data_8J3A
#
_model_server_result.job_id            kZqWsq310k6AsfOLwAYWQw 
_model_server_result.datetime_utc      '2024-11-20 01:19:07' 
_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          8j3a 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    8J3A 
#
_exptl.entry_id    8J3A 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              474.55 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide 
_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          106.944 
_cell.angle_gamma         90 
_cell.entry_id            8J3A 
_cell.length_a            54.872 
_cell.length_b            99.926 
_cell.length_c            58.712 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8J3A 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    'P 2yb' 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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
? 2 C N N 
? 2 D 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
covale ? covale1 A SG CYS 143 A CYS 145 1_555 C C34 V2M . A V2M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? 
covale ? covale2 B SG CYS 143 B CYS 145 1_555 D C34 V2M . B V2M 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.824 ? 
#
_chem_comp.formula           'C24 H34 N4 O6' 
_chem_comp.formula_weight    474.55 
_chem_comp.id                V2M 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              N-[(2S)-1-({(2S,3S)-3,4-dihydroxy-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'N-[(2S)-1-({(2S)-4-hydroxy-3-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}amino)-4-methyl-1-oxopentan-2-yl]-4-methoxy-1H-indole-2-carboxamide, bound form' 
#
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
O37 C36 V2M sing 358 n n 
C36 C34 V2M sing 359 n n 
O35 C34 V2M sing 360 n n 
C20 C18 V2M sing 361 n n 
C34 C24 V2M sing 362 n n 
O22 C21 V2M doub 363 n n 
C17 C18 V2M sing 364 n n 
C17 C15 V2M sing 365 n n 
C18 C19 V2M sing 366 n n 
C24 N23 V2M sing 367 n n 
C24 C26 V2M sing 368 n n 
C21 N23 V2M sing 369 n n 
C21 C15 V2M sing 370 n n 
C1 O2 V2M sing 371 n n 
C15 N14 V2M sing 372 n n 
C29 C30 V2M sing 373 n n 
C29 C27 V2M sing 374 n n 
O2 C3 V2M sing 375 n n 
N14 C12 V2M sing 376 n n 
C26 C27 V2M sing 377 n n 
C10 C11 V2M sing 378 n y 
C10 C9 V2M doub 379 n y 
C30 N31 V2M sing 380 n n 
C27 C32 V2M sing 381 n n 
C3 C11 V2M doub 382 n y 
C3 C4 V2M sing 383 n y 
C12 C9 V2M sing 384 n n 
C12 O13 V2M doub 385 n n 
C11 C7 V2M sing 386 n y 
C9 N8 V2M sing 387 n y 
C4 C5 V2M doub 388 n y 
N31 C32 V2M sing 389 n n 
C32 O33 V2M doub 390 n n 
C7 N8 V2M sing 391 n y 
C7 C6 V2M doub 392 n y 
C5 C6 V2M sing 393 n y 
C1 H1 V2M sing 394 n n 
C1 H2 V2M sing 395 n n 
C1 H3 V2M sing 396 n n 
C4 H4 V2M sing 397 n n 
C5 H5 V2M sing 398 n n 
C6 H6 V2M sing 399 n n 
N8 H7 V2M sing 400 n n 
C10 H8 V2M sing 401 n n 
N14 H9 V2M sing 402 n n 
C15 H10 V2M sing 403 n n 
C17 H11 V2M sing 404 n n 
C17 H12 V2M sing 405 n n 
C18 H13 V2M sing 406 n n 
C19 H14 V2M sing 407 n n 
C19 H15 V2M sing 408 n n 
C19 H16 V2M sing 409 n n 
C20 H17 V2M sing 410 n n 
C20 H18 V2M sing 411 n n 
C20 H19 V2M sing 412 n n 
N23 H20 V2M sing 413 n n 
C24 H21 V2M sing 414 n n 
C26 H22 V2M sing 415 n n 
C26 H23 V2M sing 416 n n 
C27 H24 V2M sing 417 n n 
C29 H25 V2M sing 418 n n 
C29 H26 V2M sing 419 n n 
C30 H27 V2M sing 420 n n 
C30 H28 V2M sing 421 n n 
N31 H29 V2M sing 422 n n 
C34 H30 V2M sing 423 n n 
O35 H31 V2M sing 424 n n 
C36 H32 V2M sing 425 n n 
C36 H33 V2M sing 426 n n 
O37 H34 V2M sing 427 n n 
#
_atom_sites.entry_id                     8J3A 
_atom_sites.fract_transf_matrix[1][1]    0.018224 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.005552 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010007 
_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]    0.017805 
_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
C 2 V2M A 1 401 401 V2M V2M . 
D 2 V2M B 1 401 401 V2M V2M . 
E 3 HOH A 1 501 36 HOH HOH . 
E 3 HOH A 2 502 72 HOH HOH . 
E 3 HOH A 3 503 18 HOH HOH . 
E 3 HOH A 4 504 29 HOH HOH . 
E 3 HOH A 5 505 70 HOH HOH . 
E 3 HOH A 6 506 55 HOH HOH . 
E 3 HOH A 7 507 6 HOH HOH . 
E 3 HOH A 8 508 34 HOH HOH . 
E 3 HOH A 9 509 41 HOH HOH . 
E 3 HOH A 10 510 57 HOH HOH . 
E 3 HOH A 11 511 27 HOH HOH . 
E 3 HOH A 12 512 28 HOH HOH . 
E 3 HOH A 13 513 74 HOH HOH . 
E 3 HOH A 14 514 43 HOH HOH . 
E 3 HOH A 15 515 60 HOH HOH . 
E 3 HOH A 16 516 2 HOH HOH . 
E 3 HOH A 17 517 32 HOH HOH . 
E 3 HOH A 18 518 17 HOH HOH . 
E 3 HOH A 19 519 30 HOH HOH . 
E 3 HOH A 20 520 7 HOH HOH . 
E 3 HOH A 21 521 53 HOH HOH . 
E 3 HOH A 22 522 24 HOH HOH . 
E 3 HOH A 23 523 16 HOH HOH . 
E 3 HOH A 24 524 69 HOH HOH . 
E 3 HOH A 25 525 54 HOH HOH . 
E 3 HOH A 26 526 50 HOH HOH . 
E 3 HOH A 27 527 42 HOH HOH . 
E 3 HOH A 28 528 68 HOH HOH . 
E 3 HOH A 29 529 1 HOH HOH . 
E 3 HOH A 30 530 3 HOH HOH . 
E 3 HOH A 31 531 39 HOH HOH . 
E 3 HOH A 32 532 35 HOH HOH . 
E 3 HOH A 33 533 62 HOH HOH . 
E 3 HOH A 34 534 13 HOH HOH . 
E 3 HOH A 35 535 63 HOH HOH . 
E 3 HOH A 36 536 33 HOH HOH . 
E 3 HOH A 37 537 9 HOH HOH . 
E 3 HOH A 38 538 40 HOH HOH . 
E 3 HOH A 39 539 71 HOH HOH . 
E 3 HOH A 40 540 64 HOH HOH . 
E 3 HOH A 41 541 56 HOH HOH . 
F 3 HOH B 1 501 51 HOH HOH . 
F 3 HOH B 2 502 38 HOH HOH . 
F 3 HOH B 3 503 23 HOH HOH . 
F 3 HOH B 4 504 10 HOH HOH . 
F 3 HOH B 5 505 12 HOH HOH . 
F 3 HOH B 6 506 8 HOH HOH . 
F 3 HOH B 7 507 48 HOH HOH . 
F 3 HOH B 8 508 58 HOH HOH . 
F 3 HOH B 9 509 25 HOH HOH . 
F 3 HOH B 10 510 49 HOH HOH . 
F 3 HOH B 11 511 5 HOH HOH . 
F 3 HOH B 12 512 67 HOH HOH . 
F 3 HOH B 13 513 15 HOH HOH . 
F 3 HOH B 14 514 52 HOH HOH . 
F 3 HOH B 15 515 26 HOH HOH . 
F 3 HOH B 16 516 21 HOH HOH . 
F 3 HOH B 17 517 4 HOH HOH . 
F 3 HOH B 18 518 47 HOH HOH . 
F 3 HOH B 19 519 59 HOH HOH . 
F 3 HOH B 20 520 31 HOH HOH . 
F 3 HOH B 21 521 20 HOH HOH . 
F 3 HOH B 22 522 46 HOH HOH . 
F 3 HOH B 23 523 45 HOH HOH . 
F 3 HOH B 24 524 73 HOH HOH . 
F 3 HOH B 25 525 61 HOH HOH . 
F 3 HOH B 26 526 19 HOH HOH . 
F 3 HOH B 27 527 37 HOH HOH . 
F 3 HOH B 28 528 11 HOH HOH . 
F 3 HOH B 29 529 44 HOH HOH . 
F 3 HOH B 30 530 14 HOH HOH . 
F 3 HOH B 31 531 66 HOH HOH . 
F 3 HOH B 32 532 22 HOH HOH . 
F 3 HOH B 33 533 65 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 V2M . . . C 2 -24.585 -10.672 -3.637 1 34.68 ? C1 V2M 401 A 1 
HETATM 2 O O2 V2M . . . C 2 -24.157 -10.4 -2.312 1 32.55 ? O2 V2M 401 A 1 
HETATM 3 C C3 V2M . . . C 2 -23.519 -9.216 -2.086 1 34.2 ? C3 V2M 401 A 1 
HETATM 4 C C4 V2M . . . C 2 -23.54 -8.16 -2.964 1 29.99 ? C4 V2M 401 A 1 
HETATM 5 C C5 V2M . . . C 2 -22.859 -6.975 -2.662 1 33.02 ? C5 V2M 401 A 1 
HETATM 6 C C6 V2M . . . C 2 -22.149 -6.817 -1.505 1 32.38 ? C6 V2M 401 A 1 
HETATM 7 C C7 V2M . . . C 2 -22.124 -7.886 -0.617 1 32.25 ? C7 V2M 401 A 1 
HETATM 8 N N8 V2M . . . C 2 -21.504 -8.02 0.592 1 30.64 ? N8 V2M 401 A 1 
HETATM 9 C C9 V2M . . . C 2 -21.768 -9.27 1.097 1 29.17 ? C9 V2M 401 A 1 
HETATM 10 C C10 V2M . . . C 2 -22.561 -9.952 0.213 1 29.43 ? C10 V2M 401 A 1 
HETATM 11 C C11 V2M . . . C 2 -22.803 -9.091 -0.888 1 30.74 ? C11 V2M 401 A 1 
HETATM 12 C C12 V2M . . . C 2 -21.198 -9.632 2.396 1 29.61 ? C12 V2M 401 A 1 
HETATM 13 O O13 V2M . . . C 2 -20.5 -8.843 3.026 1 29.52 ? O13 V2M 401 A 1 
HETATM 14 N N14 V2M . . . C 2 -21.495 -10.856 2.844 1 28.63 ? N14 V2M 401 A 1 
HETATM 15 C C15 V2M . . . C 2 -20.887 -11.39 4.049 1 26.13 ? C15 V2M 401 A 1 
HETATM 16 C C17 V2M . . . C 2 -21.528 -12.738 4.371 1 26.21 ? C17 V2M 401 A 1 
HETATM 17 C C18 V2M . . . C 2 -23.028 -12.693 4.651 1 28 ? C18 V2M 401 A 1 
HETATM 18 C C19 V2M . . . C 2 -23.629 -14.086 4.623 1 26.41 ? C19 V2M 401 A 1 
HETATM 19 C C20 V2M . . . C 2 -23.309 -12.012 5.979 1 27.31 ? C20 V2M 401 A 1 
HETATM 20 C C21 V2M . . . C 2 -19.376 -11.561 3.888 1 30.34 ? C21 V2M 401 A 1 
HETATM 21 O O22 V2M . . . C 2 -18.912 -11.977 2.835 1 29.44 ? O22 V2M 401 A 1 
HETATM 22 N N23 V2M . . . C 2 -18.61 -11.294 4.948 1 25.16 ? N23 V2M 401 A 1 
HETATM 23 C C24 V2M . . . C 2 -17.207 -11.257 5.114 1 28.82 ? C24 V2M 401 A 1 
HETATM 24 C C26 V2M . . . C 2 -16.539 -10.049 5.306 1 27.26 ? C26 V2M 401 A 1 
HETATM 25 C C27 V2M . . . C 2 -16.561 -9.103 4.117 1 31.06 ? C27 V2M 401 A 1 
HETATM 26 C C29 V2M . . . C 2 -15.8 -9.678 2.939 1 27.41 ? C29 V2M 401 A 1 
HETATM 27 C C30 V2M . . . C 2 -15.181 -8.478 2.257 1 29.1 ? C30 V2M 401 A 1 
HETATM 28 N N31 V2M . . . C 2 -15.105 -7.498 3.33 1 30.6 ? N31 V2M 401 A 1 
HETATM 29 C C32 V2M . . . C 2 -15.866 -7.78 4.363 1 29.31 ? C32 V2M 401 A 1 
HETATM 30 O O33 V2M . . . C 2 -16.044 -7.063 5.322 1 24.96 ? O33 V2M 401 A 1 
HETATM 31 C C34 V2M . . . C 2 -16.952 -12.286 6.418 1 30.97 ? C34 V2M 401 A 1 
HETATM 32 O O35 V2M . . . C 2 -15.637 -12.481 6.29 1 27.48 ? O35 V2M 401 A 1 
HETATM 33 C C36 V2M . . . C 2 -17.682 -13.328 6.083 1 28.41 ? C36 V2M 401 A 1 
HETATM 34 O O37 V2M . . . C 2 -17.846 -14.597 7.013 1 28.81 ? O37 V2M 401 A 1 
#
_model_server_stats.io_time_ms              114 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           34 
#