data_1Y13
#
_model_server_result.job_id            Z1SBL_dOY_1e5mZgIpRwxA 
_model_server_result.datetime_utc      '2024-11-14 15:57:18' 
_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          1y13 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":175}' 
#
_entry.id    1Y13 
#
_exptl.entry_id    1Y13 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              237.215 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            BIOPTERIN 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            1Y13 
_cell.length_a            103.319 
_cell.length_b            103.319 
_cell.length_c            131.111 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1Y13 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
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 hexameric 6 author_and_software_defined_assembly 1 
PQS trimeric 3 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,B,C,D,E,F,G,H,I,J,K,L 1 1,2 
A,B,C,D,E,F,G,H,I,J,K,L 2 1 
#
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' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 103.319 103.319 65.5555 
#
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 G 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
covale ? covale1 A C GLU 149 A GLU 141 1_555 A N MSE 150 A MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C MSE 150 A MSE 142 1_555 A N ASP 151 A ASP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 B C GLU 149 B GLU 141 1_555 B N MSE 150 B MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale4 B C MSE 150 B MSE 142 1_555 B N ASP 151 B ASP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale5 C C GLU 149 C GLU 141 1_555 C N MSE 150 C MSE 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
covale ? covale6 C C MSE 150 C MSE 142 1_555 C N ASP 151 C ASP 143 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
metalc ? metalc1 A NE2 HIS 37 A HIS 29 1_555 D ZN ZN . A ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc2 A NE2 HIS 49 A HIS 41 1_555 D ZN ZN . A ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc3 A NE2 HIS 51 A HIS 43 1_555 D ZN ZN . A ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc4 D ZN ZN . A ZN 174 1_555 E O9 BIO . A BIO 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc5 D ZN ZN . A ZN 174 1_555 E O10 BIO . A BIO 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
metalc ? metalc6 B NE2 HIS 37 B HIS 29 1_555 F ZN ZN . B ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc7 B NE2 HIS 49 B HIS 41 1_555 F ZN ZN . B ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? 
metalc ? metalc8 B NE2 HIS 51 B HIS 43 1_555 F ZN ZN . B ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? 
metalc ? metalc9 F ZN ZN . B ZN 174 1_555 G O9 BIO . B BIO 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? 
metalc ? metalc10 F ZN ZN . B ZN 174 1_555 G O10 BIO . B BIO 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? 
metalc ? metalc11 C NE2 HIS 37 C HIS 29 1_555 H ZN ZN . C ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc12 C NE2 HIS 49 C HIS 41 1_555 H ZN ZN . C ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? 
metalc ? metalc13 C NE2 HIS 51 C HIS 43 1_555 H ZN ZN . C ZN 174 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.239 ? 
metalc ? metalc14 H ZN ZN . C ZN 174 1_555 I O9 BIO . C BIO 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? 
metalc ? metalc15 H ZN ZN . C ZN 174 1_555 I O10 BIO . C BIO 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? 
#
_chem_comp.formula           'C9 H11 N5 O3' 
_chem_comp.formula_weight    237.215 
_chem_comp.id                BIO 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              BIOPTERIN 
_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 BIO doub 70 n y 
N1 C8A BIO sing 71 n y 
N2 C2 BIO sing 72 n n 
N2 HN21 BIO sing 73 n n 
N2 HN22 BIO sing 74 n n 
C2 N3 BIO sing 75 n y 
N3 C4 BIO sing 76 n y 
N3 H3 BIO sing 77 n n 
C4 O4 BIO doub 78 n n 
C4 C4A BIO sing 79 n y 
C4A C8A BIO sing 80 n y 
C4A N5 BIO doub 81 n y 
C8A N8 BIO doub 82 n y 
N8 C7 BIO sing 83 n y 
C7 C6 BIO doub 84 n y 
C7 H7 BIO sing 85 n n 
C6 N5 BIO sing 86 n y 
C6 C9 BIO sing 87 n n 
C9 O9 BIO sing 88 n n 
C9 C10 BIO sing 89 n n 
C9 H9 BIO sing 90 n n 
O9 HO9 BIO sing 91 n n 
C10 O10 BIO sing 92 n n 
C10 C11 BIO sing 93 n n 
C10 H10 BIO sing 94 n n 
O10 HO1 BIO sing 95 n n 
C11 H111 BIO sing 96 n n 
C11 H112 BIO sing 97 n n 
C11 H113 BIO sing 98 n n 
#
_atom_sites.entry_id                     1Y13 
_atom_sites.fract_transf_matrix[1][1]    0.009679 
_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]    0.009679 
_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]    0.007627 
_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 1 174 174 ZN ZN . 
E 3 BIO A 1 175 175 BIO BIO . 
F 2 ZN B 1 174 174 ZN ZN . 
G 3 BIO B 1 175 175 BIO BIO . 
H 2 ZN C 1 174 174 ZN ZN . 
I 3 BIO C 1 175 175 BIO BIO . 
J 4 HOH A 1 176 3 HOH HOH . 
J 4 HOH A 2 177 7 HOH HOH . 
J 4 HOH A 3 178 8 HOH HOH . 
J 4 HOH A 4 179 11 HOH HOH . 
J 4 HOH A 5 180 13 HOH HOH . 
J 4 HOH A 6 181 14 HOH HOH . 
J 4 HOH A 7 182 18 HOH HOH . 
J 4 HOH A 8 183 19 HOH HOH . 
J 4 HOH A 9 184 20 HOH HOH . 
J 4 HOH A 10 185 21 HOH HOH . 
J 4 HOH A 11 186 22 HOH HOH . 
J 4 HOH A 12 187 23 HOH HOH . 
J 4 HOH A 13 188 24 HOH HOH . 
J 4 HOH A 14 189 28 HOH HOH . 
J 4 HOH A 15 190 31 HOH HOH . 
J 4 HOH A 16 191 32 HOH HOH . 
J 4 HOH A 17 192 33 HOH HOH . 
J 4 HOH A 18 193 37 HOH HOH . 
J 4 HOH A 19 194 38 HOH HOH . 
J 4 HOH A 20 195 41 HOH HOH . 
J 4 HOH A 21 196 42 HOH HOH . 
J 4 HOH A 22 197 43 HOH HOH . 
J 4 HOH A 23 198 46 HOH HOH . 
J 4 HOH A 24 199 48 HOH HOH . 
J 4 HOH A 25 200 49 HOH HOH . 
J 4 HOH A 26 201 50 HOH HOH . 
J 4 HOH A 27 202 51 HOH HOH . 
J 4 HOH A 28 203 56 HOH HOH . 
J 4 HOH A 29 204 58 HOH HOH . 
J 4 HOH A 30 205 59 HOH HOH . 
J 4 HOH A 31 206 61 HOH HOH . 
J 4 HOH A 32 207 62 HOH HOH . 
J 4 HOH A 33 208 63 HOH HOH . 
J 4 HOH A 34 209 64 HOH HOH . 
J 4 HOH A 35 210 69 HOH HOH . 
J 4 HOH A 36 211 70 HOH HOH . 
J 4 HOH A 37 212 71 HOH HOH . 
J 4 HOH A 38 213 72 HOH HOH . 
J 4 HOH A 39 214 78 HOH HOH . 
J 4 HOH A 40 215 79 HOH HOH . 
J 4 HOH A 41 216 81 HOH HOH . 
J 4 HOH A 42 217 83 HOH HOH . 
J 4 HOH A 43 218 84 HOH HOH . 
J 4 HOH A 44 219 91 HOH HOH . 
J 4 HOH A 45 220 98 HOH HOH . 
J 4 HOH A 46 221 103 HOH HOH . 
J 4 HOH A 47 222 107 HOH HOH . 
J 4 HOH A 48 223 109 HOH HOH . 
J 4 HOH A 49 224 111 HOH HOH . 
J 4 HOH A 50 225 112 HOH HOH . 
J 4 HOH A 51 226 114 HOH HOH . 
J 4 HOH A 52 227 115 HOH HOH . 
J 4 HOH A 53 228 116 HOH HOH . 
J 4 HOH A 54 229 117 HOH HOH . 
J 4 HOH A 55 230 119 HOH HOH . 
J 4 HOH A 56 231 121 HOH HOH . 
J 4 HOH A 57 232 125 HOH HOH . 
K 4 HOH B 1 176 1 HOH HOH . 
K 4 HOH B 2 177 2 HOH HOH . 
K 4 HOH B 3 178 4 HOH HOH . 
K 4 HOH B 4 179 5 HOH HOH . 
K 4 HOH B 5 180 6 HOH HOH . 
K 4 HOH B 6 181 10 HOH HOH . 
K 4 HOH B 7 182 12 HOH HOH . 
K 4 HOH B 8 183 15 HOH HOH . 
K 4 HOH B 9 184 17 HOH HOH . 
K 4 HOH B 10 185 27 HOH HOH . 
K 4 HOH B 11 186 29 HOH HOH . 
K 4 HOH B 12 187 30 HOH HOH . 
K 4 HOH B 13 188 34 HOH HOH . 
K 4 HOH B 14 189 35 HOH HOH . 
K 4 HOH B 15 190 36 HOH HOH . 
K 4 HOH B 16 191 39 HOH HOH . 
K 4 HOH B 17 192 40 HOH HOH . 
K 4 HOH B 18 193 44 HOH HOH . 
K 4 HOH B 19 194 52 HOH HOH . 
K 4 HOH B 20 195 53 HOH HOH . 
K 4 HOH B 21 196 54 HOH HOH . 
K 4 HOH B 22 197 55 HOH HOH . 
K 4 HOH B 23 198 57 HOH HOH . 
K 4 HOH B 24 199 60 HOH HOH . 
K 4 HOH B 25 200 65 HOH HOH . 
K 4 HOH B 26 201 67 HOH HOH . 
K 4 HOH B 27 202 68 HOH HOH . 
K 4 HOH B 28 203 73 HOH HOH . 
K 4 HOH B 29 204 77 HOH HOH . 
K 4 HOH B 30 205 80 HOH HOH . 
K 4 HOH B 31 206 82 HOH HOH . 
K 4 HOH B 32 207 85 HOH HOH . 
K 4 HOH B 33 208 86 HOH HOH . 
K 4 HOH B 34 209 87 HOH HOH . 
K 4 HOH B 35 210 88 HOH HOH . 
K 4 HOH B 36 211 89 HOH HOH . 
K 4 HOH B 37 212 92 HOH HOH . 
K 4 HOH B 38 213 95 HOH HOH . 
K 4 HOH B 39 214 96 HOH HOH . 
K 4 HOH B 40 215 100 HOH HOH . 
K 4 HOH B 41 216 104 HOH HOH . 
K 4 HOH B 42 217 106 HOH HOH . 
K 4 HOH B 43 218 110 HOH HOH . 
K 4 HOH B 44 219 113 HOH HOH . 
K 4 HOH B 45 220 118 HOH HOH . 
K 4 HOH B 46 221 122 HOH HOH . 
K 4 HOH B 47 222 123 HOH HOH . 
K 4 HOH B 48 223 124 HOH HOH . 
K 4 HOH B 49 224 126 HOH HOH . 
K 4 HOH B 50 225 127 HOH HOH . 
L 4 HOH C 1 176 9 HOH HOH . 
L 4 HOH C 2 177 16 HOH HOH . 
L 4 HOH C 3 178 25 HOH HOH . 
L 4 HOH C 4 179 45 HOH HOH . 
L 4 HOH C 5 180 47 HOH HOH . 
L 4 HOH C 6 181 66 HOH HOH . 
L 4 HOH C 7 182 74 HOH HOH . 
L 4 HOH C 8 183 75 HOH HOH . 
L 4 HOH C 9 184 76 HOH HOH . 
L 4 HOH C 10 185 90 HOH HOH . 
L 4 HOH C 11 186 93 HOH HOH . 
L 4 HOH C 12 187 94 HOH HOH . 
L 4 HOH C 13 188 97 HOH HOH . 
L 4 HOH C 14 189 99 HOH HOH . 
L 4 HOH C 15 190 101 HOH HOH . 
L 4 HOH C 16 191 102 HOH HOH . 
L 4 HOH C 17 192 105 HOH HOH . 
L 4 HOH C 18 193 108 HOH HOH . 
L 4 HOH C 19 194 120 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 BIO . . . E 3 73.545 1.116 21.924 1 56.68 ? N1 BIO 175 A 1 
HETATM 2 N N2 BIO . . . E 3 74.231 2.158 19.961 1 56.08 ? N2 BIO 175 A 1 
HETATM 3 C C2 BIO . . . E 3 73.519 2.198 21.122 1 57.3 ? C2 BIO 175 A 1 
HETATM 4 N N3 BIO . . . E 3 72.794 3.271 21.507 1 57.74 ? N3 BIO 175 A 1 
HETATM 5 C C4A BIO . . . E 3 72.033 2.231 23.566 1 57.36 ? C4A BIO 175 A 1 
HETATM 6 C C8A BIO . . . E 3 72.841 1.087 23.096 1 55.39 ? C8A BIO 175 A 1 
HETATM 7 N N8 BIO . . . E 3 72.869 -0.027 23.876 1 65.13 ? N8 BIO 175 A 1 
HETATM 8 C C7 BIO . . . E 3 72.199 -0.115 25.047 1 60.89 ? C7 BIO 175 A 1 
HETATM 9 C C6 BIO . . . E 3 71.457 0.951 25.51 1 57.2 ? C6 BIO 175 A 1 
HETATM 10 N N5 BIO . . . E 3 71.392 2.08 24.751 1 64.66 ? N5 BIO 175 A 1 
HETATM 11 C C9 BIO . . . E 3 70.702 0.865 26.821 1 67.94 ? C9 BIO 175 A 1 
HETATM 12 O O9 BIO . . . E 3 69.501 1.726 26.843 1 57.58 ? O9 BIO 175 A 1 
HETATM 13 C C10 BIO . . . E 3 71.584 1.151 28.085 1 76.8 ? C10 BIO 175 A 1 
HETATM 14 O O10 BIO . . . E 3 71.502 2.538 28.468 1 60.99 ? O10 BIO 175 A 1 
HETATM 15 C C11 BIO . . . E 3 73.071 0.764 27.992 1 78.44 ? C11 BIO 175 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           249 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           15 
#