data_3P13
#
_model_server_result.job_id            Fgf9-YusxTxe8VOB5oOqgQ 
_model_server_result.datetime_utc      '2024-10-12 20:21:50' 
_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          3p13 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":201}' 
#
_entry.id    3P13 
#
_exptl.entry_id    3P13 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              150.13 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            beta-D-ribopyranose 
_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         120 
_cell.entry_id            3P13 
_cell.length_a            124.27 
_cell.length_b            124.27 
_cell.length_c            86.21 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3P13 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        172 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 64' 
#
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 dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_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,D,E,H,I,L 1 1 
B,C,F,G,J,K 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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
#
_chem_comp.formula           'C5 H10 O5' 
_chem_comp.formula_weight    150.13 
_chem_comp.id                RIP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              beta-D-ribopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     'beta-D-ribose;D-ribose;ribose;RIBOSE(PYRANOSE FORM)' 
#
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
C1 C2 RIP sing 264 n n 
C1 O1 RIP sing 265 n n 
C1 O5 RIP sing 266 n n 
C1 H1 RIP sing 267 n n 
C2 C3 RIP sing 268 n n 
C2 O2 RIP sing 269 n n 
C2 H2 RIP sing 270 n n 
C3 C4 RIP sing 271 n n 
C3 O3 RIP sing 272 n n 
C3 H3 RIP sing 273 n n 
C4 C5 RIP sing 274 n n 
C4 O4 RIP sing 275 n n 
C4 H4 RIP sing 276 n n 
C5 O5 RIP sing 277 n n 
C5 H51 RIP sing 278 n n 
C5 H52 RIP sing 279 n n 
O1 HO1 RIP sing 280 n n 
O2 HO2 RIP sing 281 n n 
O3 HO3 RIP sing 282 n n 
O4 HO4 RIP sing 283 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
RIP DRibpb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
RIP b-D-ribopyranose 'COMMON NAME' GMML 1 
RIP b-D-Ribp 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
RIP Rib 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     3P13 
_atom_sites.fract_transf_matrix[1][1]    0.008047 
_atom_sites.fract_transf_matrix[1][2]    0.004646 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009292 
_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]    0.0116 
_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
E 2 RIP A 1 201 201 RIP RIP . 
F 2 RIP B 1 201 201 RIP RIP . 
G 2 RIP C 1 201 201 RIP RIP . 
H 2 RIP D 1 201 201 RIP RIP . 
I 3 HOH A 1 145 8 HOH HOH . 
I 3 HOH A 2 146 9 HOH HOH . 
I 3 HOH A 3 147 15 HOH HOH . 
I 3 HOH A 4 148 16 HOH HOH . 
I 3 HOH A 5 149 17 HOH HOH . 
I 3 HOH A 6 150 19 HOH HOH . 
I 3 HOH A 7 151 22 HOH HOH . 
I 3 HOH A 8 152 27 HOH HOH . 
I 3 HOH A 9 153 29 HOH HOH . 
I 3 HOH A 10 154 34 HOH HOH . 
I 3 HOH A 11 155 39 HOH HOH . 
I 3 HOH A 12 156 44 HOH HOH . 
I 3 HOH A 13 157 47 HOH HOH . 
I 3 HOH A 14 158 50 HOH HOH . 
I 3 HOH A 15 159 56 HOH HOH . 
I 3 HOH A 16 160 59 HOH HOH . 
I 3 HOH A 17 161 70 HOH HOH . 
I 3 HOH A 18 162 74 HOH HOH . 
I 3 HOH A 19 163 76 HOH HOH . 
I 3 HOH A 20 164 81 HOH HOH . 
I 3 HOH A 21 165 82 HOH HOH . 
I 3 HOH A 22 166 92 HOH HOH . 
I 3 HOH A 23 167 95 HOH HOH . 
I 3 HOH A 24 168 97 HOH HOH . 
I 3 HOH A 25 169 98 HOH HOH . 
I 3 HOH A 26 170 99 HOH HOH . 
I 3 HOH A 27 171 100 HOH HOH . 
I 3 HOH A 28 172 104 HOH HOH . 
I 3 HOH A 29 173 106 HOH HOH . 
I 3 HOH A 30 174 109 HOH HOH . 
I 3 HOH A 31 175 112 HOH HOH . 
I 3 HOH A 32 176 118 HOH HOH . 
I 3 HOH A 33 177 119 HOH HOH . 
I 3 HOH A 34 178 120 HOH HOH . 
I 3 HOH A 35 179 121 HOH HOH . 
I 3 HOH A 36 180 138 HOH HOH . 
J 3 HOH B 1 145 5 HOH HOH . 
J 3 HOH B 2 146 6 HOH HOH . 
J 3 HOH B 3 147 13 HOH HOH . 
J 3 HOH B 4 148 18 HOH HOH . 
J 3 HOH B 5 149 24 HOH HOH . 
J 3 HOH B 6 150 26 HOH HOH . 
J 3 HOH B 7 151 32 HOH HOH . 
J 3 HOH B 8 152 38 HOH HOH . 
J 3 HOH B 9 153 41 HOH HOH . 
J 3 HOH B 10 154 43 HOH HOH . 
J 3 HOH B 11 155 45 HOH HOH . 
J 3 HOH B 12 156 48 HOH HOH . 
J 3 HOH B 13 157 52 HOH HOH . 
J 3 HOH B 14 158 57 HOH HOH . 
J 3 HOH B 15 159 58 HOH HOH . 
J 3 HOH B 16 160 63 HOH HOH . 
J 3 HOH B 17 161 64 HOH HOH . 
J 3 HOH B 18 162 65 HOH HOH . 
J 3 HOH B 19 163 72 HOH HOH . 
J 3 HOH B 20 164 75 HOH HOH . 
J 3 HOH B 21 165 78 HOH HOH . 
J 3 HOH B 22 166 80 HOH HOH . 
J 3 HOH B 23 167 83 HOH HOH . 
J 3 HOH B 24 168 86 HOH HOH . 
J 3 HOH B 25 169 87 HOH HOH . 
J 3 HOH B 26 170 93 HOH HOH . 
J 3 HOH B 27 171 94 HOH HOH . 
J 3 HOH B 28 172 108 HOH HOH . 
J 3 HOH B 29 173 111 HOH HOH . 
J 3 HOH B 30 174 113 HOH HOH . 
J 3 HOH B 31 175 115 HOH HOH . 
J 3 HOH B 32 176 122 HOH HOH . 
J 3 HOH B 33 177 123 HOH HOH . 
J 3 HOH B 34 178 124 HOH HOH . 
J 3 HOH B 35 179 139 HOH HOH . 
J 3 HOH B 36 180 142 HOH HOH . 
J 3 HOH B 37 181 36 HOH HOH . 
K 3 HOH C 1 145 2 HOH HOH . 
K 3 HOH C 2 146 3 HOH HOH . 
K 3 HOH C 3 147 4 HOH HOH . 
K 3 HOH C 4 148 7 HOH HOH . 
K 3 HOH C 5 149 12 HOH HOH . 
K 3 HOH C 6 150 21 HOH HOH . 
K 3 HOH C 7 151 25 HOH HOH . 
K 3 HOH C 8 152 31 HOH HOH . 
K 3 HOH C 9 153 33 HOH HOH . 
K 3 HOH C 10 154 35 HOH HOH . 
K 3 HOH C 11 156 51 HOH HOH . 
K 3 HOH C 12 157 54 HOH HOH . 
K 3 HOH C 13 158 62 HOH HOH . 
K 3 HOH C 14 159 67 HOH HOH . 
K 3 HOH C 15 160 68 HOH HOH . 
K 3 HOH C 16 161 69 HOH HOH . 
K 3 HOH C 17 162 71 HOH HOH . 
K 3 HOH C 18 163 73 HOH HOH . 
K 3 HOH C 19 164 77 HOH HOH . 
K 3 HOH C 20 165 79 HOH HOH . 
K 3 HOH C 21 166 88 HOH HOH . 
K 3 HOH C 22 167 89 HOH HOH . 
K 3 HOH C 23 168 91 HOH HOH . 
K 3 HOH C 24 169 96 HOH HOH . 
K 3 HOH C 25 170 101 HOH HOH . 
K 3 HOH C 26 171 102 HOH HOH . 
K 3 HOH C 27 172 105 HOH HOH . 
K 3 HOH C 28 173 107 HOH HOH . 
K 3 HOH C 29 174 116 HOH HOH . 
K 3 HOH C 30 175 125 HOH HOH . 
K 3 HOH C 31 176 126 HOH HOH . 
K 3 HOH C 32 177 127 HOH HOH . 
K 3 HOH C 33 178 128 HOH HOH . 
K 3 HOH C 34 179 129 HOH HOH . 
K 3 HOH C 35 180 130 HOH HOH . 
K 3 HOH C 36 181 131 HOH HOH . 
K 3 HOH C 37 182 132 HOH HOH . 
K 3 HOH C 38 183 133 HOH HOH . 
K 3 HOH C 39 184 143 HOH HOH . 
K 3 HOH C 40 185 144 HOH HOH . 
L 3 HOH D 1 145 1 HOH HOH . 
L 3 HOH D 2 146 10 HOH HOH . 
L 3 HOH D 3 147 11 HOH HOH . 
L 3 HOH D 4 148 14 HOH HOH . 
L 3 HOH D 5 149 20 HOH HOH . 
L 3 HOH D 6 150 23 HOH HOH . 
L 3 HOH D 7 151 28 HOH HOH . 
L 3 HOH D 8 152 30 HOH HOH . 
L 3 HOH D 9 153 37 HOH HOH . 
L 3 HOH D 10 154 40 HOH HOH . 
L 3 HOH D 11 155 42 HOH HOH . 
L 3 HOH D 12 156 46 HOH HOH . 
L 3 HOH D 13 157 49 HOH HOH . 
L 3 HOH D 14 158 53 HOH HOH . 
L 3 HOH D 15 159 55 HOH HOH . 
L 3 HOH D 16 160 60 HOH HOH . 
L 3 HOH D 17 161 61 HOH HOH . 
L 3 HOH D 18 162 66 HOH HOH . 
L 3 HOH D 19 163 84 HOH HOH . 
L 3 HOH D 20 164 85 HOH HOH . 
L 3 HOH D 21 165 90 HOH HOH . 
L 3 HOH D 22 166 103 HOH HOH . 
L 3 HOH D 23 167 110 HOH HOH . 
L 3 HOH D 24 168 114 HOH HOH . 
L 3 HOH D 25 169 117 HOH HOH . 
L 3 HOH D 26 170 134 HOH HOH . 
L 3 HOH D 27 171 135 HOH HOH . 
L 3 HOH D 28 172 136 HOH HOH . 
L 3 HOH D 29 173 137 HOH HOH . 
L 3 HOH D 30 174 140 HOH HOH . 
L 3 HOH D 31 175 141 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 C C1 RIP . . . F 2 39.993 31.982 22.937 1 46.01 ? C1 RIP 201 B 1 
HETATM 2 C C2 RIP . . . F 2 39.753 33.074 23.985 1 45.3 ? C2 RIP 201 B 1 
HETATM 3 C C3 RIP . . . F 2 41.045 33.473 24.697 1 45.26 ? C3 RIP 201 B 1 
HETATM 4 C C4 RIP . . . F 2 42.203 33.732 23.741 1 46.05 ? C4 RIP 201 B 1 
HETATM 5 C C5 RIP . . . F 2 42.315 32.655 22.656 1 46.73 ? C5 RIP 201 B 1 
HETATM 6 O O1 RIP . . . F 2 40.212 30.726 23.555 1 45.44 ? O1 RIP 201 B 1 
HETATM 7 O O2 RIP . . . F 2 39.184 34.203 23.352 1 45.76 ? O2 RIP 201 B 1 
HETATM 8 O O3 RIP . . . F 2 40.835 34.654 25.418 1 44.91 ? O3 RIP 201 B 1 
HETATM 9 O O4 RIP . . . F 2 42.034 35.01 23.169 1 46.97 ? O4 RIP 201 B 1 
HETATM 10 O O5 RIP . . . F 2 41.061 32.337 22.061 1 46.47 ? O5 RIP 201 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           10 
#