data_2ZFF # _model_server_result.job_id NBHXZCUcXf1jAZmoERiR3w _model_server_result.datetime_utc '2024-12-27 01:59:41' _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 2zff # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":2001}' # _entry.id 2ZFF # _exptl.entry_id 2ZFF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 351.442 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-phenylalanyl-N-benzyl-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 100.3 _cell.angle_gamma 90 _cell.entry_id 2ZFF _cell.length_a 70.1 _cell.length_b 71.5 _cell.length_c 72.5 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZFF _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 5 _struct_asym.id F _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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? covale ? covale1 C C GLU 9 I GLU 62 1_555 C N TYS 10 I TYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? # _chem_comp.formula 'C21 H25 N3 O2' _chem_comp.formula_weight 351.442 _chem_comp.id 53U _chem_comp.mon_nstd_flag . _chem_comp.name D-phenylalanyl-N-benzyl-L-prolinamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms (2S)-1-((2R)-2-amino-3-phenyl-propanoyl)-N-(phenylmethyl)pyrrolidine-2-carboxamide # 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 C1 C2 53U sing 1 n n C1 C16 53U sing 2 n n N1 C2 53U sing 3 n n C2 C3 53U sing 4 n n C3 O1 53U doub 5 n n C3 N2 53U sing 6 n n N2 C4 53U sing 7 n n N2 C7 53U sing 8 n n C4 C5 53U sing 9 n n C5 C6 53U sing 10 n n C6 C7 53U sing 11 n n C7 C8 53U sing 12 n n C8 N3 53U sing 13 n n C8 O2 53U doub 14 n n N3 C9 53U sing 15 n n C9 C10 53U sing 16 n n C10 C11 53U doub 17 n y C10 C15 53U sing 18 n y C11 C12 53U sing 19 n y C12 C13 53U doub 20 n y C13 C14 53U sing 21 n y C14 C15 53U doub 22 n y C16 C17 53U doub 23 n y C16 C21 53U sing 24 n y C17 C18 53U sing 25 n y C18 C19 53U doub 26 n y C19 C20 53U sing 27 n y C20 C21 53U doub 28 n y C1 H1 53U sing 29 n n C1 H1A 53U sing 30 n n N1 HN1 53U sing 31 n n N1 HN1A 53U sing 32 n n C2 H2 53U sing 33 n n C4 H4 53U sing 34 n n C4 H4A 53U sing 35 n n C5 H5 53U sing 36 n n C5 H5A 53U sing 37 n n C6 H6 53U sing 38 n n C6 H6A 53U sing 39 n n C7 H7 53U sing 40 n n N3 HN3 53U sing 41 n n C9 H9 53U sing 42 n n C9 H9A 53U sing 43 n n C11 H11 53U sing 44 n n C12 H12 53U sing 45 n n C13 H13 53U sing 46 n n C14 H14 53U sing 47 n n C15 H15 53U sing 48 n n C17 H17 53U sing 49 n n C18 H18 53U sing 50 n n C19 H19 53U sing 51 n n C20 H20 53U sing 52 n n C21 H21 53U sing 53 n n # _atom_sites.entry_id 2ZFF _atom_sites.fract_transf_matrix[1][1] 0.014259 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002602 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013993 _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] 0.01403 _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 D 4 NA H 1 2002 2002 NA NA . E 4 NA H 1 2003 2003 NA NA . F 5 53U H 1 2001 2001 53U 53U . G 6 HOH L 1 3015 3015 HOH HOH . G 6 HOH L 2 3019 3019 HOH HOH . G 6 HOH L 3 3020 3020 HOH HOH . G 6 HOH L 4 3021 3021 HOH HOH . G 6 HOH L 5 3031 3031 HOH HOH . G 6 HOH L 6 3046 3046 HOH HOH . G 6 HOH L 7 3053 3053 HOH HOH . G 6 HOH L 8 3055 3055 HOH HOH . G 6 HOH L 9 3059 3059 HOH HOH . G 6 HOH L 10 3063 3063 HOH HOH . G 6 HOH L 11 3075 3075 HOH HOH . G 6 HOH L 12 3077 3077 HOH HOH . G 6 HOH L 13 3090 3090 HOH HOH . G 6 HOH L 14 3106 3106 HOH HOH . G 6 HOH L 15 3117 3117 HOH HOH . G 6 HOH L 16 3120 3120 HOH HOH . G 6 HOH L 17 3121 3121 HOH HOH . G 6 HOH L 18 3122 3122 HOH HOH . G 6 HOH L 19 3137 3137 HOH HOH . G 6 HOH L 20 3150 3150 HOH HOH . G 6 HOH L 21 3155 3155 HOH HOH . G 6 HOH L 22 3158 3158 HOH HOH . G 6 HOH L 23 3159 3159 HOH HOH . H 6 HOH H 1 3001 3001 HOH HOH . H 6 HOH H 2 3002 3002 HOH HOH . H 6 HOH H 3 3003 3003 HOH HOH . H 6 HOH H 4 3004 3004 HOH HOH . H 6 HOH H 5 3005 3005 HOH HOH . H 6 HOH H 6 3006 3006 HOH HOH . H 6 HOH H 7 3007 3007 HOH HOH . H 6 HOH H 8 3008 3008 HOH HOH . H 6 HOH H 9 3009 3009 HOH HOH . H 6 HOH H 10 3010 3010 HOH HOH . H 6 HOH H 11 3011 3011 HOH HOH . H 6 HOH H 12 3012 3012 HOH HOH . H 6 HOH H 13 3013 3013 HOH HOH . H 6 HOH H 14 3014 3014 HOH HOH . H 6 HOH H 15 3016 3016 HOH HOH . H 6 HOH H 16 3017 3017 HOH HOH . H 6 HOH H 17 3018 3018 HOH HOH . H 6 HOH H 18 3022 3022 HOH HOH . H 6 HOH H 19 3023 3023 HOH HOH . H 6 HOH H 20 3024 3024 HOH HOH . H 6 HOH H 21 3025 3025 HOH HOH . H 6 HOH H 22 3026 3026 HOH HOH . H 6 HOH H 23 3027 3027 HOH HOH . H 6 HOH H 24 3028 3028 HOH HOH . H 6 HOH H 25 3029 3029 HOH HOH . H 6 HOH H 26 3030 3030 HOH HOH . H 6 HOH H 27 3032 3032 HOH HOH . H 6 HOH H 28 3033 3033 HOH HOH . H 6 HOH H 29 3034 3034 HOH HOH . H 6 HOH H 30 3035 3035 HOH HOH . H 6 HOH H 31 3036 3036 HOH HOH . H 6 HOH H 32 3037 3037 HOH HOH . H 6 HOH H 33 3038 3038 HOH HOH . H 6 HOH H 34 3039 3039 HOH HOH . H 6 HOH H 35 3040 3040 HOH HOH . H 6 HOH H 36 3041 3041 HOH HOH . H 6 HOH H 37 3042 3042 HOH HOH . H 6 HOH H 38 3043 3043 HOH HOH . H 6 HOH H 39 3044 3044 HOH HOH . H 6 HOH H 40 3045 3045 HOH HOH . H 6 HOH H 41 3047 3047 HOH HOH . H 6 HOH H 42 3048 3048 HOH HOH . H 6 HOH H 43 3049 3049 HOH HOH . H 6 HOH H 44 3050 3050 HOH HOH . H 6 HOH H 45 3051 3051 HOH HOH . H 6 HOH H 46 3052 3052 HOH HOH . H 6 HOH H 47 3054 3054 HOH HOH . H 6 HOH H 48 3056 3056 HOH HOH . H 6 HOH H 49 3057 3057 HOH HOH . H 6 HOH H 50 3058 3058 HOH HOH . H 6 HOH H 51 3060 3060 HOH HOH . H 6 HOH H 52 3061 3061 HOH HOH . H 6 HOH H 53 3062 3062 HOH HOH . H 6 HOH H 54 3064 3064 HOH HOH . H 6 HOH H 55 3065 3065 HOH HOH . H 6 HOH H 56 3066 3066 HOH HOH . H 6 HOH H 57 3067 3067 HOH HOH . H 6 HOH H 58 3068 3068 HOH HOH . H 6 HOH H 59 3069 3069 HOH HOH . H 6 HOH H 60 3070 3070 HOH HOH . H 6 HOH H 61 3071 3071 HOH HOH . H 6 HOH H 62 3072 3072 HOH HOH . H 6 HOH H 63 3073 3073 HOH HOH . H 6 HOH H 64 3074 3074 HOH HOH . H 6 HOH H 65 3076 3076 HOH HOH . H 6 HOH H 66 3078 3078 HOH HOH . H 6 HOH H 67 3079 3079 HOH HOH . H 6 HOH H 68 3080 3080 HOH HOH . H 6 HOH H 69 3081 3081 HOH HOH . H 6 HOH H 70 3082 3082 HOH HOH . H 6 HOH H 71 3083 3083 HOH HOH . H 6 HOH H 72 3084 3084 HOH HOH . H 6 HOH H 73 3085 3085 HOH HOH . H 6 HOH H 74 3086 3086 HOH HOH . H 6 HOH H 75 3087 3087 HOH HOH . H 6 HOH H 76 3088 3088 HOH HOH . H 6 HOH H 77 3089 3089 HOH HOH . H 6 HOH H 78 3091 3091 HOH HOH . H 6 HOH H 79 3092 3092 HOH HOH . H 6 HOH H 80 3093 3093 HOH HOH . H 6 HOH H 81 3094 3094 HOH HOH . H 6 HOH H 82 3095 3095 HOH HOH . H 6 HOH H 83 3096 3096 HOH HOH . H 6 HOH H 84 3097 3097 HOH HOH . H 6 HOH H 85 3098 3098 HOH HOH . H 6 HOH H 86 3099 3099 HOH HOH . H 6 HOH H 87 3100 3100 HOH HOH . H 6 HOH H 88 3101 3101 HOH HOH . H 6 HOH H 89 3102 3102 HOH HOH . H 6 HOH H 90 3103 3103 HOH HOH . H 6 HOH H 91 3104 3104 HOH HOH . H 6 HOH H 92 3105 3105 HOH HOH . H 6 HOH H 93 3107 3107 HOH HOH . H 6 HOH H 94 3108 3108 HOH HOH . H 6 HOH H 95 3109 3109 HOH HOH . H 6 HOH H 96 3110 3110 HOH HOH . H 6 HOH H 97 3111 3111 HOH HOH . H 6 HOH H 98 3112 3112 HOH HOH . H 6 HOH H 99 3113 3113 HOH HOH . H 6 HOH H 100 3114 3114 HOH HOH . H 6 HOH H 101 3115 3115 HOH HOH . H 6 HOH H 102 3116 3116 HOH HOH . H 6 HOH H 103 3118 3118 HOH HOH . H 6 HOH H 104 3119 3119 HOH HOH . H 6 HOH H 105 3123 3123 HOH HOH . H 6 HOH H 106 3124 3124 HOH HOH . H 6 HOH H 107 3125 3125 HOH HOH . H 6 HOH H 108 3126 3126 HOH HOH . H 6 HOH H 109 3127 3127 HOH HOH . H 6 HOH H 110 3128 3128 HOH HOH . H 6 HOH H 111 3129 3129 HOH HOH . H 6 HOH H 112 3131 3131 HOH HOH . H 6 HOH H 113 3132 3132 HOH HOH . H 6 HOH H 114 3133 3133 HOH HOH . H 6 HOH H 115 3134 3134 HOH HOH . H 6 HOH H 116 3136 3136 HOH HOH . H 6 HOH H 117 3138 3138 HOH HOH . H 6 HOH H 118 3139 3139 HOH HOH . H 6 HOH H 119 3140 3140 HOH HOH . H 6 HOH H 120 3141 3141 HOH HOH . H 6 HOH H 121 3142 3142 HOH HOH . H 6 HOH H 122 3143 3143 HOH HOH . H 6 HOH H 123 3144 3144 HOH HOH . H 6 HOH H 124 3145 3145 HOH HOH . H 6 HOH H 125 3146 3146 HOH HOH . H 6 HOH H 126 3147 3147 HOH HOH . H 6 HOH H 127 3148 3148 HOH HOH . H 6 HOH H 128 3149 3149 HOH HOH . H 6 HOH H 129 3152 3152 HOH HOH . H 6 HOH H 130 3154 3154 HOH HOH . H 6 HOH H 131 3157 3157 HOH HOH . H 6 HOH H 132 3160 3160 HOH HOH . H 6 HOH H 133 3161 3161 HOH HOH . H 6 HOH H 134 3162 3162 HOH HOH . I 6 HOH I 1 3130 3130 HOH HOH . I 6 HOH I 2 3151 3151 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 N1 53U . . . F 5 16.39 -15.783 23.16 1 24.74 ? N1 53U 2001 H 1 HETATM 2 C C2 53U . . . F 5 17.657 -15.012 23.146 1 24.61 ? C2 53U 2001 H 1 HETATM 3 C C3 53U . . . F 5 17.436 -13.631 22.568 1 22.98 ? C3 53U 2001 H 1 HETATM 4 O O1 53U . . . F 5 16.506 -12.945 23.032 1 21.51 ? O1 53U 2001 H 1 HETATM 5 C C1 53U . . . F 5 18.172 -14.917 24.595 1 24.52 ? C1 53U 2001 H 1 HETATM 6 C C16 53U . . . F 5 19.592 -14.371 24.744 1 25.56 ? C16 53U 2001 H 1 HETATM 7 C C17 53U . . . F 5 20.691 -14.964 24.089 1 29.02 ? C17 53U 2001 H 1 HETATM 8 C C21 53U . . . F 5 19.822 -13.249 25.551 1 25.48 ? C21 53U 2001 H 1 HETATM 9 C C18 53U . . . F 5 21.986 -14.454 24.235 1 30.34 ? C18 53U 2001 H 1 HETATM 10 C C20 53U . . . F 5 21.101 -12.741 25.697 1 24.18 ? C20 53U 2001 H 1 HETATM 11 C C19 53U . . . F 5 22.189 -13.333 25.046 1 27.23 ? C19 53U 2001 H 1 HETATM 12 N N2 53U . . . F 5 18.245 -13.171 21.589 1 23.28 ? N2 53U 2001 H 1 HETATM 13 C C7 53U . . . F 5 18.028 -11.822 21.062 1 24.94 ? C7 53U 2001 H 1 HETATM 14 C C8 53U . . . F 5 16.609 -11.729 20.528 1 22.87 ? C8 53U 2001 H 1 HETATM 15 O O2 53U . . . F 5 16.215 -12.728 19.926 1 30.89 ? O2 53U 2001 H 1 HETATM 16 C C6 53U . . . F 5 18.944 -11.895 19.803 1 27.09 ? C6 53U 2001 H 1 HETATM 17 C C5 53U . . . F 5 20.104 -12.767 20.317 1 26.58 ? C5 53U 2001 H 1 HETATM 18 C C4 53U . . . F 5 19.376 -13.939 21.023 1 25.8 ? C4 53U 2001 H 1 HETATM 19 N N3 53U . . . F 5 15.971 -10.576 20.754 1 23.31 ? N3 53U 2001 H 1 HETATM 20 C C9 53U . . . F 5 14.659 -10.43 20.113 1 24.46 ? C9 53U 2001 H 1 HETATM 21 C C10 53U . . . F 5 13.567 -10.492 21.19 1 26.13 ? C10 53U 2001 H 1 HETATM 22 C C11 53U . . . F 5 13.386 -9.397 22.037 1 27.72 ? C11 53U 2001 H 1 HETATM 23 C C12 53U . . . F 5 12.402 -9.443 23.015 1 27.55 ? C12 53U 2001 H 1 HETATM 24 C C13 53U . . . F 5 11.589 -10.567 23.164 1 29.17 ? C13 53U 2001 H 1 HETATM 25 C C14 53U . . . F 5 11.779 -11.663 22.309 1 29.81 ? C14 53U 2001 H 1 HETATM 26 C C15 53U . . . F 5 12.77 -11.613 21.327 1 32.55 ? C15 53U 2001 H 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 231 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #