data_1OGD
#
_model_server_result.job_id            -y3y-5yWf4VdASa2i0RcRw 
_model_server_result.datetime_utc      '2024-10-11 04:23:34' 
_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          1ogd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1134}' 
#
_entry.id    1OGD 
#
_exptl.entry_id    1OGD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              150.13 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            beta-D-ribopyranose 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          128.68 
_cell.angle_gamma         90 
_cell.entry_id            1OGD 
_cell.length_a            123.515 
_cell.length_b            108.656 
_cell.length_c            83.308 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1OGD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PQS 
_pdbx_struct_assembly.oligomeric_details    decameric 
_pdbx_struct_assembly.oligomeric_count      10 
_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,M,N,O,P,Q 
_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' 2_655 -x+1,y,-z -1 0 0 0 1 0 0 0 -1 123.515 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 L 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 277 n n 
C1 O1 RIP sing 278 n n 
C1 O5 RIP sing 279 n n 
C1 H1 RIP sing 280 n n 
C2 C3 RIP sing 281 n n 
C2 O2 RIP sing 282 n n 
C2 H2 RIP sing 283 n n 
C3 C4 RIP sing 284 n n 
C3 O3 RIP sing 285 n n 
C3 H3 RIP sing 286 n n 
C4 C5 RIP sing 287 n n 
C4 O4 RIP sing 288 n n 
C4 H4 RIP sing 289 n n 
C5 O5 RIP sing 290 n n 
C5 H51 RIP sing 291 n n 
C5 H52 RIP sing 292 n n 
O1 HO1 RIP sing 293 n n 
O2 HO2 RIP sing 294 n n 
O3 HO3 RIP sing 295 n n 
O4 HO4 RIP sing 296 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                     1OGD 
_atom_sites.fract_transf_matrix[1][1]    0.008096 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.006482 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009203 
_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]    0.015377 
_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
F 2 CL A 1 1132 1132 CL CL . 
G 3 RIP A 1 1134 1134 RIP RIP . 
H 3 RIP B 1 1132 1132 RIP RIP . 
I 3 RIP C 1 1132 1132 RIP RIP . 
J 3 RIP D 1 1132 1132 RIP RIP . 
K 2 CL D 1 1133 1133 CL CL . 
L 3 RIP E 1 1132 1132 RIP RIP . 
M 4 HOH A 1 2001 2001 HOH HOH . 
M 4 HOH A 2 2002 2002 HOH HOH . 
M 4 HOH A 3 2003 2003 HOH HOH . 
M 4 HOH A 4 2004 2004 HOH HOH . 
M 4 HOH A 5 2005 2005 HOH HOH . 
M 4 HOH A 6 2006 2006 HOH HOH . 
M 4 HOH A 7 2007 2007 HOH HOH . 
M 4 HOH A 8 2008 2008 HOH HOH . 
M 4 HOH A 9 2009 2009 HOH HOH . 
M 4 HOH A 10 2010 2010 HOH HOH . 
M 4 HOH A 11 2011 2011 HOH HOH . 
M 4 HOH A 12 2012 2012 HOH HOH . 
M 4 HOH A 13 2013 2013 HOH HOH . 
M 4 HOH A 14 2014 2014 HOH HOH . 
M 4 HOH A 15 2015 2015 HOH HOH . 
M 4 HOH A 16 2016 2016 HOH HOH . 
M 4 HOH A 17 2017 2017 HOH HOH . 
M 4 HOH A 18 2018 2018 HOH HOH . 
M 4 HOH A 19 2019 2019 HOH HOH . 
M 4 HOH A 20 2020 2020 HOH HOH . 
M 4 HOH A 21 2021 2021 HOH HOH . 
M 4 HOH A 22 2022 2022 HOH HOH . 
M 4 HOH A 23 2023 2023 HOH HOH . 
M 4 HOH A 24 2024 2024 HOH HOH . 
M 4 HOH A 25 2025 2025 HOH HOH . 
M 4 HOH A 26 2026 2026 HOH HOH . 
M 4 HOH A 27 2027 2027 HOH HOH . 
M 4 HOH A 28 2028 2028 HOH HOH . 
M 4 HOH A 29 2029 2029 HOH HOH . 
M 4 HOH A 30 2030 2030 HOH HOH . 
M 4 HOH A 31 2031 2031 HOH HOH . 
M 4 HOH A 32 2032 2032 HOH HOH . 
M 4 HOH A 33 2033 2033 HOH HOH . 
N 4 HOH B 1 2001 2001 HOH HOH . 
N 4 HOH B 2 2002 2002 HOH HOH . 
N 4 HOH B 3 2003 2003 HOH HOH . 
N 4 HOH B 4 2004 2004 HOH HOH . 
N 4 HOH B 5 2005 2005 HOH HOH . 
N 4 HOH B 6 2006 2006 HOH HOH . 
N 4 HOH B 7 2007 2007 HOH HOH . 
N 4 HOH B 8 2008 2008 HOH HOH . 
N 4 HOH B 9 2009 2009 HOH HOH . 
N 4 HOH B 10 2010 2010 HOH HOH . 
N 4 HOH B 11 2011 2011 HOH HOH . 
N 4 HOH B 12 2012 2012 HOH HOH . 
N 4 HOH B 13 2013 2013 HOH HOH . 
N 4 HOH B 14 2014 2014 HOH HOH . 
N 4 HOH B 15 2015 2015 HOH HOH . 
N 4 HOH B 16 2016 2016 HOH HOH . 
N 4 HOH B 17 2017 2017 HOH HOH . 
N 4 HOH B 18 2018 2018 HOH HOH . 
N 4 HOH B 19 2019 2019 HOH HOH . 
N 4 HOH B 20 2020 2020 HOH HOH . 
N 4 HOH B 21 2021 2021 HOH HOH . 
N 4 HOH B 22 2022 2022 HOH HOH . 
N 4 HOH B 23 2023 2023 HOH HOH . 
N 4 HOH B 24 2024 2024 HOH HOH . 
N 4 HOH B 25 2025 2025 HOH HOH . 
N 4 HOH B 26 2026 2026 HOH HOH . 
N 4 HOH B 27 2027 2027 HOH HOH . 
N 4 HOH B 28 2028 2028 HOH HOH . 
N 4 HOH B 29 2029 2029 HOH HOH . 
N 4 HOH B 30 2030 2030 HOH HOH . 
N 4 HOH B 31 2031 2031 HOH HOH . 
N 4 HOH B 32 2032 2032 HOH HOH . 
N 4 HOH B 33 2033 2033 HOH HOH . 
N 4 HOH B 34 2034 2034 HOH HOH . 
O 4 HOH C 1 2001 2001 HOH HOH . 
O 4 HOH C 2 2002 2002 HOH HOH . 
O 4 HOH C 3 2003 2003 HOH HOH . 
O 4 HOH C 4 2004 2004 HOH HOH . 
O 4 HOH C 5 2005 2005 HOH HOH . 
O 4 HOH C 6 2006 2006 HOH HOH . 
O 4 HOH C 7 2007 2007 HOH HOH . 
O 4 HOH C 8 2008 2008 HOH HOH . 
O 4 HOH C 9 2009 2009 HOH HOH . 
O 4 HOH C 10 2010 2010 HOH HOH . 
O 4 HOH C 11 2011 2011 HOH HOH . 
O 4 HOH C 12 2012 2012 HOH HOH . 
O 4 HOH C 13 2013 2013 HOH HOH . 
O 4 HOH C 14 2014 2014 HOH HOH . 
O 4 HOH C 15 2015 2015 HOH HOH . 
O 4 HOH C 16 2016 2016 HOH HOH . 
O 4 HOH C 17 2017 2017 HOH HOH . 
O 4 HOH C 18 2018 2018 HOH HOH . 
O 4 HOH C 19 2019 2019 HOH HOH . 
O 4 HOH C 20 2020 2020 HOH HOH . 
O 4 HOH C 21 2021 2021 HOH HOH . 
O 4 HOH C 22 2022 2022 HOH HOH . 
O 4 HOH C 23 2023 2023 HOH HOH . 
O 4 HOH C 24 2024 2024 HOH HOH . 
O 4 HOH C 25 2025 2025 HOH HOH . 
O 4 HOH C 26 2026 2026 HOH HOH . 
O 4 HOH C 27 2027 2027 HOH HOH . 
O 4 HOH C 28 2028 2028 HOH HOH . 
O 4 HOH C 29 2029 2029 HOH HOH . 
O 4 HOH C 30 2030 2030 HOH HOH . 
O 4 HOH C 31 2031 2031 HOH HOH . 
O 4 HOH C 32 2032 2032 HOH HOH . 
O 4 HOH C 33 2033 2033 HOH HOH . 
O 4 HOH C 34 2034 2034 HOH HOH . 
O 4 HOH C 35 2035 2035 HOH HOH . 
O 4 HOH C 36 2036 2036 HOH HOH . 
O 4 HOH C 37 2037 2037 HOH HOH . 
O 4 HOH C 38 2038 2038 HOH HOH . 
O 4 HOH C 39 2039 2039 HOH HOH . 
O 4 HOH C 40 2040 2040 HOH HOH . 
O 4 HOH C 41 2041 2041 HOH HOH . 
O 4 HOH C 42 2042 2042 HOH HOH . 
O 4 HOH C 43 2043 2043 HOH HOH . 
O 4 HOH C 44 2044 2044 HOH HOH . 
O 4 HOH C 45 2045 2045 HOH HOH . 
O 4 HOH C 46 2046 2046 HOH HOH . 
O 4 HOH C 47 2047 2047 HOH HOH . 
P 4 HOH D 1 2001 2001 HOH HOH . 
P 4 HOH D 2 2002 2002 HOH HOH . 
P 4 HOH D 3 2003 2003 HOH HOH . 
P 4 HOH D 4 2004 2004 HOH HOH . 
P 4 HOH D 5 2005 2005 HOH HOH . 
P 4 HOH D 6 2006 2006 HOH HOH . 
P 4 HOH D 7 2007 2007 HOH HOH . 
P 4 HOH D 8 2008 2008 HOH HOH . 
P 4 HOH D 9 2009 2009 HOH HOH . 
P 4 HOH D 10 2010 2010 HOH HOH . 
P 4 HOH D 11 2011 2011 HOH HOH . 
P 4 HOH D 12 2012 2012 HOH HOH . 
P 4 HOH D 13 2013 2013 HOH HOH . 
P 4 HOH D 14 2014 2014 HOH HOH . 
P 4 HOH D 15 2015 2015 HOH HOH . 
P 4 HOH D 16 2016 2016 HOH HOH . 
P 4 HOH D 17 2017 2017 HOH HOH . 
P 4 HOH D 18 2018 2018 HOH HOH . 
P 4 HOH D 19 2019 2019 HOH HOH . 
P 4 HOH D 20 2020 2020 HOH HOH . 
P 4 HOH D 21 2021 2021 HOH HOH . 
P 4 HOH D 22 2022 2022 HOH HOH . 
P 4 HOH D 23 2023 2023 HOH HOH . 
P 4 HOH D 24 2024 2024 HOH HOH . 
P 4 HOH D 25 2025 2025 HOH HOH . 
P 4 HOH D 26 2026 2026 HOH HOH . 
P 4 HOH D 27 2027 2027 HOH HOH . 
P 4 HOH D 28 2028 2028 HOH HOH . 
P 4 HOH D 29 2029 2029 HOH HOH . 
P 4 HOH D 30 2030 2030 HOH HOH . 
P 4 HOH D 31 2031 2031 HOH HOH . 
P 4 HOH D 32 2032 2032 HOH HOH . 
P 4 HOH D 33 2033 2033 HOH HOH . 
P 4 HOH D 34 2034 2034 HOH HOH . 
P 4 HOH D 35 2035 2035 HOH HOH . 
P 4 HOH D 36 2036 2036 HOH HOH . 
P 4 HOH D 37 2037 2037 HOH HOH . 
P 4 HOH D 38 2038 2038 HOH HOH . 
P 4 HOH D 39 2039 2039 HOH HOH . 
P 4 HOH D 40 2040 2040 HOH HOH . 
P 4 HOH D 41 2041 2041 HOH HOH . 
P 4 HOH D 42 2042 2042 HOH HOH . 
P 4 HOH D 43 2043 2043 HOH HOH . 
P 4 HOH D 44 2044 2044 HOH HOH . 
P 4 HOH D 45 2045 2045 HOH HOH . 
Q 4 HOH E 1 2001 2001 HOH HOH . 
Q 4 HOH E 2 2002 2002 HOH HOH . 
Q 4 HOH E 3 2003 2003 HOH HOH . 
Q 4 HOH E 4 2004 2004 HOH HOH . 
Q 4 HOH E 5 2005 2005 HOH HOH . 
Q 4 HOH E 6 2006 2006 HOH HOH . 
Q 4 HOH E 7 2007 2007 HOH HOH . 
Q 4 HOH E 8 2008 2008 HOH HOH . 
Q 4 HOH E 9 2009 2009 HOH HOH . 
Q 4 HOH E 10 2010 2010 HOH HOH . 
Q 4 HOH E 11 2011 2011 HOH HOH . 
Q 4 HOH E 12 2012 2012 HOH HOH . 
Q 4 HOH E 13 2013 2013 HOH HOH . 
Q 4 HOH E 14 2014 2014 HOH HOH . 
Q 4 HOH E 15 2015 2015 HOH HOH . 
Q 4 HOH E 16 2016 2016 HOH HOH . 
Q 4 HOH E 17 2017 2017 HOH HOH . 
Q 4 HOH E 18 2018 2018 HOH HOH . 
Q 4 HOH E 19 2019 2019 HOH HOH . 
Q 4 HOH E 20 2020 2020 HOH HOH . 
Q 4 HOH E 21 2021 2021 HOH HOH . 
Q 4 HOH E 22 2022 2022 HOH HOH . 
Q 4 HOH E 23 2023 2023 HOH HOH . 
Q 4 HOH E 24 2024 2024 HOH HOH . 
Q 4 HOH E 25 2025 2025 HOH HOH . 
Q 4 HOH E 26 2026 2026 HOH HOH . 
Q 4 HOH E 27 2027 2027 HOH HOH . 
Q 4 HOH E 28 2028 2028 HOH HOH . 
Q 4 HOH E 29 2029 2029 HOH HOH . 
Q 4 HOH E 30 2030 2030 HOH HOH . 
Q 4 HOH E 31 2031 2031 HOH HOH . 
Q 4 HOH E 32 2032 2032 HOH HOH . 
Q 4 HOH E 33 2033 2033 HOH HOH . 
Q 4 HOH E 34 2034 2034 HOH HOH . 
Q 4 HOH E 35 2035 2035 HOH HOH . 
Q 4 HOH E 36 2036 2036 HOH HOH . 
Q 4 HOH E 37 2037 2037 HOH HOH . 
Q 4 HOH E 38 2038 2038 HOH HOH . 
Q 4 HOH E 39 2039 2039 HOH HOH . 
Q 4 HOH E 40 2040 2040 HOH HOH . 
Q 4 HOH E 41 2041 2041 HOH HOH . 
Q 4 HOH E 42 2042 2042 HOH HOH . 
Q 4 HOH E 43 2043 2043 HOH HOH . 
Q 4 HOH E 44 2044 2044 HOH HOH . 
Q 4 HOH E 45 2045 2045 HOH HOH . 
Q 4 HOH E 46 2046 2046 HOH HOH . 
Q 4 HOH E 47 2047 2047 HOH HOH . 
Q 4 HOH E 48 2048 2048 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 . . . G 3 51.205 4.267 26.522 1 39.76 ? C1 RIP 1134 A 1 
HETATM 2 C C2 RIP . . . G 3 52.098 4.849 27.588 1 37.21 ? C2 RIP 1134 A 1 
HETATM 3 C C3 RIP . . . G 3 51.391 4.786 28.933 1 39.24 ? C3 RIP 1134 A 1 
HETATM 4 C C4 RIP . . . G 3 50.897 3.394 29.308 1 39.61 ? C4 RIP 1134 A 1 
HETATM 5 C C5 RIP . . . G 3 50.011 2.898 28.171 1 40.55 ? C5 RIP 1134 A 1 
HETATM 6 O O1 RIP . . . G 3 50.096 5.104 26.264 1 41.81 ? O1 RIP 1134 A 1 
HETATM 7 O O2 RIP . . . G 3 53.294 4.099 27.602 1 35.15 ? O2 RIP 1134 A 1 
HETATM 8 O O3 RIP . . . G 3 52.218 5.301 29.944 1 38.13 ? O3 RIP 1134 A 1 
HETATM 9 O O4 RIP . . . G 3 51.975 2.491 29.46 1 40.64 ? O4 RIP 1134 A 1 
HETATM 10 O O5 RIP . . . G 3 50.667 2.968 26.886 1 39.91 ? O5 RIP 1134 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           10 
#