data_3RI5
#
_model_server_result.job_id            J5h-ePnaug85NseiFtiDqw 
_model_server_result.datetime_utc      '2024-11-24 17:29:55' 
_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          3ri5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"FA","auth_seq_id":351}' 
#
_entry.id    3RI5 
#
_exptl.entry_id    3RI5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              292.284 
_entity.id                          10 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione' 
_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            3RI5 
_cell.length_a            154.843 
_cell.length_b            154.843 
_cell.length_c            573.473 
_cell.Z_PDB               40 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RI5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    pentadecameric 
_pdbx_struct_assembly.oligomeric_count      15 
_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                      10 
_struct_asym.id                             FA 
_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
disulf ? disulf1 A SG CYS 130 A CYS 130 1_555 A SG CYS 144 A CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf2 A SG CYS 191 A CYS 191 1_555 A SG CYS 202 A CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf3 B SG CYS 130 B CYS 130 1_555 B SG CYS 144 B CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf4 B SG CYS 191 B CYS 191 1_555 B SG CYS 202 B CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf5 C SG CYS 130 C CYS 130 1_555 C SG CYS 144 C CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf6 C SG CYS 191 C CYS 191 1_555 C SG CYS 202 C CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf7 D SG CYS 130 D CYS 130 1_555 D SG CYS 144 D CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf8 D SG CYS 191 D CYS 191 1_555 D SG CYS 202 D CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf9 E SG CYS 130 E CYS 130 1_555 E SG CYS 144 E CYS 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf10 E SG CYS 191 E CYS 191 1_555 E SG CYS 202 E CYS 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf11 F SG CYS 22 F CYS 22 1_555 F SG CYS 96 F CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf12 F SG CYS 149 F CYS 149 1_555 F SG CYS 204 F CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf13 G SG CYS 22 G CYS 22 1_555 G SG CYS 96 G CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf14 G SG CYS 149 G CYS 149 1_555 G SG CYS 204 G CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf15 H SG CYS 22 H CYS 22 1_555 H SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf16 H SG CYS 149 H CYS 149 1_555 H SG CYS 204 H CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf17 I SG CYS 22 I CYS 22 1_555 I SG CYS 96 I CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf18 I SG CYS 149 I CYS 149 1_555 I SG CYS 204 I CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf19 J SG CYS 22 J CYS 22 1_555 J SG CYS 96 J CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf20 J SG CYS 149 J CYS 149 1_555 J SG CYS 204 J CYS 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf21 K SG CYS 22 K CYS 22 1_555 K SG CYS 90 K CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf22 K SG CYS 137 K CYS 137 1_555 K SG CYS 196 K CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf23 L SG CYS 22 L CYS 22 1_555 L SG CYS 90 L CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf24 L SG CYS 137 L CYS 137 1_555 L SG CYS 196 L CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf25 M SG CYS 22 M CYS 22 1_555 M SG CYS 90 M CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf26 M SG CYS 137 M CYS 137 1_555 M SG CYS 196 M CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf27 N SG CYS 22 N CYS 22 1_555 N SG CYS 90 N CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf28 O SG CYS 22 O CYS 22 1_555 O SG CYS 90 O CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf29 O SG CYS 137 O CYS 137 1_555 O SG CYS 196 O CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
covale ? covale1 B ND2 ASN 185 B ASN 185 1_555 S C1 NAG . B NAG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? 
covale ? covale2 C ND2 ASN 185 C ASN 185 1_555 X C1 NAG . C NAG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.468 ? 
covale ? covale3 E ND2 ASN 185 E ASN 185 1_555 CA C1 NAG . E NAG 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.466 ? 
#
_chem_comp.formula           'C15 H16 O6' 
_chem_comp.formula_weight    292.284 
_chem_comp.id                RI5 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     PICROTOXIN 
#
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
C01 C02 RI5 sing 554 n n 
C01 H01 RI5 sing 555 n n 
C01 H01A RI5 sing 556 n n 
C01 H01B RI5 sing 557 n n 
C02 C03 RI5 doub 558 n n 
C02 C04 RI5 sing 559 n n 
C03 H03 RI5 sing 560 n n 
C03 H03A RI5 sing 561 n n 
C05 C04 RI5 sing 562 n n 
C04 C09 RI5 sing 563 n n 
C04 H04 RI5 sing 564 n n 
C06 C05 RI5 sing 565 n n 
C05 O12 RI5 sing 566 n n 
C05 H05 RI5 sing 567 n n 
C06 O19 RI5 sing 568 n n 
C06 C07 RI5 sing 569 n n 
C06 H06 RI5 sing 570 n n 
C21 C07 RI5 sing 571 n n 
C07 C15 RI5 sing 572 n n 
C07 C08 RI5 sing 573 n n 
O20 C08 RI5 sing 574 n n 
C08 C09 RI5 sing 575 n n 
C08 C13 RI5 sing 576 n n 
C09 C10 RI5 sing 577 n n 
C09 H09 RI5 sing 578 n n 
O12 C10 RI5 sing 579 n n 
C10 O11 RI5 doub 580 n n 
C14 C13 RI5 sing 581 n n 
C13 H13 RI5 sing 582 n n 
C13 H13A RI5 sing 583 n n 
C15 C14 RI5 sing 584 n n 
O16 C14 RI5 sing 585 n n 
C14 H14 RI5 sing 586 n n 
C17 C15 RI5 sing 587 n n 
C15 O16 RI5 sing 588 n n 
O19 C17 RI5 sing 589 n n 
C17 O18 RI5 doub 590 n n 
O20 HO20 RI5 sing 591 n n 
C21 H21 RI5 sing 592 n n 
C21 H21A RI5 sing 593 n n 
C21 H21B RI5 sing 594 n n 
#
_atom_sites.entry_id                     3RI5 
_atom_sites.fract_transf_matrix[1][1]    0.006458 
_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]    0.006458 
_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]    0.001744 
_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
P 4 IVM A 1 349 1 IVM IVM . 
Q 5 LMT A 1 350 1 LMT LMT . 
R 5 LMT A 1 351 1 LMT LMT . 
S 6 NAG B 1 400 400 NAG NAG . 
T 4 IVM B 1 349 1 IVM IVM . 
U 5 LMT B 1 350 1 LMT LMT . 
V 7 OCT B 1 351 1 OCT OCT . 
W 8 UND B 1 352 1 UND UND . 
X 6 NAG C 1 400 400 NAG NAG . 
Y 9 CL C 1 349 1 CL CL . 
Z 4 IVM C 1 350 1 IVM IVM . 
AA 4 IVM D 1 349 1 IVM IVM . 
BA 7 OCT D 1 350 1 OCT OCT . 
CA 6 NAG E 1 400 400 NAG NAG . 
DA 4 IVM E 1 349 1 IVM IVM . 
EA 7 OCT E 1 350 1 OCT OCT . 
FA 10 RI5 E 1 351 1 RI5 RI5 . 
#
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 C01 RI5 . . . FA 10 14.599 121.202 31.516 1 213.36 ? C01 RI5 351 E 1 
HETATM 2 C C02 RI5 . . . FA 10 14.35 121.174 32.994 1 213.36 ? C02 RI5 351 E 1 
HETATM 3 C C03 RI5 . . . FA 10 13.297 121.798 33.477 1 213.36 ? C03 RI5 351 E 1 
HETATM 4 C C04 RI5 . . . FA 10 15.326 120.487 33.906 1 213.36 ? C04 RI5 351 E 1 
HETATM 5 C C05 RI5 . . . FA 10 16.084 119.356 33.236 1 213.36 ? C05 RI5 351 E 1 
HETATM 6 C C06 RI5 . . . FA 10 15.158 118.233 32.785 1 213.36 ? C06 RI5 351 E 1 
HETATM 7 C C07 RI5 . . . FA 10 13.826 118.066 33.55 1 213.36 ? C07 RI5 351 E 1 
HETATM 8 C C08 RI5 . . . FA 10 13.594 118.895 34.801 1 213.36 ? C08 RI5 351 E 1 
HETATM 9 C C09 RI5 . . . FA 10 14.764 119.8 35.138 1 213.36 ? C09 RI5 351 E 1 
HETATM 10 C C10 RI5 . . . FA 10 15.932 118.915 35.422 1 213.36 ? C10 RI5 351 E 1 
HETATM 11 O O11 RI5 . . . FA 10 16.126 118.313 36.464 1 213.36 ? O11 RI5 351 E 1 
HETATM 12 O O12 RI5 . . . FA 10 16.853 118.828 34.307 1 213.36 ? O12 RI5 351 E 1 
HETATM 13 C C13 RI5 . . . FA 10 13.306 117.931 35.941 1 213.36 ? C13 RI5 351 E 1 
HETATM 14 C C14 RI5 . . . FA 10 13.628 116.513 35.488 1 213.36 ? C14 RI5 351 E 1 
HETATM 15 C C15 RI5 . . . FA 10 13.849 116.618 33.986 1 213.36 ? C15 RI5 351 E 1 
HETATM 16 O O16 RI5 . . . FA 10 12.713 115.956 34.538 1 213.36 ? O16 RI5 351 E 1 
HETATM 17 C C17 RI5 . . . FA 10 15.177 116.054 33.676 1 213.36 ? C17 RI5 351 E 1 
HETATM 18 O O18 RI5 . . . FA 10 15.616 114.988 34.065 1 213.36 ? O18 RI5 351 E 1 
HETATM 19 O O19 RI5 . . . FA 10 15.92 117.013 32.883 1 213.36 ? O19 RI5 351 E 1 
HETATM 20 O O20 RI5 . . . FA 10 12.405 119.666 34.622 1 213.36 ? O20 RI5 351 E 1 
HETATM 21 C C21 RI5 . . . FA 10 12.664 118.314 32.601 1 213.36 ? C21 RI5 351 E 1 
#
_model_server_stats.io_time_ms              86 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    63 
_model_server_stats.query_time_ms           342 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           21 
#