data_8WMO
#
_model_server_result.job_id            D1BU5MT3TxQwfmctAJwx0Q 
_model_server_result.datetime_utc      '2024-11-01 20:40:58' 
_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          8wmo 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":504}' 
#
_entry.id    8WMO 
#
_exptl.entry_id    8WMO 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              508.543 
_entity.id                          11 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6-f][1,3]benzodioxol-8-one 
_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            8WMO 
_cell.length_a            103.82 
_cell.length_b            156.446 
_cell.length_c            179.393 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8WMO 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    'P 2ac 2ab' 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_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,Z,AA,BA,CA,DA,EA,FA 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      11 
_struct_asym.id                             N 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc2 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc3 K O1A GDP . B GDP 501 1_555 L MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc4 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.9 ? 
metalc ? metalc5 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc6 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc7 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
metalc ? metalc8 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc9 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? 
metalc ? metalc10 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc11 P O1G GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? 
metalc ? metalc12 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? 
metalc ? metalc13 W O1A GTP . D GTP 501 1_555 X MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
#
_chem_comp.formula           'C26 H24 N2 O7 S' 
_chem_comp.formula_weight    508.543 
_chem_comp.id                WIW 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (5~{S},5~{a}~{R},8~{a}~{R},9~{R})-5-pyrimidin-2-ylsulfanyl-9-(3,4,5-trimethoxyphenyl)-5~{a},6,8~{a},9-tetrahydro-5~{H}-[2]benzofuro[5,6-f][1,3]benzodioxol-8-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
C26 O5' WIW sing 572 n n 
O5' C5' WIW sing 573 n n 
C25 O4' WIW sing 574 n n 
O4' C17 WIW sing 575 n n 
C5' C17 WIW doub 576 n y 
C5' C19 WIW sing 577 n y 
C17 C16 WIW sing 578 n y 
C19 C14 WIW doub 579 n y 
O6 C6 WIW doub 580 n n 
C6 O1 WIW sing 581 n n 
C6 C5 WIW sing 582 n n 
C14 C15 WIW sing 583 n y 
C14 C7 WIW sing 584 n n 
C16 C15 WIW doub 585 n y 
C16 OP3 WIW sing 586 n n 
O1 C12 WIW sing 587 n n 
C7 C5 WIW sing 588 n n 
C7 CAB WIW sing 589 n n 
OP3 C24 WIW sing 590 n n 
C5 C9 WIW sing 591 n n 
C12 C9 WIW sing 592 n n 
C9 C10 WIW sing 593 n n 
CAB C4 WIW doub 594 n y 
CAB CAA WIW sing 595 n y 
C4 C2' WIW sing 596 n y 
C10 CAA WIW sing 597 n n 
C10 S1 WIW sing 598 n n 
CAA C1 WIW doub 599 n y 
C2' O2' WIW sing 600 n n 
C2' C3' WIW doub 601 n y 
O2' C13 WIW sing 602 n n 
S1 C20 WIW sing 603 n n 
C1 C3' WIW sing 604 n y 
C3' O3' WIW sing 605 n n 
C20 N2 WIW doub 606 n y 
C20 N9 WIW sing 607 n y 
C13 O3' WIW sing 608 n n 
N2 C2 WIW sing 609 n y 
N9 C8 WIW doub 610 n y 
C2 C22 WIW doub 611 n y 
C8 C22 WIW sing 612 n y 
C4 H1 WIW sing 613 n n 
C5 H2 WIW sing 614 n n 
C7 H3 WIW sing 615 n n 
C8 H4 WIW sing 616 n n 
C10 H5 WIW sing 617 n n 
C13 H6 WIW sing 618 n n 
C13 H7 WIW sing 619 n n 
C15 H8 WIW sing 620 n n 
C22 H9 WIW sing 621 n n 
C24 H10 WIW sing 622 n n 
C24 H11 WIW sing 623 n n 
C24 H12 WIW sing 624 n n 
C26 H13 WIW sing 625 n n 
C26 H14 WIW sing 626 n n 
C26 H15 WIW sing 627 n n 
C1 H16 WIW sing 628 n n 
C12 H17 WIW sing 629 n n 
C12 H18 WIW sing 630 n n 
C19 H19 WIW sing 631 n n 
C2 H20 WIW sing 632 n n 
C25 H21 WIW sing 633 n n 
C25 H22 WIW sing 634 n n 
C25 H23 WIW sing 635 n n 
C9 H24 WIW sing 636 n n 
#
_atom_sites.entry_id                     8WMO 
_atom_sites.fract_transf_matrix[1][1]    0.009632 
_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]    0.006392 
_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]    0.005574 
_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 EDO A 1 503 505 EDO EDO . 
J 8 PEG A 1 504 506 PEG PEG . 
K 9 GDP B 1 501 501 GDP GDP . 
L 6 MG B 1 502 502 MG MG . 
M 10 MES B 1 503 503 MES MES . 
N 11 WIW B 1 504 504 WIW B1N . 
O 7 EDO B 1 505 505 EDO EDO . 
P 5 GTP C 1 501 501 GTP GTP . 
Q 6 MG C 1 502 502 MG MG . 
R 12 CA C 1 503 503 CA CA . 
S 7 EDO C 1 504 504 EDO EDO . 
T 7 EDO C 1 505 505 EDO EDO . 
U 7 EDO C 1 506 506 EDO EDO . 
V 7 EDO C 1 507 507 EDO EDO . 
W 5 GTP D 1 501 501 GTP GTP . 
X 6 MG D 1 502 502 MG MG . 
Y 7 EDO D 1 503 503 EDO EDO . 
Z 7 EDO D 1 504 504 EDO EDO . 
AA 13 ACP F 1 401 401 ACP ACP . 
BA 14 HOH A 1 601 31 HOH HOH . 
BA 14 HOH A 2 602 30 HOH HOH . 
BA 14 HOH A 3 603 17 HOH HOH . 
BA 14 HOH A 4 604 11 HOH HOH . 
BA 14 HOH A 5 605 26 HOH HOH . 
BA 14 HOH A 6 606 27 HOH HOH . 
BA 14 HOH A 7 607 29 HOH HOH . 
CA 14 HOH B 1 601 18 HOH HOH . 
CA 14 HOH B 2 602 5 HOH HOH . 
CA 14 HOH B 3 603 1 HOH HOH . 
CA 14 HOH B 4 604 28 HOH HOH . 
CA 14 HOH B 5 605 25 HOH HOH . 
CA 14 HOH B 6 606 2 HOH HOH . 
DA 14 HOH C 1 601 12 HOH HOH . 
DA 14 HOH C 2 602 3 HOH HOH . 
DA 14 HOH C 3 603 4 HOH HOH . 
DA 14 HOH C 4 604 6 HOH HOH . 
DA 14 HOH C 5 605 24 HOH HOH . 
DA 14 HOH C 6 606 7 HOH HOH . 
EA 14 HOH D 1 601 9 HOH HOH . 
EA 14 HOH D 2 602 13 HOH HOH . 
EA 14 HOH D 3 603 22 HOH HOH . 
EA 14 HOH D 4 604 23 HOH HOH . 
EA 14 HOH D 5 605 10 HOH HOH . 
EA 14 HOH D 6 606 21 HOH HOH . 
EA 14 HOH D 7 607 16 HOH HOH . 
EA 14 HOH D 8 608 14 HOH HOH . 
EA 14 HOH D 9 609 8 HOH HOH . 
FA 14 HOH F 1 501 19 HOH HOH . 
FA 14 HOH F 2 502 15 HOH HOH . 
FA 14 HOH F 3 503 20 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 C4 WIW . . . N 11 -17.998 62.992 -43.852 0.85 57.48 ? C4 WIW 504 B 1 
HETATM 2 C C5 WIW . . . N 11 -19.4 66.353 -42.713 0.85 57.46 ? C5 WIW 504 B 1 
HETATM 3 C C6 WIW . . . N 11 -19.784 67.243 -41.592 0.85 64.78 ? C6 WIW 504 B 1 
HETATM 4 C C7 WIW . . . N 11 -18.581 65.078 -42.419 0.85 51.82 ? C7 WIW 504 B 1 
HETATM 5 C C8 WIW . . . N 11 -21.049 70.447 -48.194 0.85 64.7 ? C8 WIW 504 B 1 
HETATM 6 C C10 WIW . . . N 11 -18.501 66.75 -45.008 0.85 61.97 ? C10 WIW 504 B 1 
HETATM 7 C C13 WIW . . . N 11 -17.422 60.905 -46.839 0.85 52.07 ? C13 WIW 504 B 1 
HETATM 8 C C15 WIW . . . N 11 -17.371 65.195 -40.179 0.85 60.97 ? C15 WIW 504 B 1 
HETATM 9 C C17 WIW . . . N 11 -15.013 65.743 -39.978 0.85 49.49 ? C17 WIW 504 B 1 
HETATM 10 C C20 WIW . . . N 11 -19.963 68.765 -46.995 0.85 67.39 ? C20 WIW 504 B 1 
HETATM 11 C C22 WIW . . . N 11 -19.823 70.914 -48.669 0.85 65.19 ? C22 WIW 504 B 1 
HETATM 12 C C24 WIW . . . N 11 -16.464 66.436 -37.244 0.85 61.02 ? C24 WIW 504 B 1 
HETATM 13 C C26 WIW . . . N 11 -13.585 65.87 -43.363 0.85 51.93 ? C26 WIW 504 B 1 
HETATM 14 C C1 WIW . . . N 11 -17.938 64.517 -46.254 0.85 59.09 ? C1 WIW 504 B 1 
HETATM 15 C C12 WIW . . . N 11 -19.278 68.662 -43.302 0.85 61.84 ? C12 WIW 504 B 1 
HETATM 16 C C14 WIW . . . N 11 -17.322 65.331 -41.573 0.85 52.08 ? C14 WIW 504 B 1 
HETATM 17 C C16 WIW . . . N 11 -16.233 65.399 -39.385 0.85 60.61 ? C16 WIW 504 B 1 
HETATM 18 C C19 WIW . . . N 11 -16.072 65.666 -42.167 0.85 52.04 ? C19 WIW 504 B 1 
HETATM 19 C C2 WIW . . . N 11 -18.676 70.232 -48.246 0.85 65.66 ? C2 WIW 504 B 1 
HETATM 20 C C2' WIW . . . N 11 -17.715 62.378 -45.081 0.85 54.84 ? C2' WIW 504 B 1 
HETATM 21 C C25 WIW . . . N 11 -13.031 64.805 -39.157 0.85 60.67 ? C25 WIW 504 B 1 
HETATM 22 C C3' WIW . . . N 11 -17.686 63.132 -46.263 0.85 54.87 ? C3' WIW 504 B 1 
HETATM 23 C C5' WIW . . . N 11 -14.933 65.872 -41.37 0.85 55.15 ? C5' WIW 504 B 1 
HETATM 24 C C9 WIW . . . N 11 -18.588 67.307 -43.575 0.85 64.19 ? C9 WIW 504 B 1 
HETATM 25 C CAA WIW . . . N 11 -18.232 65.176 -45.026 0.85 59.54 ? CAA WIW 504 B 1 
HETATM 26 C CAB WIW . . . N 11 -18.267 64.391 -43.82 0.85 56.28 ? CAB WIW 504 B 1 
HETATM 27 N N2 WIW . . . N 11 -18.731 69.16 -47.415 0.85 74.83 ? N2 WIW 504 B 1 
HETATM 28 N N9 WIW . . . N 11 -21.128 69.379 -47.361 0.85 66.29 ? N9 WIW 504 B 1 
HETATM 29 O O1 WIW . . . N 11 -19.799 68.527 -41.978 0.85 69.19 ? O1 WIW 504 B 1 
HETATM 30 O O2' WIW . . . N 11 -17.429 61.046 -45.42 0.85 48.39 ? O2' WIW 504 B 1 
HETATM 31 O O3' WIW . . . N 11 -17.378 62.249 -47.313 0.85 56.67 ? O3' WIW 504 B 1 
HETATM 32 O O4' WIW . . . N 11 -13.895 65.931 -39.183 0.85 53.67 ? O4' WIW 504 B 1 
HETATM 33 O O5' WIW . . . N 11 -13.725 66.21 -41.989 0.85 56.57 ? O5' WIW 504 B 1 
HETATM 34 O O6 WIW . . . N 11 -20.057 66.874 -40.434 0.85 68.46 ? O6 WIW 504 B 1 
HETATM 35 O OP3 WIW . . . N 11 -16.387 65.248 -38.008 0.85 61.37 ? OP3 WIW 504 B 1 
HETATM 36 S S1 WIW . . . N 11 -20.067 67.332 -45.883 0.85 84.25 ? S1 WIW 504 B 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    22 
_model_server_stats.query_time_ms           289 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           36 
#