data_4NFF # _model_server_result.job_id LMFHAnmajA0AI6bg5EhMmQ _model_server_result.datetime_utc '2024-11-05 11:02:38' _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 4nff # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4NFF # _exptl.entry_id 4NFF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.986 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide _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 4NFF _cell.length_a 60.1 _cell.length_b 60.74 _cell.length_c 66.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NFF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 7 A CYS 22 1_555 A SG CYS 149 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 26 A CYS 42 1_555 A SG CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 128 A CYS 136 1_555 A SG CYS 195 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 A SG CYS 160 A CYS 168 1_555 A SG CYS 174 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? disulf ? disulf5 A SG CYS 185 A CYS 191 1_555 A SG CYS 210 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale1 A NE2 HIS 41 A HIS 57 1_555 B C3 0G6 . A 0G6 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.495 ? covale ? covale2 A OG SER 189 A SER 195 1_555 B C2 0G6 . A 0G6 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.404 ? # _chem_comp.formula 'C21 H34 Cl N6 O3 1' _chem_comp.formula_weight 453.986 _chem_comp.id 0G6 _chem_comp.mon_nstd_flag . _chem_comp.name D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms PPACK # 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 N CA 0G6 sing 1 n n N H 0G6 sing 2 n n N H2 0G6 sing 3 n n CA C 0G6 sing 4 n n CA CB 0G6 sing 5 n n CA HA 0G6 sing 6 n n C O 0G6 doub 7 n n C N1 0G6 sing 8 n n CB CG 0G6 sing 9 n n CB HB2 0G6 sing 10 n n CB HB3 0G6 sing 11 n n CG CD1 0G6 doub 12 n y CG CD2 0G6 sing 13 n y CD1 CE1 0G6 sing 14 n y CD1 HD1 0G6 sing 15 n n CD2 CE2 0G6 doub 16 n y CD2 HD2 0G6 sing 17 n n CE1 CZ 0G6 doub 18 n y CE1 HE1 0G6 sing 19 n n CE2 CZ 0G6 sing 20 n y CE2 HE2 0G6 sing 21 n n CZ HZ 0G6 sing 22 n n N1 CA1 0G6 sing 23 n n N1 CD 0G6 sing 24 n n CA1 C1 0G6 sing 25 n n CA1 CB1 0G6 sing 26 n n CA1 HA1 0G6 sing 27 n n C1 O1 0G6 doub 28 n n C1 N2 0G6 sing 29 n n CB1 CG1 0G6 sing 30 n n CB1 HB21 0G6 sing 31 n n CB1 HB31 0G6 sing 32 n n CG1 CD 0G6 sing 33 n n CG1 HG2 0G6 sing 34 n n CG1 HG3 0G6 sing 35 n n CD HD21 0G6 sing 36 n n CD HD3 0G6 sing 37 n n N2 CA2 0G6 sing 38 n n N2 H1 0G6 sing 39 n n CA2 C2 0G6 sing 40 n n CA2 CB2 0G6 sing 41 n n CA2 HA2 0G6 sing 42 n n C2 O2 0G6 sing 43 n n C2 C3 0G6 sing 44 n n CB2 CG2 0G6 sing 45 n n CB2 HB22 0G6 sing 46 n n CB2 HB32 0G6 sing 47 n n CG2 CD3 0G6 sing 48 n n CG2 HG21 0G6 sing 49 n n CG2 HG31 0G6 sing 50 n n CD3 NE 0G6 sing 51 n n CD3 HD22 0G6 sing 52 n n CD3 HD31 0G6 sing 53 n n NE CZ1 0G6 sing 54 n n NE HE 0G6 sing 55 n n CZ1 NH1 0G6 sing 56 n n CZ1 NH2 0G6 doub 57 n n NH1 HH11 0G6 sing 58 n n NH1 HH12 0G6 sing 59 n n NH2 HH21 0G6 sing 60 n n NH2 HH22 0G6 sing 61 n n C3 H11 0G6 sing 62 n n C3 H21 0G6 sing 63 n n CL C3 0G6 sing 64 n n C2 H33 0G6 sing 65 n n O2 H34 0G6 sing 66 n n # _atom_sites.entry_id 4NFF _atom_sites.fract_transf_matrix[1][1] 0.016639 _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] 0.016464 _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] 0.01497 _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 B 2 0G6 A 1 301 1 0G6 0G6 . C 3 HOH A 1 401 1 HOH HOH . C 3 HOH A 2 402 2 HOH HOH . C 3 HOH A 3 403 3 HOH HOH . C 3 HOH A 4 404 4 HOH HOH . C 3 HOH A 5 405 5 HOH HOH . C 3 HOH A 6 406 6 HOH HOH . C 3 HOH A 7 407 7 HOH HOH . C 3 HOH A 8 408 8 HOH HOH . C 3 HOH A 9 409 9 HOH HOH . C 3 HOH A 10 410 10 HOH HOH . C 3 HOH A 11 411 11 HOH HOH . C 3 HOH A 12 412 12 HOH HOH . C 3 HOH A 13 413 13 HOH HOH . C 3 HOH A 14 414 14 HOH HOH . C 3 HOH A 15 415 15 HOH HOH . C 3 HOH A 16 416 16 HOH HOH . C 3 HOH A 17 417 17 HOH HOH . C 3 HOH A 18 418 18 HOH HOH . C 3 HOH A 19 419 19 HOH HOH . C 3 HOH A 20 420 20 HOH HOH . C 3 HOH A 21 421 21 HOH HOH . C 3 HOH A 22 422 22 HOH HOH . C 3 HOH A 23 423 23 HOH HOH . C 3 HOH A 24 424 24 HOH HOH . C 3 HOH A 25 425 25 HOH HOH . C 3 HOH A 26 426 26 HOH HOH . C 3 HOH A 27 427 27 HOH HOH . C 3 HOH A 28 428 28 HOH HOH . C 3 HOH A 29 429 29 HOH HOH . C 3 HOH A 30 430 30 HOH HOH . C 3 HOH A 31 431 31 HOH HOH . C 3 HOH A 32 432 32 HOH HOH . C 3 HOH A 33 433 33 HOH HOH . C 3 HOH A 34 434 34 HOH HOH . C 3 HOH A 35 435 35 HOH HOH . C 3 HOH A 36 436 36 HOH HOH . C 3 HOH A 37 437 37 HOH HOH . C 3 HOH A 38 438 38 HOH HOH . C 3 HOH A 39 439 39 HOH HOH . C 3 HOH A 40 440 40 HOH HOH . C 3 HOH A 41 441 41 HOH HOH . C 3 HOH A 42 442 42 HOH HOH . C 3 HOH A 43 443 43 HOH HOH . C 3 HOH A 44 444 44 HOH HOH . C 3 HOH A 45 445 45 HOH HOH . C 3 HOH A 46 446 46 HOH HOH . C 3 HOH A 47 447 47 HOH HOH . C 3 HOH A 48 448 48 HOH HOH . C 3 HOH A 49 449 49 HOH HOH . C 3 HOH A 50 450 50 HOH HOH . C 3 HOH A 51 451 51 HOH HOH . C 3 HOH A 52 452 52 HOH HOH . C 3 HOH A 53 453 53 HOH HOH . C 3 HOH A 54 454 54 HOH HOH . C 3 HOH A 55 455 55 HOH HOH . C 3 HOH A 56 456 56 HOH HOH . C 3 HOH A 57 457 57 HOH HOH . C 3 HOH A 58 458 58 HOH HOH . C 3 HOH A 59 459 59 HOH HOH . C 3 HOH A 60 460 60 HOH HOH . C 3 HOH A 61 461 61 HOH HOH . C 3 HOH A 62 462 62 HOH HOH . C 3 HOH A 63 463 63 HOH HOH . C 3 HOH A 64 464 64 HOH HOH . C 3 HOH A 65 465 65 HOH HOH . C 3 HOH A 66 466 66 HOH HOH . C 3 HOH A 67 467 67 HOH HOH . C 3 HOH A 68 468 68 HOH HOH . C 3 HOH A 69 469 69 HOH HOH . C 3 HOH A 70 470 70 HOH HOH . C 3 HOH A 71 471 71 HOH HOH . C 3 HOH A 72 472 72 HOH HOH . C 3 HOH A 73 473 73 HOH HOH . C 3 HOH A 74 474 74 HOH HOH . C 3 HOH A 75 475 75 HOH HOH . C 3 HOH A 76 476 76 HOH HOH . C 3 HOH A 77 477 77 HOH HOH . C 3 HOH A 78 478 78 HOH HOH . C 3 HOH A 79 479 79 HOH HOH . C 3 HOH A 80 480 80 HOH HOH . C 3 HOH A 81 481 81 HOH HOH . C 3 HOH A 82 482 82 HOH HOH . C 3 HOH A 83 483 83 HOH HOH . C 3 HOH A 84 484 84 HOH HOH . C 3 HOH A 85 485 85 HOH HOH . C 3 HOH A 86 486 86 HOH HOH . C 3 HOH A 87 487 87 HOH HOH . C 3 HOH A 88 488 88 HOH HOH . C 3 HOH A 89 489 89 HOH HOH . C 3 HOH A 90 490 90 HOH HOH . C 3 HOH A 91 491 91 HOH HOH . C 3 HOH A 92 492 92 HOH HOH . C 3 HOH A 93 493 93 HOH HOH . C 3 HOH A 94 494 94 HOH HOH . C 3 HOH A 95 495 95 HOH HOH . C 3 HOH A 96 496 96 HOH HOH . C 3 HOH A 97 497 97 HOH HOH . C 3 HOH A 98 498 98 HOH HOH . C 3 HOH A 99 499 99 HOH HOH . C 3 HOH A 100 500 100 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 N N 0G6 . . . B 2 -3.171 19.613 17.542 1 14.27 ? N 0G6 301 A 1 HETATM 2 C CA 0G6 . . . B 2 -4.304 19.541 16.626 1 14.79 ? CA 0G6 301 A 1 HETATM 3 C C 0G6 . . . B 2 -3.818 20.013 15.266 1 13.69 ? C 0G6 301 A 1 HETATM 4 O O 0G6 . . . B 2 -2.654 19.763 14.953 1 12.89 ? O 0G6 301 A 1 HETATM 5 C CB 0G6 . . . B 2 -4.712 18.053 16.654 1 18.52 ? CB 0G6 301 A 1 HETATM 6 C CG 0G6 . . . B 2 -5.973 17.754 15.888 1 23.93 ? CG 0G6 301 A 1 HETATM 7 C CD1 0G6 . . . B 2 -5.913 16.838 14.821 1 26.88 ? CD1 0G6 301 A 1 HETATM 8 C CD2 0G6 . . . B 2 -7.204 18.355 16.239 1 26.64 ? CD2 0G6 301 A 1 HETATM 9 C CE1 0G6 . . . B 2 -7.06 16.546 14.076 1 29.23 ? CE1 0G6 301 A 1 HETATM 10 C CE2 0G6 . . . B 2 -8.356 18.059 15.499 1 30.14 ? CE2 0G6 301 A 1 HETATM 11 C CZ 0G6 . . . B 2 -8.275 17.164 14.419 1 30.35 ? CZ 0G6 301 A 1 HETATM 12 N N1 0G6 . . . B 2 -4.622 20.699 14.419 1 12.92 ? N1 0G6 301 A 1 HETATM 13 C CA1 0G6 . . . B 2 -4.163 21.03 13.065 1 12.2 ? CA1 0G6 301 A 1 HETATM 14 C C1 0G6 . . . B 2 -3.003 21.99 13.1 1 11.16 ? C1 0G6 301 A 1 HETATM 15 O O1 0G6 . . . B 2 -2.874 22.777 14.029 1 10.19 ? O1 0G6 301 A 1 HETATM 16 C CB1 0G6 . . . B 2 -5.412 21.611 12.364 1 13.65 ? CB1 0G6 301 A 1 HETATM 17 C CG1 0G6 . . . B 2 -6.576 21.141 13.222 1 14.89 ? CG1 0G6 301 A 1 HETATM 18 C CD 0G6 . . . B 2 -5.982 21.209 14.643 1 13.69 ? CD 0G6 301 A 1 HETATM 19 N N2 0G6 . . . B 2 -2.101 21.903 12.113 1 10.36 ? N2 0G6 301 A 1 HETATM 20 C CA2 0G6 . . . B 2 -0.968 22.803 12.033 1 9.54 ? CA2 0G6 301 A 1 HETATM 21 C C2 0G6 . . . B 2 -1.051 23.57 10.7 1 9.78 ? C2 0G6 301 A 1 HETATM 22 O O2 0G6 . . . B 2 -0.095 24.636 10.816 1 9.08 ? O2 0G6 301 A 1 HETATM 23 C CB2 0G6 . . . B 2 0.35 21.977 12.12 1 9.18 ? CB2 0G6 301 A 1 HETATM 24 C CG2 0G6 . . . B 2 0.626 21.562 13.574 1 8.97 ? CG2 0G6 301 A 1 HETATM 25 C CD3 0G6 . . . B 2 1.667 20.428 13.59 1 8.42 ? CD3 0G6 301 A 1 HETATM 26 N NE 0G6 . . . B 2 2.04 20.035 14.953 1 8.11 ? NE 0G6 301 A 1 HETATM 27 C CZ1 0G6 . . . B 2 2.924 19.02 15.129 1 7.83 ? CZ1 0G6 301 A 1 HETATM 28 N NH1 0G6 . . . B 2 3.472 18.4 14.069 1 7.25 ? NH1 0G6 301 A 1 HETATM 29 N NH2 0G6 . . . B 2 3.239 18.669 16.369 1 7.57 ? NH2 0G6 301 A 1 HETATM 30 C C3 0G6 . . . B 2 -2.374 24.276 10.358 1 11.33 ? C3 0G6 301 A 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 218 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #