data_4X1Y # _model_server_result.job_id 3MqXs4wGGkXTjmxtvUaWCw _model_server_result.datetime_utc '2024-11-13 06:06:50' _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 4x1y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":503}' # _entry.id 4X1Y # _exptl.entry_id 4X1Y _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 717.936 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description N,2-dimethyl-L-alanyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide _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 90 _cell.angle_gamma 90 _cell.entry_id 4X1Y _cell.length_a 66.61 _cell.length_b 127.86 _cell.length_c 255.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X1Y _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 pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_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 _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 ? 8 J N N ? 8 O 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 metalc ? metalc1 A OG1 THR 145 A THR 145 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc2 F O2G GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 F O2B GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc4 K O2G GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc5 K O2B GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? # _chem_comp.formula 'C38 H63 N5 O8' _chem_comp.formula_weight 717.936 _chem_comp.id 3WV _chem_comp.mon_nstd_flag . _chem_comp.name N,2-dimethyl-L-alanyl-N-[(3R,4S,5S)-1-{(2S)-2-[(1R,2R)-3-{[(1S)-1-carboxy-2-phenylethyl]amino}-1-methoxy-2-methyl-3-oxopropyl]pyrrolidin-1-yl}-3-methoxy-5-methyl-1-oxoheptan-4-yl]-N-methyl-L-valinamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms ? # 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 C12 C13 3WV sing 1 n n C12 C10 3WV sing 2 n n O4 C11 3WV doub 3 n n C14 C13 3WV doub 4 n y C14 C15 3WV sing 5 n y O3 C11 3WV sing 6 n n C13 C18 3WV sing 7 n y C11 C10 3WV sing 8 n n C15 C16 3WV doub 9 n y C10 N2 3WV sing 10 n n C18 C17 3WV doub 11 n y C16 C17 3WV sing 12 n y N2 C8 3WV sing 13 n n C8 O2 3WV doub 14 n n C8 C6 3WV sing 15 n n C3 C4 3WV sing 16 n n C3 C2 3WV sing 17 n n C6 C7 3WV sing 18 n n C6 C5 3WV sing 19 n n C4 C1 3WV sing 20 n n C9 O1 3WV sing 21 n n C2 C5 3WV sing 22 n n C2 N1 3WV sing 23 n n C5 O1 3WV sing 24 n n C1 N1 3WV sing 25 n n N1 C27 3WV sing 26 n n O6 C27 3WV doub 27 n n C27 C26 3WV sing 28 n n C26 C20 3WV sing 29 n n C20 O5 3WV sing 30 n n C20 C19 3WV sing 31 n n C28 O5 3WV sing 32 n n C22 C21 3WV sing 33 n n C19 C21 3WV sing 34 n n C19 N3 3WV sing 35 n n C21 C23 3WV sing 36 n n C23 C24 3WV sing 37 n n C32 C31 3WV sing 38 n n N3 C25 3WV sing 39 n n N3 C29 3WV sing 40 n n C31 C30 3WV sing 41 n n C31 C33 3WV sing 42 n n C30 C29 3WV sing 43 n n C30 N4 3WV sing 44 n n C29 O7 3WV doub 45 n n O8 C35 3WV doub 46 n n N4 C35 3WV sing 47 n n C35 C34 3WV sing 48 n n N5 C34 3WV sing 49 n n N5 C38 3WV sing 50 n n C34 C36 3WV sing 51 n n C34 C37 3WV sing 52 n n C36 H1 3WV sing 53 n n C36 H2 3WV sing 54 n n C36 H3 3WV sing 55 n n C33 H4 3WV sing 56 n n C33 H5 3WV sing 57 n n C33 H6 3WV sing 58 n n C37 H7 3WV sing 59 n n C37 H8 3WV sing 60 n n C37 H9 3WV sing 61 n n C32 H10 3WV sing 62 n n C32 H11 3WV sing 63 n n C32 H12 3WV sing 64 n n C4 H13 3WV sing 65 n n C4 H14 3WV sing 66 n n N2 H15 3WV sing 67 n n C7 H16 3WV sing 68 n n C7 H17 3WV sing 69 n n C7 H18 3WV sing 70 n n C6 H19 3WV sing 71 n n C9 H20 3WV sing 72 n n C9 H21 3WV sing 73 n n C9 H22 3WV sing 74 n n C20 H23 3WV sing 75 n n C21 H24 3WV sing 76 n n N5 H25 3WV sing 77 n n C18 H27 3WV sing 78 n n C16 H28 3WV sing 79 n n C19 H29 3WV sing 80 n n C26 H30 3WV sing 81 n n C26 H31 3WV sing 82 n n C2 H32 3WV sing 83 n n C3 H33 3WV sing 84 n n C3 H34 3WV sing 85 n n C1 H35 3WV sing 86 n n C1 H36 3WV sing 87 n n C5 H37 3WV sing 88 n n C30 H38 3WV sing 89 n n N4 H39 3WV sing 90 n n C23 H40 3WV sing 91 n n C23 H41 3WV sing 92 n n C24 H42 3WV sing 93 n n C24 H43 3WV sing 94 n n C24 H44 3WV sing 95 n n C22 H45 3WV sing 96 n n C22 H46 3WV sing 97 n n C22 H47 3WV sing 98 n n C31 H48 3WV sing 99 n n C25 H49 3WV sing 100 n n C25 H50 3WV sing 101 n n C25 H51 3WV sing 102 n n C28 H52 3WV sing 103 n n C28 H53 3WV sing 104 n n C28 H54 3WV sing 105 n n C38 H55 3WV sing 106 n n C38 H56 3WV sing 107 n n C38 H57 3WV sing 108 n n C10 H58 3WV sing 109 n n C12 H59 3WV sing 110 n n C12 H60 3WV sing 111 n n C14 H61 3WV sing 112 n n C15 H62 3WV sing 113 n n C17 H63 3WV sing 114 n n O3 H64 3WV sing 115 n n # _atom_sites.entry_id 4X1Y _atom_sites.fract_transf_matrix[1][1] 0.015013 _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] 0.007822 _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] 0.003922 _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 F 4 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 GDP B 1 501 600 GDP GDP . I 7 LOC B 1 502 601 LOC 618 . J 8 3WV B 1 503 1 3WV PFE . K 4 GTP C 1 600 600 GTP GTP . L 5 MG C 1 601 601 MG MG . M 6 GDP D 1 501 600 GDP GDP . N 7 LOC D 1 502 601 LOC 618 . O 8 3WV D 1 503 1 3WV PFE . # 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 C36 3WV . . . O 8 -39.893 161.119 135.702 1 122 ? C36 3WV 503 D 1 HETATM 2 C C35 3WV . . . O 8 -37.712 160.962 134.496 1 119.77 ? C35 3WV 503 D 1 HETATM 3 C C37 3WV . . . O 8 -38.484 159.064 135.964 1 120.92 ? C37 3WV 503 D 1 HETATM 4 C C34 3WV . . . O 8 -38.939 160.157 134.991 1 121.2 ? C34 3WV 503 D 1 HETATM 5 N N5 3WV . . . O 8 -39.588 159.588 133.746 1 121.5 ? N5 3WV 503 D 1 HETATM 6 O O8 3WV . . . O 8 -36.615 160.815 135.026 1 121.33 ? O8 3WV 503 D 1 HETATM 7 C C38 3WV . . . O 8 -39.822 158.118 133.64 1 120.93 ? C38 3WV 503 D 1 HETATM 8 N N4 3WV . . . O 8 -37.944 161.823 133.492 1 116.21 ? N4 3WV 503 D 1 HETATM 9 C C30 3WV . . . O 8 -36.961 162.719 132.886 1 115.64 ? C30 3WV 503 D 1 HETATM 10 C C29 3WV . . . O 8 -35.995 161.988 131.937 1 116.4 ? C29 3WV 503 D 1 HETATM 11 O O7 3WV . . . O 8 -36.561 161.463 130.994 1 121.29 ? O7 3WV 503 D 1 HETATM 12 C C31 3WV . . . O 8 -36.46 163.954 133.681 1 114.45 ? C31 3WV 503 D 1 HETATM 13 C C33 3WV . . . O 8 -35.697 163.668 134.97 1 115.07 ? C33 3WV 503 D 1 HETATM 14 C C32 3WV . . . O 8 -35.739 164.977 132.816 1 113.24 ? C32 3WV 503 D 1 HETATM 15 N N3 3WV . . . O 8 -34.647 161.847 132.077 1 110.33 ? N3 3WV 503 D 1 HETATM 16 C C20 3WV . . . O 8 -33.577 162.059 129.692 1 98.72 ? C20 3WV 503 D 1 HETATM 17 C C21 3WV . . . O 8 -34.248 159.579 130.711 1 91.87 ? C21 3WV 503 D 1 HETATM 18 C C19 3WV . . . O 8 -33.867 161.106 130.917 1 101.92 ? C19 3WV 503 D 1 HETATM 19 C C26 3WV . . . O 8 -34.437 162.038 128.421 1 98.5 ? C26 3WV 503 D 1 HETATM 20 C C27 3WV . . . O 8 -33.58 162.256 127.192 1 102.15 ? C27 3WV 503 D 1 HETATM 21 O O5 3WV . . . O 8 -33.21 163.333 130.223 1 101.26 ? O5 3WV 503 D 1 HETATM 22 O O6 3WV . . . O 8 -32.437 161.844 127.162 1 106.29 ? O6 3WV 503 D 1 HETATM 23 C C23 3WV . . . O 8 -34.125 158.823 132.03 1 88.21 ? C23 3WV 503 D 1 HETATM 24 C C24 3WV . . . O 8 -35.414 158.701 132.786 1 88.02 ? C24 3WV 503 D 1 HETATM 25 C C22 3WV . . . O 8 -33.502 158.866 129.589 1 90.52 ? C22 3WV 503 D 1 HETATM 26 C C25 3WV . . . O 8 -33.711 162.125 133.171 1 109.03 ? C25 3WV 503 D 1 HETATM 27 C C28 3WV . . . O 8 -33.866 164.459 129.632 1 107.01 ? C28 3WV 503 D 1 HETATM 28 C C4 3WV . . . O 8 -35.383 163.713 124.435 1 104.09 ? C4 3WV 503 D 1 HETATM 29 C C7 3WV . . . O 8 -29.569 165.467 125.249 1 113.61 ? C7 3WV 503 D 1 HETATM 30 C C6 3WV . . . O 8 -30.821 164.826 124.646 1 114 ? C6 3WV 503 D 1 HETATM 31 C C9 3WV . . . O 8 -32.794 166.688 126.05 1 113.83 ? C9 3WV 503 D 1 HETATM 32 C C8 3WV . . . O 8 -30.295 163.531 123.933 1 119.03 ? C8 3WV 503 D 1 HETATM 33 N N1 3WV . . . O 8 -33.993 163.031 126.16 1 102.72 ? N1 3WV 503 D 1 HETATM 34 C C2 3WV . . . O 8 -33.048 163.534 125.156 1 105.73 ? C2 3WV 503 D 1 HETATM 35 C C3 3WV . . . O 8 -33.963 164.097 124.049 1 104.17 ? C3 3WV 503 D 1 HETATM 36 C C1 3WV . . . O 8 -35.345 163.55 125.928 1 104.14 ? C1 3WV 503 D 1 HETATM 37 C C5 3WV . . . O 8 -31.922 164.424 125.683 1 111.03 ? C5 3WV 503 D 1 HETATM 38 O O1 3WV . . . O 8 -32.306 165.452 126.604 1 112.9 ? O1 3WV 503 D 1 HETATM 39 O O2 3WV . . . O 8 -29.75 162.62 124.562 1 121.48 ? O2 3WV 503 D 1 HETATM 40 N N2 3WV . . . O 8 -30.513 163.488 122.611 1 120.34 ? N2 3WV 503 D 1 HETATM 41 C C10 3WV . . . O 8 -30.223 162.312 121.8 1 121.28 ? C10 3WV 503 D 1 HETATM 42 C C11 3WV . . . O 8 -28.757 162.197 121.396 1 125.51 ? C11 3WV 503 D 1 HETATM 43 O O4 3WV . . . O 8 -28.524 161.264 120.507 1 126.52 ? O4 3WV 503 D 1 HETATM 44 C C12 3WV . . . O 8 -31.165 162.232 120.583 1 118.28 ? C12 3WV 503 D 1 HETATM 45 C C13 3WV . . . O 8 -32.526 161.678 120.93 1 117.1 ? C13 3WV 503 D 1 HETATM 46 C C18 3WV . . . O 8 -32.664 160.395 121.445 1 116.45 ? C18 3WV 503 D 1 HETATM 47 C C14 3WV . . . O 8 -33.66 162.471 120.834 1 117.38 ? C14 3WV 503 D 1 HETATM 48 C C17 3WV . . . O 8 -33.892 159.94 121.897 1 115.68 ? C17 3WV 503 D 1 HETATM 49 C C15 3WV . . . O 8 -34.89 162.008 121.278 1 116.42 ? C15 3WV 503 D 1 HETATM 50 C C16 3WV . . . O 8 -35.001 160.749 121.822 1 116.09 ? C16 3WV 503 D 1 HETATM 51 O O3 3WV . . . O 8 -27.885 162.878 121.901 1 128.25 ? O3 3WV 503 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 51 #