data_2HBM # _model_server_result.job_id c-VU-GoHD8bHqd7xJN6xrQ _model_server_result.datetime_utc '2024-12-12 02:15:33' _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 2hbm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":3001}' # _entry.id 2HBM # _exptl.entry_id 2HBM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 120 _cell.entry_id 2HBM _cell.length_a 110.577 _cell.length_b 110.577 _cell.length_c 79.33 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2HBM _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,D,E _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 4 _struct_asym.id D _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 metalc ? metalc1 A OD1 ASP 112 A ASP 238 1_555 C MN MN . A MN 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc2 A OE2 GLU 114 A GLU 240 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc3 A OD2 ASP 239 A ASP 365 1_555 B ZN ZN . A ZN 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc4 B ZN ZN . A ZN 1001 1_555 D O2P U5P . A U5P 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc5 B ZN ZN . A ZN 1001 1_555 E O HOH . A HOH 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc6 C MN MN . A MN 1002 1_555 D O1P U5P . A U5P 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.137 ? metalc ? metalc7 C MN MN . A MN 1002 1_555 E O HOH . A HOH 3004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc8 C MN MN . A MN 1002 1_555 E O HOH . A HOH 3005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc9 C MN MN . A MN 1002 1_555 E O HOH . A HOH 3006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.71 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _chem_comp.type non-polymer _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 N1 C2 U5P sing 358 n n N1 C6 U5P sing 359 n n N1 C1' U5P sing 360 n n C2 N3 U5P sing 361 n n C2 O2 U5P doub 362 n n N3 C4 U5P sing 363 n n N3 HN3 U5P sing 364 n n C4 C5 U5P sing 365 n n C4 O4 U5P doub 366 n n C5 C6 U5P doub 367 n n C5 H5 U5P sing 368 n n C6 H6 U5P sing 369 n n C1' C2' U5P sing 370 n n C1' O4' U5P sing 371 n n C1' H1' U5P sing 372 n n C2' O2' U5P sing 373 n n C2' C3' U5P sing 374 n n C2' H2' U5P sing 375 n n O2' HO2' U5P sing 376 n n C3' C4' U5P sing 377 n n C3' O3' U5P sing 378 n n C3' H3' U5P sing 379 n n C4' O4' U5P sing 380 n n C4' C5' U5P sing 381 n n C4' H4' U5P sing 382 n n O3' HO3' U5P sing 383 n n C5' O5' U5P sing 384 n n C5' "H5'1" U5P sing 385 n n C5' "H5'2" U5P sing 386 n n O5' P U5P sing 387 n n P O1P U5P doub 388 n n P O2P U5P sing 389 n n P O3P U5P sing 390 n n O2P HOP2 U5P sing 391 n n O3P HOP3 U5P sing 392 n n # _atom_sites.entry_id 2HBM _atom_sites.fract_transf_matrix[1][1] 0.009043 _atom_sites.fract_transf_matrix[1][2] 0.005221 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010443 _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] 0.012606 _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 ZN A 1 1001 1001 ZN ZN2 . C 3 MN A 1 1002 1002 MN MN . D 4 U5P A 1 3001 1 U5P U . E 5 HOH A 1 3002 1 HOH WAT . E 5 HOH A 2 3003 2 HOH WAT . E 5 HOH A 3 3004 3 HOH WAT . E 5 HOH A 4 3005 4 HOH WAT . E 5 HOH A 5 3006 5 HOH WAT . E 5 HOH A 6 3007 6 HOH WAT . E 5 HOH A 7 3008 7 HOH WAT . E 5 HOH A 8 3009 8 HOH WAT . E 5 HOH A 9 3010 9 HOH WAT . E 5 HOH A 10 3011 10 HOH WAT . E 5 HOH A 11 3012 11 HOH WAT . E 5 HOH A 12 3013 12 HOH WAT . E 5 HOH A 13 3014 13 HOH WAT . E 5 HOH A 14 3015 14 HOH WAT . E 5 HOH A 15 3016 15 HOH WAT . E 5 HOH A 16 3017 16 HOH WAT . E 5 HOH A 17 3018 17 HOH WAT . E 5 HOH A 18 3019 18 HOH WAT . E 5 HOH A 19 3020 19 HOH WAT . E 5 HOH A 20 3021 20 HOH WAT . E 5 HOH A 21 3022 21 HOH WAT . E 5 HOH A 22 3023 22 HOH WAT . E 5 HOH A 23 3024 23 HOH WAT . E 5 HOH A 24 3025 24 HOH WAT . E 5 HOH A 25 3026 25 HOH WAT . E 5 HOH A 26 3027 26 HOH WAT . E 5 HOH A 27 3028 27 HOH WAT . E 5 HOH A 28 3029 28 HOH WAT . E 5 HOH A 29 3030 29 HOH WAT . E 5 HOH A 30 3031 30 HOH WAT . E 5 HOH A 31 3032 31 HOH WAT . E 5 HOH A 32 3033 32 HOH WAT . E 5 HOH A 33 3034 33 HOH WAT . E 5 HOH A 34 3035 34 HOH WAT . E 5 HOH A 35 3036 35 HOH WAT . E 5 HOH A 36 3037 36 HOH WAT . E 5 HOH A 37 3038 37 HOH WAT . E 5 HOH A 38 3039 38 HOH WAT . E 5 HOH A 39 3040 39 HOH WAT . E 5 HOH A 40 3041 40 HOH WAT . E 5 HOH A 41 3042 41 HOH WAT . E 5 HOH A 42 3043 42 HOH WAT . E 5 HOH A 43 3044 43 HOH WAT . E 5 HOH A 44 3045 44 HOH WAT . E 5 HOH A 45 3046 45 HOH WAT . E 5 HOH A 46 3047 46 HOH WAT . E 5 HOH A 47 3048 47 HOH WAT . E 5 HOH A 48 3049 48 HOH WAT . E 5 HOH A 49 3050 49 HOH WAT . E 5 HOH A 50 3051 50 HOH WAT . E 5 HOH A 51 3052 51 HOH WAT . E 5 HOH A 52 3053 52 HOH WAT . E 5 HOH A 53 3054 53 HOH WAT . E 5 HOH A 54 3055 54 HOH WAT . E 5 HOH A 55 3056 55 HOH WAT . E 5 HOH A 56 3057 56 HOH WAT . E 5 HOH A 57 3058 57 HOH WAT . E 5 HOH A 58 3059 58 HOH WAT . E 5 HOH A 59 3060 59 HOH WAT . E 5 HOH A 60 3061 60 HOH WAT . E 5 HOH A 61 3062 61 HOH WAT . E 5 HOH A 62 3063 62 HOH WAT . E 5 HOH A 63 3064 63 HOH WAT . E 5 HOH A 64 3065 64 HOH WAT . E 5 HOH A 65 3066 65 HOH WAT . E 5 HOH A 66 3067 66 HOH WAT . E 5 HOH A 67 3068 67 HOH WAT . E 5 HOH A 68 3069 68 HOH WAT . E 5 HOH A 69 3070 69 HOH WAT . E 5 HOH A 70 3071 70 HOH WAT . E 5 HOH A 71 3072 71 HOH WAT . E 5 HOH A 72 3073 72 HOH WAT . E 5 HOH A 73 3074 73 HOH WAT . E 5 HOH A 74 3075 74 HOH WAT . E 5 HOH A 75 3076 75 HOH WAT . E 5 HOH A 76 3077 76 HOH WAT . E 5 HOH A 77 3078 77 HOH WAT . E 5 HOH A 78 3079 78 HOH WAT . E 5 HOH A 79 3080 79 HOH WAT . E 5 HOH A 80 3081 80 HOH WAT . E 5 HOH A 81 3082 81 HOH WAT . E 5 HOH A 82 3083 82 HOH WAT . E 5 HOH A 83 3084 83 HOH WAT . E 5 HOH A 84 3085 85 HOH WAT . E 5 HOH A 85 3086 86 HOH WAT . E 5 HOH A 86 3087 87 HOH WAT . E 5 HOH A 87 3088 89 HOH WAT . E 5 HOH A 88 3089 90 HOH WAT . E 5 HOH A 89 3090 91 HOH WAT . E 5 HOH A 90 3091 92 HOH WAT . E 5 HOH A 91 3092 93 HOH WAT . E 5 HOH A 92 3093 94 HOH WAT . E 5 HOH A 93 3094 95 HOH WAT . E 5 HOH A 94 3095 96 HOH WAT . E 5 HOH A 95 3096 97 HOH WAT . E 5 HOH A 96 3097 98 HOH WAT . E 5 HOH A 97 3098 99 HOH WAT . E 5 HOH A 98 3099 100 HOH WAT . E 5 HOH A 99 3100 101 HOH WAT . E 5 HOH A 100 3101 102 HOH WAT . E 5 HOH A 101 3102 103 HOH WAT . E 5 HOH A 102 3103 104 HOH WAT . E 5 HOH A 103 3104 105 HOH WAT . E 5 HOH A 104 3105 106 HOH WAT . E 5 HOH A 105 3106 107 HOH WAT . E 5 HOH A 106 3107 108 HOH WAT . E 5 HOH A 107 3108 110 HOH WAT . E 5 HOH A 108 3109 111 HOH WAT . E 5 HOH A 109 3110 112 HOH WAT . E 5 HOH A 110 3111 114 HOH WAT . E 5 HOH A 111 3112 115 HOH WAT . E 5 HOH A 112 3113 116 HOH WAT . E 5 HOH A 113 3114 117 HOH WAT . E 5 HOH A 114 3115 118 HOH WAT . E 5 HOH A 115 3116 119 HOH WAT . E 5 HOH A 116 3117 120 HOH WAT . E 5 HOH A 117 3118 121 HOH WAT . E 5 HOH A 118 3119 122 HOH WAT . E 5 HOH A 119 3120 123 HOH WAT . E 5 HOH A 120 3121 124 HOH WAT . E 5 HOH A 121 3122 125 HOH WAT . E 5 HOH A 122 3123 127 HOH WAT . E 5 HOH A 123 3124 128 HOH WAT . E 5 HOH A 124 3125 129 HOH WAT . E 5 HOH A 125 3126 130 HOH WAT . E 5 HOH A 126 3127 131 HOH WAT . E 5 HOH A 127 3128 133 HOH WAT . E 5 HOH A 128 3129 134 HOH WAT . E 5 HOH A 129 3130 135 HOH WAT . E 5 HOH A 130 3131 136 HOH WAT . E 5 HOH A 131 3132 137 HOH WAT . E 5 HOH A 132 3133 138 HOH WAT . E 5 HOH A 133 3134 140 HOH WAT . E 5 HOH A 134 3135 141 HOH WAT . E 5 HOH A 135 3136 142 HOH WAT . # 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 U5P . . . D 4 66.781 13.443 12.303 1 88.84 ? N1 U5P 3001 A 1 HETATM 2 C C2 U5P . . . D 4 65.42 13.327 12.496 1 88.87 ? C2 U5P 3001 A 1 HETATM 3 N N3 U5P . . . D 4 64.94 13.921 13.638 1 88.81 ? N3 U5P 3001 A 1 HETATM 4 C C4 U5P . . . D 4 65.67 14.61 14.585 1 89.26 ? C4 U5P 3001 A 1 HETATM 5 C C5 U5P . . . D 4 67.076 14.689 14.311 1 89.39 ? C5 U5P 3001 A 1 HETATM 6 C C6 U5P . . . D 4 67.57 14.116 13.207 1 88.86 ? C6 U5P 3001 A 1 HETATM 7 O O2 U5P . . . D 4 64.696 12.744 11.71 1 89.39 ? O2 U5P 3001 A 1 HETATM 8 O O4 U5P . . . D 4 65.094 15.094 15.563 1 89.07 ? O4 U5P 3001 A 1 HETATM 9 C C1' U5P . . . D 4 67.343 12.817 11.098 1 88.58 ? C1' U5P 3001 A 1 HETATM 10 C C2' U5P . . . D 4 67.055 13.589 9.806 1 88.05 ? C2' U5P 3001 A 1 HETATM 11 O O2' U5P . . . D 4 66.779 12.667 8.773 1 87.78 ? O2' U5P 3001 A 1 HETATM 12 C C3' U5P . . . D 4 68.368 14.338 9.601 1 88.01 ? C3' U5P 3001 A 1 HETATM 13 C C4' U5P . . . D 4 69.391 13.327 10.091 1 87.57 ? C4' U5P 3001 A 1 HETATM 14 O O3' U5P . . . D 4 68.619 14.788 8.262 1 86.61 ? O3' U5P 3001 A 1 HETATM 15 O O4' U5P . . . D 4 68.751 12.731 11.246 1 88.07 ? O4' U5P 3001 A 1 HETATM 16 C C5' U5P . . . D 4 70.731 13.885 10.503 1 87.61 ? C5' U5P 3001 A 1 HETATM 17 O O5' U5P . . . D 4 70.616 14.597 11.749 1 86.65 ? O5' U5P 3001 A 1 HETATM 18 P P U5P . . . D 4 71.94 14.949 12.632 1 86.76 ? P U5P 3001 A 1 HETATM 19 O O1P U5P . . . D 4 72.621 13.622 12.931 1 87.87 ? O1P U5P 3001 A 1 HETATM 20 O O2P U5P . . . D 4 72.8 15.843 11.75 1 88.12 ? O2P U5P 3001 A 1 HETATM 21 O O3P U5P . . . D 4 71.426 15.65 13.881 1 86.57 ? O3P U5P 3001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #