data_3CM7 # _model_server_result.job_id EneJgNDEX5IzoVyFQWXMSA _model_server_result.datetime_utc '2025-07-31 02:30:06' _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 3cm7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":600}' # _entry.id 3CM7 # _exptl.entry_id 3CM7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 492.61 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide _entity.pdbx_number_of_molecules 6 _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 3CM7 _cell.length_a 92.39 _cell.length_b 92.39 _cell.length_c 175.151 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CM7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 ? monomeric 1 author_defined_assembly 5 ? monomeric 1 author_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression C,D,I,J,K,L,M,N,Q,R 1 1 A,E,F,O 2 2 B,G,H,P 2 1 A,E,F,O 3 1 B,G,H,P 4 1 C,I,J,Q 5 1 D,K,L,M,N,R 6 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L N N ? 3 M N N ? 3 N 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 disulf ? disulf1 B SG CYS 77 A CYS 303 1_555 B SG CYS 101 A CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? disulf ? disulf2 C SG CYS 125 B CYS 351 1_555 D SG CYS 125 D CYS 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc1 E ZN ZN . C ZN 4 1_555 A SG CYS 74 C CYS 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc2 E ZN ZN . C ZN 4 1_555 A SG CYS 77 C CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc3 E ZN ZN . C ZN 4 1_555 A NE2 HIS 94 C HIS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 E ZN ZN . C ZN 4 1_555 A SG CYS 101 C CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? metalc ? metalc5 G ZN ZN . A ZN 6 1_555 B SG CYS 74 A CYS 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc6 G ZN ZN . A ZN 6 1_555 B NE2 HIS 94 A HIS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc7 I ZN ZN . B ZN 5 1_555 C SG CYS 74 B CYS 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc8 I ZN ZN . B ZN 5 1_555 C SG CYS 77 B CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc9 I ZN ZN . B ZN 5 1_555 C NE2 HIS 94 B HIS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc10 I ZN ZN . B ZN 5 1_555 C SG CYS 101 B CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc11 K ZN ZN . D ZN 3 1_555 D SG CYS 74 D CYS 300 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc12 K ZN ZN . D ZN 3 1_555 D SG CYS 77 D CYS 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.513 ? metalc ? metalc13 K ZN ZN . D ZN 3 1_555 D NE2 HIS 94 D HIS 320 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc14 K ZN ZN . D ZN 3 1_555 D SG CYS 101 D CYS 327 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? # _chem_comp.formula 'C28 H36 N4 O4' _chem_comp.formula_weight 492.61 _chem_comp.id X22 _chem_comp.mon_nstd_flag . _chem_comp.name (3S,6S,7S,9aS)-6-{[(2S)-2-aminobutanoyl]amino}-N-(diphenylmethyl)-7-(hydroxymethyl)-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2(S),3(S),6(S),7(S),9a(S) 6-(2-Amino-butyrylamino)-7-hydroxymethyl-5-oxo-octahydro-pyrrolo[1,2-a]azepine-3-carboxylic acid benzhydryl-amide' # 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 CAA CB X22 sing 376 n n CB CA X22 sing 377 n n CA N X22 sing 378 n n CA C X22 sing 379 n n C O X22 doub 380 n n C NAX X22 sing 381 n n NAX CBI X22 sing 382 n n CBI CBA X22 sing 383 n n CBI CBE X22 sing 384 n n CBA OAE X22 doub 385 n n CBA NBJ X22 sing 386 n n NBJ CBF X22 sing 387 n n NBJ CBG X22 sing 388 n n CBE CAR X22 sing 389 n n CBE CAS X22 sing 390 n n CAR OAF X22 sing 391 n n CAS CAT X22 sing 392 n n CAT CBF X22 sing 393 n n CBF CAU X22 sing 394 n n CAU CAV X22 sing 395 n n CAV CBG X22 sing 396 n n CBG CAZ X22 sing 397 n n CAZ OAD X22 doub 398 n n CAZ NAW X22 sing 399 n n NAW CBH X22 sing 400 n n CBH CBC X22 sing 401 n n CBH CBB X22 sing 402 n n CBC CAO X22 doub 403 n y CBC CAP X22 sing 404 n y CAO CAK X22 sing 405 n y CAK CAH X22 doub 406 n y CAH CAL X22 sing 407 n y CAL CAP X22 doub 408 n y CBB CAM X22 doub 409 n y CBB CAN X22 sing 410 n y CAM CAI X22 sing 411 n y CAI CAG X22 doub 412 n y CAG CAJ X22 sing 413 n y CAJ CAN X22 doub 414 n y CAA HAA X22 sing 415 n n CAA HAAA X22 sing 416 n n CAA HAAB X22 sing 417 n n CB HB X22 sing 418 n n CB HBA X22 sing 419 n n CA HA X22 sing 420 n n N HN X22 sing 421 n n N HNA X22 sing 422 n n NAX HNAX X22 sing 423 n n CBI HBI X22 sing 424 n n CBE HBE X22 sing 425 n n CAR HAR X22 sing 426 n n CAR HARA X22 sing 427 n n OAF HOAF X22 sing 428 n n CAS HAS X22 sing 429 n n CAS HASA X22 sing 430 n n CAT HAT X22 sing 431 n n CAT HATA X22 sing 432 n n CBF HBF X22 sing 433 n n CAU HAU X22 sing 434 n n CAU HAUA X22 sing 435 n n CAV HAV X22 sing 436 n n CAV HAVA X22 sing 437 n n CBG HBG X22 sing 438 n n NAW HNAW X22 sing 439 n n CBH HBH X22 sing 440 n n CAO HAO X22 sing 441 n n CAK HAK X22 sing 442 n n CAH HAH X22 sing 443 n n CAL HAL X22 sing 444 n n CAP HAP X22 sing 445 n n CAM HAM X22 sing 446 n n CAI HAI X22 sing 447 n n CAG HAG X22 sing 448 n n CAJ HAJ X22 sing 449 n n CAN HAN X22 sing 450 n n # _atom_sites.entry_id 3CM7 _atom_sites.fract_transf_matrix[1][1] 0.010824 _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] 0.010824 _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] 0.005709 _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 E 2 ZN C 1 4 4 ZN ZN . F 3 X22 C 1 600 600 X22 DRG . G 2 ZN A 1 6 6 ZN ZN . H 3 X22 A 1 600 600 X22 DRG . I 2 ZN B 1 5 5 ZN ZN . J 3 X22 B 1 600 600 X22 DRG . K 2 ZN D 1 3 3 ZN ZN . L 3 X22 D 1 700 700 X22 DRG . M 3 X22 D 1 600 600 X22 DRG . N 3 X22 D 1 701 700 X22 DRG . O 4 HOH C 1 9 9 HOH HOH . O 4 HOH C 2 18 18 HOH HOH . O 4 HOH C 3 19 19 HOH HOH . P 4 HOH A 1 14 14 HOH HOH . P 4 HOH A 2 16 16 HOH HOH . P 4 HOH A 3 17 17 HOH HOH . P 4 HOH A 4 25 25 HOH HOH . Q 4 HOH B 1 12 12 HOH HOH . Q 4 HOH B 2 13 13 HOH HOH . Q 4 HOH B 3 15 15 HOH HOH . Q 4 HOH B 4 20 20 HOH HOH . Q 4 HOH B 5 26 26 HOH HOH . Q 4 HOH B 6 27 27 HOH HOH . R 4 HOH D 1 7 7 HOH HOH . R 4 HOH D 2 8 8 HOH HOH . R 4 HOH D 3 22 22 HOH HOH . R 4 HOH D 4 24 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 CAA X22 . . . J 3 -38.557 -10.94 -42.758 1 53.4 ? CAA X22 600 B 1 HETATM 2 C CB X22 . . . J 3 -37.611 -10.165 -43.675 1 53.83 ? CB X22 600 B 1 HETATM 3 C CA X22 . . . J 3 -37.558 -8.638 -43.418 1 53.86 ? CA X22 600 B 1 HETATM 4 N N X22 . . . J 3 -37.054 -8.318 -42.073 1 53.99 ? N X22 600 B 1 HETATM 5 C C X22 . . . J 3 -38.931 -8.015 -43.583 1 53.81 ? C X22 600 B 1 HETATM 6 O O X22 . . . J 3 -39.794 -8.171 -42.721 1 53.88 ? O X22 600 B 1 HETATM 7 N NAX X22 . . . J 3 -39.111 -7.302 -44.685 1 53.79 ? NAX X22 600 B 1 HETATM 8 C CBI X22 . . . J 3 -40.431 -6.685 -44.884 1 53.76 ? CBI X22 600 B 1 HETATM 9 C CBA X22 . . . J 3 -41.323 -7.581 -45.791 1 53.33 ? CBA X22 600 B 1 HETATM 10 O OAE X22 . . . J 3 -40.813 -8.485 -46.465 1 52.48 ? OAE X22 600 B 1 HETATM 11 N NBJ X22 . . . J 3 -42.655 -7.422 -45.784 1 53.44 ? NBJ X22 600 B 1 HETATM 12 C CBE X22 . . . J 3 -40.364 -5.158 -45.154 1 53.86 ? CBE X22 600 B 1 HETATM 13 C CAR X22 . . . J 3 -39.692 -4.776 -46.484 1 54.94 ? CAR X22 600 B 1 HETATM 14 O OAF X22 . . . J 3 -38.278 -4.641 -46.264 1 55.25 ? OAF X22 600 B 1 HETATM 15 C CAS X22 . . . J 3 -41.723 -4.435 -44.927 1 53.27 ? CAS X22 600 B 1 HETATM 16 C CAT X22 . . . J 3 -42.974 -5.048 -45.59 1 52.55 ? CAT X22 600 B 1 HETATM 17 C CBF X22 . . . J 3 -43.378 -6.404 -45.005 1 52.62 ? CBF X22 600 B 1 HETATM 18 C CAU X22 . . . J 3 -44.865 -6.635 -45.263 1 52.62 ? CAU X22 600 B 1 HETATM 19 C CAV X22 . . . J 3 -44.959 -8.054 -45.818 1 53.38 ? CAV X22 600 B 1 HETATM 20 C CBG X22 . . . J 3 -43.612 -8.271 -46.538 1 54.05 ? CBG X22 600 B 1 HETATM 21 C CAZ X22 . . . J 3 -43.733 -7.962 -48.026 1 54.23 ? CAZ X22 600 B 1 HETATM 22 O OAD X22 . . . J 3 -44.622 -7.233 -48.454 1 54.27 ? OAD X22 600 B 1 HETATM 23 N NAW X22 . . . J 3 -42.839 -8.563 -48.793 1 55.01 ? NAW X22 600 B 1 HETATM 24 C CBH X22 . . . J 3 -42.866 -8.367 -50.251 1 56.14 ? CBH X22 600 B 1 HETATM 25 C CBC X22 . . . J 3 -41.741 -7.42 -50.728 1 57.51 ? CBC X22 600 B 1 HETATM 26 C CAO X22 . . . J 3 -41.24 -7.501 -52.036 1 57.87 ? CAO X22 600 B 1 HETATM 27 C CAK X22 . . . J 3 -40.235 -6.632 -52.466 1 58.03 ? CAK X22 600 B 1 HETATM 28 C CAH X22 . . . J 3 -39.732 -5.666 -51.591 1 58.05 ? CAH X22 600 B 1 HETATM 29 C CAL X22 . . . J 3 -40.232 -5.571 -50.287 1 58.42 ? CAL X22 600 B 1 HETATM 30 C CAP X22 . . . J 3 -41.237 -6.443 -49.857 1 58.06 ? CAP X22 600 B 1 HETATM 31 C CBB X22 . . . J 3 -42.829 -9.741 -50.918 1 55.14 ? CBB X22 600 B 1 HETATM 32 C CAM X22 . . . J 3 -43.926 -10.155 -51.665 1 54.96 ? CAM X22 600 B 1 HETATM 33 C CAI X22 . . . J 3 -43.907 -11.411 -52.275 1 55.51 ? CAI X22 600 B 1 HETATM 34 C CAG X22 . . . J 3 -42.798 -12.251 -52.133 1 55.49 ? CAG X22 600 B 1 HETATM 35 C CAJ X22 . . . J 3 -41.702 -11.831 -51.378 1 55.26 ? CAJ X22 600 B 1 HETATM 36 C CAN X22 . . . J 3 -41.724 -10.577 -50.769 1 55.06 ? CAN X22 600 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #