data_2VA5
#
_model_server_result.job_id            hXJ9G40XCLBCWmbBrjrydg 
_model_server_result.datetime_utc      '2024-12-22 02:44:16' 
_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          2va5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1389}' 
#
_entry.id    2VA5 
#
_exptl.entry_id    2VA5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              254.287 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-amino-6-[2-(1H-indol-6-yl)ethyl]pyrimidin-4(3H)-one 
_entity.pdbx_number_of_molecules    1 
_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         120 
_cell.entry_id            2VA5 
_cell.length_a            102.138 
_cell.length_b            102.138 
_cell.length_c            168.258 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2VA5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
_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 
_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' 12_555 x,x-y,-z+1/6 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 0 0 28.043 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 218 A CYS 155 1_555 A SG CYS 422 A CYS 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
disulf ? disulf2 A SG CYS 280 A CYS 217 1_555 A SG CYS 445 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? 
disulf ? disulf3 A SG CYS 332 A CYS 269 1_555 A SG CYS 382 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
#
_chem_comp.formula           'C14 H14 N4 O' 
_chem_comp.formula_weight    254.287 
_chem_comp.id                C8C 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-amino-6-[2-(1H-indol-6-yl)ethyl]pyrimidin-4(3H)-one 
_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
N1 C2 C8C sing 70 n n 
C2 N18 C8C doub 71 n n 
C2 N3 C8C sing 72 n n 
C4 C5 C8C sing 73 n n 
C4 N3 C8C sing 74 n n 
C4 O5 C8C doub 75 n n 
C5 C6 C8C doub 76 n n 
C6 C7 C8C sing 77 n n 
C6 N18 C8C sing 78 n n 
C7 C8 C8C sing 79 n n 
C8 C9 C8C sing 80 n n 
C9 C10 C8C sing 81 n y 
C9 C17 C8C doub 82 n y 
C10 C11 C8C doub 83 n y 
C11 C12 C8C sing 84 n y 
C12 C13 C8C sing 85 n y 
C12 C16 C8C doub 86 n y 
C13 C14 C8C doub 87 n y 
C14 N15 C8C sing 88 n y 
N15 C16 C8C sing 89 n y 
C16 C17 C8C sing 90 n y 
N1 H1N1 C8C sing 91 n n 
N1 H1N2 C8C sing 92 n n 
N3 H3 C8C sing 93 n n 
C5 H5 C8C sing 94 n n 
C7 H7C1 C8C sing 95 n n 
C7 H7C2 C8C sing 96 n n 
C8 H8C1 C8C sing 97 n n 
C8 H8C2 C8C sing 98 n n 
C10 H10 C8C sing 99 n n 
C17 H17 C8C sing 100 n n 
C11 H11 C8C sing 101 n n 
C13 H13 C8C sing 102 n n 
C14 H14 C8C sing 103 n n 
N15 H15 C8C sing 104 n n 
#
_atom_sites.entry_id                     2VA5 
_atom_sites.fract_transf_matrix[1][1]    0.009791 
_atom_sites.fract_transf_matrix[1][2]    0.005653 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011305 
_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]    0.005943 
_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 IOD A 1 1387 1387 IOD IOD . 
C 2 IOD A 1 1388 1388 IOD IOD . 
D 3 C8C A 1 1389 1389 C8C C8C . 
E 4 HOH A 1 2001 2001 HOH HOH . 
E 4 HOH A 2 2002 2002 HOH HOH . 
E 4 HOH A 3 2003 2003 HOH HOH . 
E 4 HOH A 4 2004 2004 HOH HOH . 
E 4 HOH A 5 2005 2005 HOH HOH . 
E 4 HOH A 6 2006 2006 HOH HOH . 
E 4 HOH A 7 2007 2007 HOH HOH . 
E 4 HOH A 8 2008 2008 HOH HOH . 
E 4 HOH A 9 2009 2009 HOH HOH . 
E 4 HOH A 10 2010 2010 HOH HOH . 
E 4 HOH A 11 2011 2011 HOH HOH . 
E 4 HOH A 12 2012 2012 HOH HOH . 
E 4 HOH A 13 2013 2013 HOH HOH . 
E 4 HOH A 14 2014 2014 HOH HOH . 
E 4 HOH A 15 2015 2015 HOH HOH . 
E 4 HOH A 16 2016 2016 HOH HOH . 
E 4 HOH A 17 2017 2017 HOH HOH . 
E 4 HOH A 18 2018 2018 HOH HOH . 
E 4 HOH A 19 2019 2019 HOH HOH . 
E 4 HOH A 20 2020 2020 HOH HOH . 
E 4 HOH A 21 2021 2021 HOH HOH . 
E 4 HOH A 22 2022 2022 HOH HOH . 
E 4 HOH A 23 2023 2023 HOH HOH . 
E 4 HOH A 24 2024 2024 HOH HOH . 
E 4 HOH A 25 2025 2025 HOH HOH . 
E 4 HOH A 26 2026 2026 HOH HOH . 
E 4 HOH A 27 2027 2027 HOH HOH . 
E 4 HOH A 28 2028 2028 HOH HOH . 
E 4 HOH A 29 2029 2029 HOH HOH . 
E 4 HOH A 30 2030 2030 HOH HOH . 
E 4 HOH A 31 2031 2031 HOH HOH . 
E 4 HOH A 32 2032 2032 HOH HOH . 
E 4 HOH A 33 2033 2033 HOH HOH . 
E 4 HOH A 34 2034 2034 HOH HOH . 
E 4 HOH A 35 2035 2035 HOH HOH . 
E 4 HOH A 36 2036 2036 HOH HOH . 
E 4 HOH A 37 2037 2037 HOH HOH . 
E 4 HOH A 38 2038 2038 HOH HOH . 
E 4 HOH A 39 2039 2039 HOH HOH . 
E 4 HOH A 40 2040 2040 HOH HOH . 
E 4 HOH A 41 2041 2041 HOH HOH . 
E 4 HOH A 42 2042 2042 HOH HOH . 
E 4 HOH A 43 2043 2043 HOH HOH . 
E 4 HOH A 44 2044 2044 HOH HOH . 
E 4 HOH A 45 2045 2045 HOH HOH . 
E 4 HOH A 46 2046 2046 HOH HOH . 
E 4 HOH A 47 2047 2047 HOH HOH . 
E 4 HOH A 48 2048 2048 HOH HOH . 
E 4 HOH A 49 2049 2049 HOH HOH . 
E 4 HOH A 50 2050 2050 HOH HOH . 
E 4 HOH A 51 2051 2051 HOH HOH . 
E 4 HOH A 52 2052 2052 HOH HOH . 
E 4 HOH A 53 2053 2053 HOH HOH . 
E 4 HOH A 54 2054 2054 HOH HOH . 
E 4 HOH A 55 2055 2055 HOH HOH . 
E 4 HOH A 56 2056 2056 HOH HOH . 
E 4 HOH A 57 2057 2057 HOH HOH . 
E 4 HOH A 58 2058 2058 HOH HOH . 
E 4 HOH A 59 2059 2059 HOH HOH . 
E 4 HOH A 60 2060 2060 HOH HOH . 
E 4 HOH A 61 2061 2061 HOH HOH . 
E 4 HOH A 62 2062 2062 HOH HOH . 
E 4 HOH A 63 2063 2063 HOH HOH . 
E 4 HOH A 64 2064 2064 HOH HOH . 
E 4 HOH A 65 2065 2065 HOH HOH . 
E 4 HOH A 66 2066 2066 HOH HOH . 
E 4 HOH A 67 2067 2067 HOH HOH . 
E 4 HOH A 68 2068 2068 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 N1 C8C . . . D 3 66.815 49.086 5.617 1 45.46 ? N1 C8C 1389 A 1 
HETATM 2 C C2 C8C . . . D 3 67.618 48.938 6.693 1 48.63 ? C2 C8C 1389 A 1 
HETATM 3 C C4 C8C . . . D 3 68.17 47.709 8.535 1 51.39 ? C4 C8C 1389 A 1 
HETATM 4 C C5 C8C . . . D 3 69.185 48.606 8.814 1 51.39 ? C5 C8C 1389 A 1 
HETATM 5 C C6 C8C . . . D 3 69.365 49.682 7.965 1 52.25 ? C6 C8C 1389 A 1 
HETATM 6 C C7 C8C . . . D 3 70.449 50.696 8.223 1 54.05 ? C7 C8C 1389 A 1 
HETATM 7 C C8 C8C . . . D 3 71.395 50.869 7.053 1 56.31 ? C8 C8C 1389 A 1 
HETATM 8 C C9 C8C . . . D 3 72.201 49.638 6.719 1 55.94 ? C9 C8C 1389 A 1 
HETATM 9 C C10 C8C . . . D 3 73.17 49.17 7.601 1 56.48 ? C10 C8C 1389 A 1 
HETATM 10 C C11 C8C . . . D 3 73.939 48.061 7.297 1 57.61 ? C11 C8C 1389 A 1 
HETATM 11 C C12 C8C . . . D 3 73.753 47.427 6.076 1 59.96 ? C12 C8C 1389 A 1 
HETATM 12 C C13 C8C . . . D 3 74.34 46.31 5.46 1 61.33 ? C13 C8C 1389 A 1 
HETATM 13 C C14 C8C . . . D 3 73.731 46.138 4.219 1 58.54 ? C14 C8C 1389 A 1 
HETATM 14 N N15 C8C . . . D 3 72.811 47.101 4.062 1 58.12 ? N15 C8C 1389 A 1 
HETATM 15 C C16 C8C . . . D 3 72.803 47.903 5.182 1 60.63 ? C16 C8C 1389 A 1 
HETATM 16 C C17 C8C . . . D 3 72.026 49.009 5.491 1 59.27 ? C17 C8C 1389 A 1 
HETATM 17 N N18 C8C . . . D 3 68.578 49.87 6.895 1 50.39 ? N18 C8C 1389 A 1 
HETATM 18 N N3 C8C . . . D 3 67.378 47.866 7.468 1 49.4 ? N3 C8C 1389 A 1 
HETATM 19 O O5 C8C . . . D 3 67.959 46.64 9.349 1 52.43 ? O5 C8C 1389 A 1 
#
_model_server_stats.io_time_ms              73 
_model_server_stats.parse_time_ms           31 
_model_server_stats.create_model_time_ms    39 
_model_server_stats.query_time_ms           798 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           19 
#