data_5M9X
#
_model_server_result.job_id            ze98rLT7Y3MsDkbpk1ZaAg 
_model_server_result.datetime_utc      '2024-11-04 22:48:07' 
_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          5m9x 
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_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":601}' 
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_entry.id    5M9X 
#
_exptl.entry_id    5M9X 
_exptl.method      'X-RAY DIFFRACTION' 
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_entity.details                     ? 
_entity.formula_weight              390.384 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(~{E})-2-(4-hydroxyphenyl)ethenyl]-5-oxidanyl-phenoxy]oxane-3,4,5-triol 
_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         90 
_cell.entry_id            5M9X 
_cell.length_a            83.103 
_cell.length_b            83.103 
_cell.length_c            157.209 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M9X 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 43 21 2' 
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_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1 
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_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C20 H22 O8' 
_chem_comp.formula_weight    390.384 
_chem_comp.id                7KP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[3-[(~{E})-2-(4-hydroxyphenyl)ethenyl]-5-oxidanyl-phenoxy]oxane-3,4 ,5-triol' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'glycosylated resveratrol' 
#
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
O2 C2 7KP sing 1 n n 
C2 C1 7KP sing 2 n n 
C2 C3 7KP sing 3 n n 
O3 C3 7KP sing 4 n n 
C1 O5 7KP sing 5 n n 
C1 O1 7KP sing 6 n n 
OBA CAI 7KP sing 7 n n 
C3 C4 7KP sing 8 n n 
O5 C5 7KP sing 9 n n 
CAH CAI 7KP doub 10 n y 
CAH CAG 7KP sing 11 n y 
CAI CAJ 7KP sing 12 n y 
C4 C5 7KP sing 13 n n 
C4 O4 7KP sing 14 n n 
O1 CAG 7KP sing 15 n n 
O6 C6 7KP sing 16 n n 
CAG CAL 7KP doub 17 n y 
C5 C6 7KP sing 18 n n 
CAJ CAK 7KP doub 19 n y 
CAL CAK 7KP sing 20 n y 
CAK CAM 7KP sing 21 n n 
CAM CAN 7KP doub 22 e n 
CAN CAT 7KP sing 23 n n 
CAS CAT 7KP doub 24 n y 
CAS CAR 7KP sing 25 n y 
CAT CAO 7KP sing 26 n y 
CAR CAQ 7KP doub 27 n y 
CAO CAP 7KP doub 28 n y 
CAQ CAP 7KP sing 29 n y 
CAQ OBB 7KP sing 30 n n 
C1 H1 7KP sing 31 n n 
C2 H2 7KP sing 32 n n 
C3 H3 7KP sing 33 n n 
C4 H4 7KP sing 34 n n 
C5 H5 7KP sing 35 n n 
C6 H6 7KP sing 36 n n 
C6 H7 7KP sing 37 n n 
CAH H8 7KP sing 38 n n 
CAJ H9 7KP sing 39 n n 
CAL H10 7KP sing 40 n n 
CAM H11 7KP sing 41 n n 
CAN H13 7KP sing 42 n n 
CAO H15 7KP sing 43 n n 
CAP H16 7KP sing 44 n n 
CAR H17 7KP sing 45 n n 
CAS H18 7KP sing 46 n n 
O2 H19 7KP sing 47 n n 
O3 H20 7KP sing 48 n n 
O4 H21 7KP sing 49 n n 
O6 H22 7KP sing 50 n n 
OBA H23 7KP sing 51 n n 
OBB H24 7KP sing 52 n n 
#
_atom_sites.entry_id                     5M9X 
_atom_sites.fract_transf_matrix[1][1]    0.012033 
_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]    0.012033 
_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]    0.006361 
_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 7KP B 1 601 1 7KP RG1 . 
C 3 HOH B 1 701 30 HOH HOH . 
C 3 HOH B 2 702 22 HOH HOH . 
C 3 HOH B 3 703 25 HOH HOH . 
C 3 HOH B 4 704 11 HOH HOH . 
C 3 HOH B 5 705 5 HOH HOH . 
C 3 HOH B 6 706 3 HOH HOH . 
C 3 HOH B 7 707 31 HOH HOH . 
C 3 HOH B 8 708 20 HOH HOH . 
C 3 HOH B 9 709 24 HOH HOH . 
C 3 HOH B 10 710 2 HOH HOH . 
C 3 HOH B 11 711 8 HOH HOH . 
C 3 HOH B 12 712 1 HOH HOH . 
C 3 HOH B 13 713 12 HOH HOH . 
C 3 HOH B 14 714 23 HOH HOH . 
C 3 HOH B 15 715 13 HOH HOH . 
C 3 HOH B 16 716 26 HOH HOH . 
C 3 HOH B 17 717 18 HOH HOH . 
C 3 HOH B 18 718 9 HOH HOH . 
C 3 HOH B 19 719 29 HOH HOH . 
C 3 HOH B 20 720 7 HOH HOH . 
C 3 HOH B 21 721 6 HOH HOH . 
C 3 HOH B 22 722 10 HOH HOH . 
C 3 HOH B 23 723 4 HOH HOH . 
C 3 HOH B 24 724 17 HOH HOH . 
C 3 HOH B 25 725 14 HOH HOH . 
C 3 HOH B 26 726 21 HOH HOH . 
C 3 HOH B 27 727 19 HOH HOH . 
C 3 HOH B 28 728 15 HOH HOH . 
C 3 HOH B 29 729 27 HOH HOH . 
C 3 HOH B 30 730 35 HOH HOH . 
C 3 HOH B 31 731 32 HOH HOH . 
C 3 HOH B 32 732 34 HOH HOH . 
C 3 HOH B 33 733 28 HOH HOH . 
C 3 HOH B 34 734 16 HOH HOH . 
C 3 HOH B 35 735 33 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 7KP . . . B 2 -12.099 -22.235 -16.884 1 80.37 ? C1 7KP 601 B 1 
HETATM 2 C C2 7KP . . . B 2 -11.264 -21.134 -17.5 1 77.81 ? C2 7KP 601 B 1 
HETATM 3 C C3 7KP . . . B 2 -10.91 -20.157 -16.397 1 78.34 ? C3 7KP 601 B 1 
HETATM 4 C C4 7KP . . . B 2 -12.199 -19.613 -15.822 1 79.15 ? C4 7KP 601 B 1 
HETATM 5 C C5 7KP . . . B 2 -13.059 -20.766 -15.32 1 80.63 ? C5 7KP 601 B 1 
HETATM 6 C C6 7KP . . . B 2 -14.377 -20.223 -14.755 1 80.74 ? C6 7KP 601 B 1 
HETATM 7 C CAG 7KP . . . B 2 -11.883 -23.997 -15.42 1 80.87 ? CAG 7KP 601 B 1 
HETATM 8 C CAH 7KP . . . B 2 -12.787 -24.648 -16.252 1 80.78 ? CAH 7KP 601 B 1 
HETATM 9 C CAI 7KP . . . B 2 -13.297 -25.883 -15.88 1 81.18 ? CAI 7KP 601 B 1 
HETATM 10 C CAJ 7KP . . . B 2 -12.9 -26.465 -14.691 1 81.8 ? CAJ 7KP 601 B 1 
HETATM 11 C CAK 7KP . . . B 2 -12.003 -25.813 -13.86 1 81.37 ? CAK 7KP 601 B 1 
HETATM 12 C CAL 7KP . . . B 2 -11.483 -24.577 -14.221 1 81.43 ? CAL 7KP 601 B 1 
HETATM 13 C CAM 7KP . . . B 2 -11.65 -26.463 -12.689 1 81.57 ? CAM 7KP 601 B 1 
HETATM 14 C CAN 7KP . . . B 2 -11.401 -25.664 -11.412 1 81.27 ? CAN 7KP 601 B 1 
HETATM 15 C CAO 7KP . . . B 2 -11.02 -26.19 -9.053 1 81.02 ? CAO 7KP 601 B 1 
HETATM 16 C CAP 7KP . . . B 2 -10.708 -27.166 -8.109 1 81.02 ? CAP 7KP 601 B 1 
HETATM 17 C CAQ 7KP . . . B 2 -10.468 -28.482 -8.499 1 81.67 ? CAQ 7KP 601 B 1 
HETATM 18 C CAR 7KP . . . B 2 -10.54 -28.837 -9.837 1 82.22 ? CAR 7KP 601 B 1 
HETATM 19 C CAS 7KP . . . B 2 -10.852 -27.866 -10.774 1 82.59 ? CAS 7KP 601 B 1 
HETATM 20 C CAT 7KP . . . B 2 -11.087 -26.552 -10.393 1 80.83 ? CAT 7KP 601 B 1 
HETATM 21 O O1 7KP . . . B 2 -11.379 -22.789 -15.777 1 79.73 ? O1 7KP 601 B 1 
HETATM 22 O O2 7KP . . . B 2 -10.072 -21.692 -18.059 1 75.72 ? O2 7KP 601 B 1 
HETATM 23 O O3 7KP . . . B 2 -10.112 -19.077 -16.913 1 78.79 ? O3 7KP 601 B 1 
HETATM 24 O O4 7KP . . . B 2 -11.891 -18.744 -14.73 1 75.58 ? O4 7KP 601 B 1 
HETATM 25 O O5 7KP . . . B 2 -13.331 -21.694 -16.386 1 81.4 ? O5 7KP 601 B 1 
HETATM 26 O O6 7KP . . . B 2 -15.095 -19.512 -15.769 1 79.4 ? O6 7KP 601 B 1 
HETATM 27 O OBA 7KP . . . B 2 -14.173 -26.536 -16.681 1 80.97 ? OBA 7KP 601 B 1 
HETATM 28 O OBB 7KP . . . B 2 -10.161 -29.437 -7.582 1 81.6 ? OBB 7KP 601 B 1 
#
_model_server_stats.io_time_ms              78 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           249 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           28 
#