data_5WMM # _model_server_result.job_id lN6-65IJIAAPc18re5x41Q _model_server_result.datetime_utc '2024-11-04 22:46:07' _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 5wmm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 5WMM # _exptl.entry_id 5WMM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 432.326 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-amino-3-methylbutanoyl (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl hydrogen (S)-phosphate' _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 5WMM _cell.length_a 136.712 _cell.length_b 136.712 _cell.length_c 228.234 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WMM _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 3 _struct_asym.id C _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 OD2 ASP 219 A ASP 198 1_555 H CA CA . A CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc2 A OD2 ASP 221 A ASP 200 1_555 H CA CA . A CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc3 A OE1 GLU 298 A GLU 277 1_555 H CA CA . A CA 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? # _chem_comp.formula 'C14 H21 N6 O8 P' _chem_comp.formula_weight 432.326 _chem_comp.id B6G _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-amino-3-methylbutanoyl (2S,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl hydrogen (S)-phosphate' _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 O2 C6 B6G sing 70 n n O3 C7 B6G sing 71 n n C6 C7 B6G sing 72 n n C6 C5 B6G sing 73 n n C7 C8 B6G sing 74 n n O6 P B6G doub 75 n n O1 C5 B6G sing 76 n n O1 P B6G sing 77 n n C5 O4 B6G sing 78 n n C8 O4 B6G sing 79 n n C8 N1 B6G sing 80 n n P O5 B6G sing 81 n n P O B6G sing 82 n n N2 C9 B6G doub 83 n y N2 C10 B6G sing 84 n y N1 C9 B6G sing 85 n y N1 C13 B6G sing 86 n y O C4 B6G sing 87 n n C9 C12 B6G sing 88 n y C10 N3 B6G doub 89 n y C13 N5 B6G doub 90 n y C4 O7 B6G doub 91 n n C4 C3 B6G sing 92 n n C12 N5 B6G sing 93 n y C12 C11 B6G doub 94 n y N3 C11 B6G sing 95 n y N C3 B6G sing 96 n n C11 N4 B6G sing 97 n n C3 C1 B6G sing 98 n n C1 C B6G sing 99 n n C1 C2 B6G sing 100 n n C8 H1 B6G sing 101 n n C5 H2 B6G sing 102 n n C6 H3 B6G sing 103 n n C2 H4 B6G sing 104 n n C2 H5 B6G sing 105 n n C2 H6 B6G sing 106 n n C3 H7 B6G sing 107 n n N H8 B6G sing 108 n n N H9 B6G sing 109 n n C1 H11 B6G sing 110 n n C H12 B6G sing 111 n n C H13 B6G sing 112 n n C H14 B6G sing 113 n n O5 H15 B6G sing 114 n n C7 H16 B6G sing 115 n n O3 H17 B6G sing 116 n n O2 H18 B6G sing 117 n n C13 H19 B6G sing 118 n n N4 H20 B6G sing 119 n n N4 H21 B6G sing 120 n n C10 H22 B6G sing 121 n n # _atom_sites.entry_id 5WMM _atom_sites.fract_transf_matrix[1][1] 0.007315 _atom_sites.fract_transf_matrix[1][2] 0.004223 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008446 _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] 0.004381 _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 C 3 B6G A 1 1001 1 B6G ADV . D 4 SAH A 1 1002 1 SAH SAH . E 5 CL A 1 1003 1 CL CL . F 5 CL A 1 1004 3 CL CL . G 5 CL A 1 1005 4 CL CL . H 6 CA A 1 1006 1 CA CA . I 6 CA A 1 1007 2 CA CA . J 6 CA A 1 1008 3 CA CA . K 7 HOH A 1 1101 1 HOH HOH . K 7 HOH A 2 1102 2 HOH HOH . K 7 HOH A 3 1103 4 HOH HOH . K 7 HOH A 4 1104 3 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 C8 B6G . . . C 3 -71.146 -1.916 -1.442 1 64.04 ? C8 B6G 1001 A 1 HETATM 2 C C5 B6G . . . C 3 -73.477 -2.203 -1.786 1 66.4 ? C5 B6G 1001 A 1 HETATM 3 C C6 B6G . . . C 3 -72.792 -2.942 -2.934 1 66.69 ? C6 B6G 1001 A 1 HETATM 4 N N1 B6G . . . C 3 -70.666 -2.562 -0.18 1 64.12 ? N1 B6G 1001 A 1 HETATM 5 C C2 B6G . . . C 3 -76.182 -3.78 4.8 1 77.69 ? C2 B6G 1001 A 1 HETATM 6 N N3 B6G . . . C 3 -67.019 -3.147 1.651 1 63.06 ? N3 B6G 1001 A 1 HETATM 7 C C4 B6G . . . C 3 -75.649 -2.136 1.334 1 77.78 ? C4 B6G 1001 A 1 HETATM 8 O O7 B6G . . . C 3 -74.875 -1.218 1.567 1 78.11 ? O7 B6G 1001 A 1 HETATM 9 C C3 B6G . . . C 3 -76.338 -2.885 2.455 1 78.19 ? C3 B6G 1001 A 1 HETATM 10 N N B6G . . . C 3 -77.235 -3.875 1.84 1 78.19 ? N B6G 1001 A 1 HETATM 11 C C1 B6G . . . C 3 -75.458 -3.658 3.458 1 78.16 ? C1 B6G 1001 A 1 HETATM 12 C C B6G . . . C 3 -74.069 -3.087 3.716 1 79.42 ? C B6G 1001 A 1 HETATM 13 O O B6G . . . C 3 -75.942 -2.513 -0.052 1 73.75 ? O B6G 1001 A 1 HETATM 14 P P B6G . . . C 3 -76.045 -1.477 -1.287 1 70.12 ? P B6G 1001 A 1 HETATM 15 O O5 B6G . . . C 3 -76.392 -0.104 -0.759 1 68.29 ? O5 B6G 1001 A 1 HETATM 16 O O6 B6G . . . C 3 -77.167 -1.935 -2.184 1 70.59 ? O6 B6G 1001 A 1 HETATM 17 O O1 B6G . . . C 3 -74.658 -1.455 -2.147 1 68.44 ? O1 B6G 1001 A 1 HETATM 18 O O4 B6G . . . C 3 -72.45 -1.357 -1.254 1 64.53 ? O4 B6G 1001 A 1 HETATM 19 C C7 B6G . . . C 3 -71.299 -2.899 -2.594 1 65.41 ? C7 B6G 1001 A 1 HETATM 20 O O3 B6G . . . C 3 -70.481 -2.477 -3.69 1 64.73 ? O3 B6G 1001 A 1 HETATM 21 O O2 B6G . . . C 3 -73.088 -2.351 -4.207 1 69.38 ? O2 B6G 1001 A 1 HETATM 22 C C13 B6G . . . C 3 -71.452 -3.142 0.757 1 64.65 ? C13 B6G 1001 A 1 HETATM 23 N N5 B6G . . . C 3 -70.725 -3.618 1.797 1 63.83 ? N5 B6G 1001 A 1 HETATM 24 C C12 B6G . . . C 3 -69.438 -3.349 1.547 1 63.6 ? C12 B6G 1001 A 1 HETATM 25 C C9 B6G . . . C 3 -69.397 -2.649 0.245 1 63.85 ? C9 B6G 1001 A 1 HETATM 26 C C11 B6G . . . C 3 -68.151 -3.592 2.247 1 63.13 ? C11 B6G 1001 A 1 HETATM 27 N N4 B6G . . . C 3 -68.118 -4.231 3.442 1 62.93 ? N4 B6G 1001 A 1 HETATM 28 C C10 B6G . . . C 3 -67.045 -2.507 0.459 1 63.94 ? C10 B6G 1001 A 1 HETATM 29 N N2 B6G . . . C 3 -68.184 -2.259 -0.23 1 64.76 ? N2 B6G 1001 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 29 #