data_6VYA
#
_model_server_result.job_id            HOvv5wEyHBj9C9Bfu5fsJQ 
_model_server_result.datetime_utc      '2024-11-26 01:17:55' 
_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          6vya 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"EB","auth_seq_id":501}' 
#
_entry.id    6VYA 
#
_exptl.entry_id    6VYA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              283.325 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione 
_entity.pdbx_number_of_molecules    24 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         78.255 
_cell.angle_beta          65.051 
_cell.angle_gamma         66.396 
_cell.entry_id            6VYA 
_cell.length_a            157.893 
_cell.length_b            163.069 
_cell.length_c            167.857 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6VYA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_defined_assembly 2 
? tetrameric 4 author_defined_assembly 3 
? tetrameric 4 author_defined_assembly 4 
? tetrameric 4 author_defined_assembly 5 
? tetrameric 4 author_defined_assembly 6 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,D,E,Y,Z,AA,BA,EA,FA,GA,HA 1 1 
C,V,W,X,CA,DA,OB,PB,QB,RB,SB,TB 2 1 
F,G,H,I,IA,JA,KA,LA,MA,NA,OA,PA 3 1 
J,K,L,M,QA,RA,SA,TA,UA,VA,WA,XA 4 1 
N,O,P,Q,YA,ZA,AB,BB,CB,DB,EB,FB 5 1 
R,S,T,U,GB,HB,IB,JB,KB,LB,MB,NB 6 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
? 2 Y N N 
? 2 AA N N 
? 2 CA N N 
? 2 EA N N 
? 2 GA N N 
? 2 IA N N 
? 2 KA N N 
? 2 MA N N 
? 2 OA N N 
? 2 QA N N 
? 2 SA N N 
? 2 UA N N 
? 2 WA N N 
? 2 YA N N 
? 2 AB N N 
? 2 CB N N 
? 2 EB N N 
? 2 GB N N 
? 2 IB N N 
? 2 KB N N 
? 2 MB N N 
? 2 OB N N 
? 2 QB N N 
? 2 SB N N 
#
_chem_comp.formula           'C16 H17 N3 O2' 
_chem_comp.formula_weight    283.325 
_chem_comp.id                QRP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (3S,8aS)-3-(1H-indol-3-ylmethyl)hexahydropyrrolo[1,2-a]pyrazine-1,4-dione 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Brevianamide F;cyclo-L-Trp-L-Pro' 
#
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
O C QRP doub 300 n n 
C CA QRP sing 301 n n 
C NAU QRP sing 302 n n 
CA N QRP sing 303 n n 
N CAN QRP sing 304 n n 
N HN QRP sing 305 n n 
CB CA QRP sing 306 n n 
CA HA QRP sing 307 n n 
CB CG QRP sing 308 n n 
CB HB QRP sing 309 n n 
CB HBA QRP sing 310 n n 
CD2 CG QRP sing 311 n y 
CG CD1 QRP doub 312 n y 
CAN OAA QRP doub 313 n n 
CAJ CAH QRP sing 314 n n 
CAH CAI QRP sing 315 n n 
CAH HAH QRP sing 316 n n 
CAH HAHA QRP sing 317 n n 
CAT CAI QRP sing 318 n n 
CAI HAI QRP sing 319 n n 
CAI HAIA QRP sing 320 n n 
NAU CAJ QRP sing 321 n n 
CAJ HAJ QRP sing 322 n n 
CAJ HAJA QRP sing 323 n n 
CAT CAN QRP sing 324 n n 
NAU CAT QRP sing 325 n n 
CAT HAT QRP sing 326 n n 
NE1 CD1 QRP sing 327 n y 
CD1 HD1 QRP sing 328 n n 
CE3 CD2 QRP doub 329 n y 
CD2 CE2 QRP sing 330 n y 
CE2 NE1 QRP sing 331 n y 
CZ2 CE2 QRP doub 332 n y 
CZ3 CE3 QRP sing 333 n y 
CE3 HE3 QRP sing 334 n n 
CZ3 CH2 QRP doub 335 n y 
CH2 CZ2 QRP sing 336 n y 
CH2 HH2 QRP sing 337 n n 
CZ2 HZ2 QRP sing 338 n n 
CZ3 HZ3 QRP sing 339 n n 
NE1 HNE1 QRP sing 340 n n 
#
_atom_sites.entry_id                     6VYA 
_atom_sites.fract_transf_matrix[1][1]    0.006333 
_atom_sites.fract_transf_matrix[1][2]    -0.002768 
_atom_sites.fract_transf_matrix[1][3]    -0.002833 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006692 
_atom_sites.fract_transf_matrix[2][3]    -0.000279 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.006576 
_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
Y 2 QRP C 1 501 501 QRP QRP . 
Z 3 DST C 1 502 601 DST DST . 
AA 2 QRP A 1 501 501 QRP QRP . 
BA 3 DST A 1 502 601 DST DST . 
CA 2 QRP V 1 501 501 QRP QRP . 
DA 3 DST V 1 502 601 DST DST . 
EA 2 QRP E 1 501 501 QRP QRP . 
FA 3 DST E 1 502 601 DST DST . 
GA 2 QRP G 1 501 501 QRP QRP . 
HA 3 DST G 1 502 601 DST DST . 
IA 2 QRP B 1 501 501 QRP QRP . 
JA 3 DST B 1 502 601 DST DST . 
KA 2 QRP D 1 501 501 QRP QRP . 
LA 3 DST D 1 502 601 DST DST . 
MA 2 QRP F 1 501 501 QRP QRP . 
NA 3 DST F 1 502 601 DST DST . 
OA 2 QRP H 1 501 501 QRP QRP . 
PA 3 DST H 1 502 601 DST DST . 
QA 2 QRP I 1 501 501 QRP QRP . 
RA 3 DST I 1 502 601 DST DST . 
SA 2 QRP J 1 501 501 QRP QRP . 
TA 3 DST J 1 502 601 DST DST . 
UA 2 QRP K 1 501 501 QRP QRP . 
VA 3 DST K 1 502 601 DST DST . 
WA 2 QRP L 1 501 501 QRP QRP . 
XA 3 DST L 1 502 601 DST DST . 
YA 2 QRP M 1 501 501 QRP QRP . 
ZA 3 DST M 1 502 601 DST DST . 
AB 2 QRP N 1 501 501 QRP QRP . 
BB 3 DST N 1 502 601 DST DST . 
CB 2 QRP O 1 501 501 QRP QRP . 
DB 3 DST O 1 502 601 DST DST . 
EB 2 QRP P 1 501 501 QRP QRP . 
FB 3 DST P 1 502 601 DST DST . 
GB 2 QRP Q 1 501 501 QRP QRP . 
HB 3 DST Q 1 502 601 DST DST . 
IB 2 QRP R 1 501 501 QRP QRP . 
JB 3 DST R 1 502 601 DST DST . 
KB 2 QRP S 1 501 501 QRP QRP . 
LB 3 DST S 1 502 601 DST DST . 
MB 2 QRP T 1 501 501 QRP QRP . 
NB 3 DST T 1 502 601 DST DST . 
OB 2 QRP U 1 501 501 QRP QRP . 
PB 3 DST U 1 502 601 DST DST . 
QB 2 QRP W 1 501 501 QRP QRP . 
RB 3 DST W 1 502 601 DST DST . 
SB 2 QRP X 1 501 501 QRP QRP . 
TB 3 DST X 1 502 601 DST DST . 
#
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 C QRP . . . EB 2 23.037 98.008 42.988 1 99.25 ? C QRP 501 P 1 
HETATM 2 N N QRP . . . EB 2 21.155 98.365 41.454 1 100.68 ? N QRP 501 P 1 
HETATM 3 O O QRP . . . EB 2 23.922 98.493 43.624 1 105.11 ? O QRP 501 P 1 
HETATM 4 C CA QRP . . . EB 2 22.619 98.527 41.615 1 102.94 ? CA QRP 501 P 1 
HETATM 5 C CB QRP . . . EB 2 23.01 99.992 41.436 1 110.76 ? CB QRP 501 P 1 
HETATM 6 C CG QRP . . . EB 2 24.234 100.125 40.524 1 113.79 ? CG QRP 501 P 1 
HETATM 7 O OAA QRP . . . EB 2 19.216 97.207 41.987 1 99.53 ? OAA QRP 501 P 1 
HETATM 8 C CAH QRP . . . EB 2 21.439 95.193 45.008 1 118.41 ? CAH QRP 501 P 1 
HETATM 9 C CAI QRP . . . EB 2 20.388 95.495 43.928 1 110.85 ? CAI QRP 501 P 1 
HETATM 10 C CAJ QRP . . . EB 2 22.563 96.308 44.904 1 113.08 ? CAJ QRP 501 P 1 
HETATM 11 C CAN QRP . . . EB 2 20.393 97.285 42.106 1 98.77 ? CAN QRP 501 P 1 
HETATM 12 C CAT QRP . . . EB 2 21.176 96.221 42.895 1 111.84 ? CAT QRP 501 P 1 
HETATM 13 N NAU QRP . . . EB 2 22.301 96.902 43.552 1 100.79 ? NAU QRP 501 P 1 
HETATM 14 C CD1 QRP . . . EB 2 24.273 100.712 39.266 1 117.98 ? CD1 QRP 501 P 1 
HETATM 15 C CD2 QRP . . . EB 2 25.627 99.771 40.828 1 101.92 ? CD2 QRP 501 P 1 
HETATM 16 N NE1 QRP . . . EB 2 25.446 100.646 38.926 1 112.91 ? NE1 QRP 501 P 1 
HETATM 17 C CE2 QRP . . . EB 2 26.324 100.162 39.67 1 110.88 ? CE2 QRP 501 P 1 
HETATM 18 C CE3 QRP . . . EB 2 26.318 99.193 41.869 1 87.46 ? CE3 QRP 501 P 1 
HETATM 19 C CH2 QRP . . . EB 2 28.402 99.403 40.599 1 97.76 ? CH2 QRP 501 P 1 
HETATM 20 C CZ2 QRP . . . EB 2 27.679 99.986 39.557 1 109.39 ? CZ2 QRP 501 P 1 
HETATM 21 C CZ3 QRP . . . EB 2 27.705 99.005 41.759 1 91.83 ? CZ3 QRP 501 P 1 
HETATM 22 H HN QRP . . . EB 2 20.662 99.017 40.877 1 120.58 ? HN QRP 501 P 1 
HETATM 23 H HA QRP . . . EB 2 23.134 97.953 40.855 1 123.29 ? HA QRP 501 P 1 
HETATM 24 H HB QRP . . . EB 2 23.243 100.418 42.407 1 132.68 ? HB QRP 501 P 1 
HETATM 25 H HBA QRP . . . EB 2 22.178 100.531 40.995 1 132.68 ? HBA QRP 501 P 1 
HETATM 26 H HAH QRP . . . EB 2 20.948 95.344 45.962 1 141.85 ? HAH QRP 501 P 1 
HETATM 27 H HAHA QRP . . . EB 2 21.91 94.259 44.723 1 141.85 ? HAHA QRP 501 P 1 
HETATM 28 H HAI QRP . . . EB 2 19.974 94.577 43.524 1 132.78 ? HAI QRP 501 P 1 
HETATM 29 H HAIA QRP . . . EB 2 19.597 96.124 44.324 1 132.78 ? HAIA QRP 501 P 1 
HETATM 30 H HAJ QRP . . . EB 2 23.553 95.866 44.948 1 135.45 ? HAJ QRP 501 P 1 
HETATM 31 H HAJA QRP . . . EB 2 22.444 97.052 45.684 1 135.45 ? HAJA QRP 501 P 1 
HETATM 32 H HAT QRP . . . EB 2 21.486 95.465 42.184 1 133.96 ? HAT QRP 501 P 1 
HETATM 33 H HD1 QRP . . . EB 2 23.447 101.135 38.708 1 141.33 ? HD1 QRP 501 P 1 
HETATM 34 H HE3 QRP . . . EB 2 25.796 98.884 42.766 1 104.71 ? HE3 QRP 501 P 1 
HETATM 35 H HH2 QRP . . . EB 2 29.472 99.26 40.52 1 117.07 ? HH2 QRP 501 P 1 
HETATM 36 H HZ2 QRP . . . EB 2 28.191 100.301 38.655 1 131.03 ? HZ2 QRP 501 P 1 
HETATM 37 H HZ3 QRP . . . EB 2 28.247 98.547 42.577 1 109.95 ? HZ3 QRP 501 P 1 
HETATM 38 H HNE1 QRP . . . EB 2 25.632 100.637 37.939 1 135.25 ? HNE1 QRP 501 P 1 
#
_model_server_stats.io_time_ms              81 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    376 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           38 
#