 HOH HOH . 
L 5 HOH B 50 2050 2050 HOH HOH . 
L 5 HOH B 51 2051 2051 HOH HOH . 
L 5 HOH B 52 2052 2052 HOH HOH . 
L 5 HOH B 53 2053 2053 HOH HOH . 
L 5 HOH B 54 2054 2054 HOH HOH . 
L 5 HOH B 55 2055 2055 HOH HOH . 
L 5 HOH B 56 2056 2056 HOH HOH . 
L 5 HOH B 57 2057 2057 HOH HOH . 
L 5 HOH B 58 2058 2058 HOH HOH . 
L 5 HOH B 59 2059 2059 HOH HOH . 
L 5 HOH B 60 2060 2060 HOH HOH . 
L 5 HOH B 61 2061 2061 HOH HOH . 
L 5 HOH B 62 2062 2062 HOH HOH . 
L 5 HOH B 63 2063 2063 HOH HOH . 
L 5 HOH B 64 2064 2064 HOH HOH . 
L 5 HOH B 65 2065 2065 HOH HOH . 
L 5 HOH B 66 2066 2066 HOH HOH . 
L 5 HOH B 67 2067 2067 HOH HOH . 
L 5 HOH B 68 2068 2068 HOH HOH . 
L 5 HOH B 69 2069 2069 HOH HOH . 
L 5 HOH B 70 2070 2070 HOH HOH . 
L 5 HOH B 71 2071 2071 HOH HOH . 
L 5 HOH B 72 2072 2072 HOH HOH . 
L 5 HOH B 73 2073 2073 HOH HOH . 
L 5 HOH B 74 2074 2074 HOH HOH . 
L 5 HOH B 75 2075 2075 HOH HOH . 
L 5 HOH B 76 2076 2076 HOH HOH . 
L 5 HOH B 77 2077 2077 HOH HOH . 
L 5 HOH B 78 2078 2078 HOH HOH . 
L 5 HOH B 79 2079 2079 HOH HOH . 
L 5 HOH B 80 2080 2080 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 N N LYS . . . H 2 81.507 50.177 158.405 0.7 66.26 ? N LYS 601 B 1 
HETATM 2 C CA LYS . . . H 2 80.407 49.198 158.668 0.7 66.39 ? CA LYS 601 B 1 
HETATM 3 C C LYS . . . H 2 80.887 47.925 159.382 0.7 66.57 ? C LYS 601 B 1 
HETATM 4 O O LYS . . . H 2 80.36 47.583 160.441 0.7 66.68 ? O LYS 601 B 1 
HETATM 5 C CB LYS . . . H 2 79.627 48.862 157.381 0.7 66.33 ? CB LYS 601 B 1 
HETATM 6 C CG LYS . . . H 2 80.429 48.254 156.228 0.7 66.3 ? CG LYS 601 B 1 
HETATM 7 C CD LYS . . . H 2 81.311 49.281 155.54 0.7 66.1 ? CD LYS 601 B 1 
HETATM 8 C CE LYS . . . H 2 82.314 48.611 154.634 0.7 66.12 ? CE LYS 601 B 1 
HETATM 9 N NZ LYS . . . H 2 83.641 49.238 154.814 0.7 65.59 ? NZ LYS 601 B 1 
HETATM 10 O OXT LYS . . . H 2 81.8 47.211 158.946 0.7 66.6 ? OXT LYS 601 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           444 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           10 
#