data_5YLJ
#
_model_server_result.job_id            w3NhKU-iUH-OHbZODxMiLA 
_model_server_result.datetime_utc      '2025-06-30 04:42:41' 
_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          5ylj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":504}' 
#
_entry.id    5YLJ 
#
_exptl.entry_id    5YLJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              350.408 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxyphenyl)prop-2-en-1-one 
_entity.pdbx_number_of_molecules    2 
_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            5YLJ 
_cell.length_a            105.231 
_cell.length_b            157.367 
_cell.length_c            182.684 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YLJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,R,S,T,U,V,W,X,Y 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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
? 11 N N N 
? 11 T 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
metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? 
metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? 
metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.013 ? 
metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? 
metalc ? metalc8 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc10 H MG MG . A MG 502 1_555 V O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc11 H MG MG . A MG 502 1_555 V O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc12 H MG MG . A MG 502 1_555 V O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc13 H MG MG . A MG 502 1_555 W O HOH . B HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? 
metalc ? metalc14 B OE1 GLN 11 B GLN 11 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.238 ? 
metalc ? metalc15 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? 
metalc ? metalc16 L MG MG . B MG 502 1_555 W O HOH . B HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? 
metalc ? metalc17 L MG MG . B MG 502 1_555 W O HOH . B HOH 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc18 L MG MG . B MG 502 1_555 W O HOH . B HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? 
metalc ? metalc19 L MG MG . B MG 502 1_555 X O HOH . C HOH 607 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc20 C OD1 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.744 ? 
metalc ? metalc21 C OD2 ASP 39 C ASP 39 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
metalc ? metalc22 C O THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.624 ? 
metalc ? metalc23 C OG1 THR 41 C THR 41 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.596 ? 
metalc ? metalc24 C O GLY 44 C GLY 44 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.427 ? 
metalc ? metalc25 C OE1 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? 
metalc ? metalc26 C OE2 GLU 55 C GLU 55 1_555 Q CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.681 ? 
metalc ? metalc27 O O1G GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? 
metalc ? metalc28 O O1B GTP . C GTP 501 1_555 P MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc29 P MG MG . C MG 502 1_555 X O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
metalc ? metalc30 P MG MG . C MG 502 1_555 X O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? 
metalc ? metalc31 P MG MG . C MG 502 1_555 X O HOH . C HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? 
metalc ? metalc32 P MG MG . C MG 502 1_555 X O HOH . C HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc33 R O1G GTP . D GTP 501 1_555 S MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? 
metalc ? metalc34 S MG MG . D MG 502 1_555 Y O HOH . D HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? 
metalc ? metalc35 S MG MG . D MG 502 1_555 Y O HOH . D HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? 
metalc ? metalc36 S MG MG . D MG 502 1_555 Y O HOH . D HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? 
#
_chem_comp.formula           'C22 H22 O4' 
_chem_comp.formula_weight    350.408 
_chem_comp.id                8X0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (E)-1-(5-methoxy-2,2-dimethyl-chromen-8-yl)-3-(4-methoxyphenyl)prop-2-en-1-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
C16 O15 8X0 sing 1 n n 
O15 C14 8X0 sing 2 n n 
C13 C14 8X0 doub 3 n y 
C13 C12 8X0 sing 4 n y 
C14 C17 8X0 sing 5 n y 
C12 C11 8X0 doub 6 n y 
C17 C18 8X0 sing 7 n n 
C17 C24 8X0 doub 8 n y 
C18 C19 8X0 doub 9 n n 
C11 C24 8X0 sing 10 n y 
C11 C9 8X0 sing 11 n n 
C24 O23 8X0 sing 12 n n 
C19 C20 8X0 sing 13 n n 
O10 C9 8X0 doub 14 n n 
C9 C8 8X0 sing 15 n n 
C22 C20 8X0 sing 16 n n 
C20 O23 8X0 sing 17 n n 
C20 C21 8X0 sing 18 n n 
C7 C8 8X0 doub 19 e n 
C7 C6 8X0 sing 20 n n 
C25 C6 8X0 doub 21 n y 
C25 C26 8X0 sing 22 n y 
C6 C5 8X0 sing 23 n y 
C26 C3 8X0 doub 24 n y 
C5 C4 8X0 doub 25 n y 
C3 C4 8X0 sing 26 n y 
C3 O2 8X0 sing 27 n n 
O2 C1 8X0 sing 28 n n 
C1 H1 8X0 sing 29 n n 
C1 H2 8X0 sing 30 n n 
C1 H3 8X0 sing 31 n n 
C4 H4 8X0 sing 32 n n 
C5 H5 8X0 sing 33 n n 
C7 H6 8X0 sing 34 n n 
C8 H7 8X0 sing 35 n n 
C12 H8 8X0 sing 36 n n 
C13 H9 8X0 sing 37 n n 
C16 H10 8X0 sing 38 n n 
C16 H11 8X0 sing 39 n n 
C16 H12 8X0 sing 40 n n 
C18 H13 8X0 sing 41 n n 
C19 H14 8X0 sing 42 n n 
C21 H15 8X0 sing 43 n n 
C21 H16 8X0 sing 44 n n 
C21 H17 8X0 sing 45 n n 
C22 H18 8X0 sing 46 n n 
C22 H19 8X0 sing 47 n n 
C22 H20 8X0 sing 48 n n 
C25 H21 8X0 sing 49 n n 
C26 H22 8X0 sing 50 n n 
#
_atom_sites.entry_id                     5YLJ 
_atom_sites.fract_transf_matrix[1][1]    0.009503 
_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]    0.006355 
_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]    0.005474 
_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
G 5 GTP A 1 501 501 GTP GTP . 
H 6 MG A 1 502 502 MG MG . 
I 7 CA A 1 503 503 CA CA . 
J 8 GOL A 1 504 601 GOL GOL . 
K 9 GDP B 1 501 501 GDP GDP . 
L 6 MG B 1 502 502 MG MG . 
M 10 MES B 1 503 505 MES MES . 
N 11 8X0 B 1 504 1 8X0 MIL . 
O 5 GTP C 1 501 501 GTP GTP . 
P 6 MG C 1 502 502 MG MG . 
Q 7 CA C 1 503 504 CA CA . 
R 5 GTP D 1 501 501 GTP GTP . 
S 6 MG D 1 502 502 MG MG . 
T 11 8X0 D 1 503 2 8X0 MIL . 
U 12 ACP F 1 401 401 ACP ACP . 
V 13 HOH A 1 601 3 HOH HOH . 
V 13 HOH A 2 602 1 HOH HOH . 
V 13 HOH A 3 603 4 HOH HOH . 
V 13 HOH A 4 604 5 HOH HOH . 
W 13 HOH B 1 601 9 HOH HOH . 
W 13 HOH B 2 602 11 HOH HOH . 
W 13 HOH B 3 603 10 HOH HOH . 
W 13 HOH B 4 604 2 HOH HOH . 
W 13 HOH B 5 605 7 HOH HOH . 
W 13 HOH B 6 606 8 HOH HOH . 
W 13 HOH B 7 607 6 HOH HOH . 
W 13 HOH B 8 608 14 HOH HOH . 
W 13 HOH B 9 609 16 HOH HOH . 
W 13 HOH B 10 610 12 HOH HOH . 
W 13 HOH B 11 611 13 HOH HOH . 
X 13 HOH C 1 601 22 HOH HOH . 
X 13 HOH C 2 602 18 HOH HOH . 
X 13 HOH C 3 603 21 HOH HOH . 
X 13 HOH C 4 604 17 HOH HOH . 
X 13 HOH C 5 605 19 HOH HOH . 
X 13 HOH C 6 606 20 HOH HOH . 
X 13 HOH C 7 607 15 HOH HOH . 
Y 13 HOH D 1 601 27 HOH HOH . 
Y 13 HOH D 2 602 23 HOH HOH . 
Y 13 HOH D 3 603 25 HOH HOH . 
Y 13 HOH D 4 604 26 HOH HOH . 
Y 13 HOH D 5 605 24 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 8X0 . . . N 11 16.399 220.69 48.443 1 82.6 ? C1 8X0 504 B 1 
HETATM 2 O O2 8X0 . . . N 11 17.06 220.181 47.321 1 78.77 ? O2 8X0 504 B 1 
HETATM 3 C C3 8X0 . . . N 11 17.387 221.08 46.281 1 77.92 ? C3 8X0 504 B 1 
HETATM 4 C C4 8X0 . . . N 11 17.885 222.351 46.525 1 76.61 ? C4 8X0 504 B 1 
HETATM 5 C C5 8X0 . . . N 11 18.217 223.242 45.411 1 75.23 ? C5 8X0 504 B 1 
HETATM 6 C C6 8X0 . . . N 11 18.049 222.775 44.102 1 75.97 ? C6 8X0 504 B 1 
HETATM 7 C C7 8X0 . . . N 11 18.378 223.664 42.833 1 75.26 ? C7 8X0 504 B 1 
HETATM 8 C C8 8X0 . . . N 11 18.842 224.994 42.845 1 78.42 ? C8 8X0 504 B 1 
HETATM 9 C C9 8X0 . . . N 11 19.057 225.69 41.474 1 80.01 ? C9 8X0 504 B 1 
HETATM 10 O O10 8X0 . . . N 11 19.887 226.608 41.362 1 82.73 ? O10 8X0 504 B 1 
HETATM 11 C C11 8X0 . . . N 11 18.26 225.251 40.286 1 81.34 ? C11 8X0 504 B 1 
HETATM 12 C C12 8X0 . . . N 11 18.89 225.081 39.034 1 81.89 ? C12 8X0 504 B 1 
HETATM 13 C C13 8X0 . . . N 11 18.138 224.654 37.907 1 80.48 ? C13 8X0 504 B 1 
HETATM 14 C C14 8X0 . . . N 11 16.757 224.388 38.029 1 82.63 ? C14 8X0 504 B 1 
HETATM 15 O O15 8X0 . . . N 11 16.031 223.952 36.894 1 84.32 ? O15 8X0 504 B 1 
HETATM 16 C C16 8X0 . . . N 11 16.179 222.553 36.651 1 85.05 ? C16 8X0 504 B 1 
HETATM 17 C C17 8X0 . . . N 11 16.094 224.55 39.32 1 83.58 ? C17 8X0 504 B 1 
HETATM 18 C C18 8X0 . . . N 11 14.65 224.287 39.503 1 83.16 ? C18 8X0 504 B 1 
HETATM 19 C C19 8X0 . . . N 11 13.948 224.881 40.651 1 85.5 ? C19 8X0 504 B 1 
HETATM 20 C C20 8X0 . . . N 11 14.757 225.609 41.75 1 86.94 ? C20 8X0 504 B 1 
HETATM 21 C C21 8X0 . . . N 11 14.165 225.475 43.123 1 87.37 ? C21 8X0 504 B 1 
HETATM 22 C C22 8X0 . . . N 11 14.813 227.129 41.627 1 87.79 ? C22 8X0 504 B 1 
HETATM 23 O O23 8X0 . . . N 11 16.176 225.148 41.767 1 85.85 ? O23 8X0 504 B 1 
HETATM 24 C C24 8X0 . . . N 11 16.838 224.975 40.405 1 83.21 ? C24 8X0 504 B 1 
HETATM 25 C C25 8X0 . . . N 11 17.532 221.46 43.851 1 77.37 ? C25 8X0 504 B 1 
HETATM 26 C C26 8X0 . . . N 11 17.21 220.613 44.922 1 77.44 ? C26 8X0 504 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           449 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           26 
#