data_2QR2 # _model_server_result.job_id UbeDTxaOJt6wSBALX2dp2Q _model_server_result.datetime_utc '2024-10-14 10:16:26' _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 2qr2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":236}' # _entry.id 2QR2 # _exptl.entry_id 2QR2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 172.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description MENADIONE _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 2QR2 _cell.length_a 83.6 _cell.length_b 106.27 _cell.length_c 56.08 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QR2 _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,PQS _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 _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 ? 4 G N N ? 4 H 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 ND1 HIS 173 A HIS 173 1_555 C ZN ZN . A ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc2 A ND1 HIS 177 A HIS 177 1_555 C ZN ZN . A ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc3 A SG CYS 222 A CYS 222 1_555 C ZN ZN . A ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc4 A O CYS 222 A CYS 222 1_555 C ZN ZN . A ZN 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc5 B ND1 HIS 173 B HIS 173 1_555 E ZN ZN . B ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc6 B ND1 HIS 177 B HIS 177 1_555 E ZN ZN . B ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc7 B SG CYS 222 B CYS 222 1_555 E ZN ZN . B ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? metalc ? metalc8 B O CYS 222 B CYS 222 1_555 E ZN ZN . B ZN 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? # _chem_comp.formula 'C11 H8 O2' _chem_comp.formula_weight 172.18 _chem_comp.id VK3 _chem_comp.mon_nstd_flag . _chem_comp.name MENADIONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN K3;2-METHYL-1,4-NAPHTHALENEDIONE' # 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 C1K O1K VK3 doub 467 n n C1K C2K VK3 sing 468 n n C1K C10 VK3 sing 469 n n C2K C3K VK3 doub 470 n n C2K H2K1 VK3 sing 471 n n C3K C4K VK3 sing 472 n n C3K C11 VK3 sing 473 n n C4K O4K VK3 doub 474 n n C4K C5K VK3 sing 475 n n C5K C6K VK3 doub 476 n y C5K C10 VK3 sing 477 n y C6K C7K VK3 sing 478 n y C6K H6K1 VK3 sing 479 n n C7K C8K VK3 doub 480 n y C7K H7K1 VK3 sing 481 n n C8K C9K VK3 sing 482 n y C8K H8K1 VK3 sing 483 n n C9K C10 VK3 doub 484 n y C9K H9K1 VK3 sing 485 n n C11 H111 VK3 sing 486 n n C11 H112 VK3 sing 487 n n C11 H113 VK3 sing 488 n n # _atom_sites.entry_id 2QR2 _atom_sites.fract_transf_matrix[1][1] 0.011962 _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] 0.00941 _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] 0.017832 _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 2 ZN A 1 231 231 ZN ZN . D 3 FAD A 1 234 2 FAD FAD . E 2 ZN B 1 232 232 ZN ZN . F 3 FAD B 1 233 1 FAD FAD . G 4 VK3 B 1 235 3 VK3 VK3 . H 4 VK3 B 1 236 4 VK3 VK3 . I 5 HOH A 1 235 9 HOH HOH . I 5 HOH A 2 236 10 HOH HOH . I 5 HOH A 3 237 11 HOH HOH . I 5 HOH A 4 238 12 HOH HOH . I 5 HOH A 5 239 15 HOH HOH . I 5 HOH A 6 240 16 HOH HOH . I 5 HOH A 7 241 17 HOH HOH . I 5 HOH A 8 242 18 HOH HOH . I 5 HOH A 9 243 19 HOH HOH . I 5 HOH A 10 244 20 HOH HOH . I 5 HOH A 11 245 21 HOH HOH . I 5 HOH A 12 246 27 HOH HOH . I 5 HOH A 13 247 28 HOH HOH . I 5 HOH A 14 248 31 HOH HOH . I 5 HOH A 15 249 32 HOH HOH . I 5 HOH A 16 250 33 HOH HOH . I 5 HOH A 17 251 34 HOH HOH . I 5 HOH A 18 252 40 HOH HOH . I 5 HOH A 19 253 41 HOH HOH . I 5 HOH A 20 254 42 HOH HOH . I 5 HOH A 21 255 43 HOH HOH . I 5 HOH A 22 256 44 HOH HOH . I 5 HOH A 23 257 45 HOH HOH . I 5 HOH A 24 258 46 HOH HOH . I 5 HOH A 25 259 47 HOH HOH . I 5 HOH A 26 260 57 HOH HOH . I 5 HOH A 27 261 58 HOH HOH . I 5 HOH A 28 262 59 HOH HOH . I 5 HOH A 29 263 60 HOH HOH . I 5 HOH A 30 264 61 HOH HOH . I 5 HOH A 31 265 62 HOH HOH . I 5 HOH A 32 266 63 HOH HOH . I 5 HOH A 33 267 71 HOH HOH . I 5 HOH A 34 268 79 HOH HOH . I 5 HOH A 35 269 81 HOH HOH . I 5 HOH A 36 270 82 HOH HOH . I 5 HOH A 37 271 83 HOH HOH . I 5 HOH A 38 272 86 HOH HOH . I 5 HOH A 39 273 87 HOH HOH . I 5 HOH A 40 274 90 HOH HOH . I 5 HOH A 41 275 91 HOH HOH . I 5 HOH A 42 276 92 HOH HOH . I 5 HOH A 43 277 93 HOH HOH . I 5 HOH A 44 278 94 HOH HOH . I 5 HOH A 45 279 95 HOH HOH . I 5 HOH A 46 280 96 HOH HOH . I 5 HOH A 47 281 99 HOH HOH . I 5 HOH A 48 282 103 HOH HOH . I 5 HOH A 49 283 104 HOH HOH . I 5 HOH A 50 284 105 HOH HOH . I 5 HOH A 51 285 106 HOH HOH . I 5 HOH A 52 286 108 HOH HOH . I 5 HOH A 53 287 110 HOH HOH . I 5 HOH A 54 288 114 HOH HOH . I 5 HOH A 55 289 120 HOH HOH . I 5 HOH A 56 290 123 HOH HOH . I 5 HOH A 57 291 124 HOH HOH . I 5 HOH A 58 292 125 HOH HOH . I 5 HOH A 59 293 126 HOH HOH . I 5 HOH A 60 294 127 HOH HOH . I 5 HOH A 61 295 128 HOH HOH . I 5 HOH A 62 296 134 HOH HOH . I 5 HOH A 63 297 135 HOH HOH . I 5 HOH A 64 298 136 HOH HOH . I 5 HOH A 65 299 137 HOH HOH . I 5 HOH A 66 300 147 HOH HOH . I 5 HOH A 67 301 149 HOH HOH . J 5 HOH B 1 237 1 HOH HOH . J 5 HOH B 2 238 2 HOH HOH . J 5 HOH B 3 239 3 HOH HOH . J 5 HOH B 4 240 4 HOH HOH . J 5 HOH B 5 241 5 HOH HOH . J 5 HOH B 6 242 6 HOH HOH . J 5 HOH B 7 243 7 HOH HOH . J 5 HOH B 8 244 8 HOH HOH . J 5 HOH B 9 245 13 HOH HOH . J 5 HOH B 10 246 14 HOH HOH . J 5 HOH B 11 247 22 HOH HOH . J 5 HOH B 12 248 23 HOH HOH . J 5 HOH B 13 249 24 HOH HOH . J 5 HOH B 14 250 25 HOH HOH . J 5 HOH B 15 251 26 HOH HOH . J 5 HOH B 16 252 29 HOH HOH . J 5 HOH B 17 253 30 HOH HOH . J 5 HOH B 18 254 35 HOH HOH . J 5 HOH B 19 255 36 HOH HOH . J 5 HOH B 20 256 37 HOH HOH . J 5 HOH B 21 257 38 HOH HOH . J 5 HOH B 22 258 39 HOH HOH . J 5 HOH B 23 259 48 HOH HOH . J 5 HOH B 24 260 49 HOH HOH . J 5 HOH B 25 261 50 HOH HOH . J 5 HOH B 26 262 51 HOH HOH . J 5 HOH B 27 263 52 HOH HOH . J 5 HOH B 28 264 53 HOH HOH . J 5 HOH B 29 265 54 HOH HOH . J 5 HOH B 30 266 55 HOH HOH . J 5 HOH B 31 267 56 HOH HOH . J 5 HOH B 32 268 64 HOH HOH . J 5 HOH B 33 269 65 HOH HOH . J 5 HOH B 34 270 66 HOH HOH . J 5 HOH B 35 271 67 HOH HOH . J 5 HOH B 36 272 68 HOH HOH . J 5 HOH B 37 273 69 HOH HOH . J 5 HOH B 38 274 70 HOH HOH . J 5 HOH B 39 275 72 HOH HOH . J 5 HOH B 40 276 73 HOH HOH . J 5 HOH B 41 277 74 HOH HOH . J 5 HOH B 42 278 75 HOH HOH . J 5 HOH B 43 279 76 HOH HOH . J 5 HOH B 44 280 77 HOH HOH . J 5 HOH B 45 281 78 HOH HOH . J 5 HOH B 46 282 80 HOH HOH . J 5 HOH B 47 283 84 HOH HOH . J 5 HOH B 48 284 85 HOH HOH . J 5 HOH B 49 285 88 HOH HOH . J 5 HOH B 50 286 89 HOH HOH . J 5 HOH B 51 287 97 HOH HOH . J 5 HOH B 52 288 98 HOH HOH . J 5 HOH B 53 289 100 HOH HOH . J 5 HOH B 54 290 101 HOH HOH . J 5 HOH B 55 291 102 HOH HOH . J 5 HOH B 56 292 107 HOH HOH . J 5 HOH B 57 293 109 HOH HOH . J 5 HOH B 58 294 111 HOH HOH . J 5 HOH B 59 295 112 HOH HOH . J 5 HOH B 60 296 113 HOH HOH . J 5 HOH B 61 297 115 HOH HOH . J 5 HOH B 62 298 116 HOH HOH . J 5 HOH B 63 299 117 HOH HOH . J 5 HOH B 64 300 118 HOH HOH . J 5 HOH B 65 301 119 HOH HOH . J 5 HOH B 66 302 121 HOH HOH . J 5 HOH B 67 303 122 HOH HOH . J 5 HOH B 68 304 129 HOH HOH . J 5 HOH B 69 305 130 HOH HOH . J 5 HOH B 70 306 131 HOH HOH . J 5 HOH B 71 307 132 HOH HOH . J 5 HOH B 72 308 133 HOH HOH . J 5 HOH B 73 309 138 HOH HOH . J 5 HOH B 74 310 139 HOH HOH . J 5 HOH B 75 311 140 HOH HOH . J 5 HOH B 76 312 141 HOH HOH . J 5 HOH B 77 313 142 HOH HOH . J 5 HOH B 78 314 143 HOH HOH . J 5 HOH B 79 315 144 HOH HOH . J 5 HOH B 80 316 145 HOH HOH . J 5 HOH B 81 317 146 HOH HOH . J 5 HOH B 82 318 148 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 C1K VK3 . . . H 4 34.006 14.994 33.258 1 37.18 ? C1K VK3 236 B 1 HETATM 2 O O1K VK3 . . . H 4 33.215 14.48 34.059 1 37.86 ? O1K VK3 236 B 1 HETATM 3 C C2K VK3 . . . H 4 33.423 15.86 32.227 1 36.2 ? C2K VK3 236 B 1 HETATM 4 C C3K VK3 . . . H 4 34.233 16.448 31.282 1 36.27 ? C3K VK3 236 B 1 HETATM 5 C C4K VK3 . . . H 4 35.699 16.281 31.319 1 36.41 ? C4K VK3 236 B 1 HETATM 6 O O4K VK3 . . . H 4 36.312 16.87 30.414 1 36.46 ? O4K VK3 236 B 1 HETATM 7 C C5K VK3 . . . H 4 36.261 15.514 32.408 1 36.07 ? C5K VK3 236 B 1 HETATM 8 C C6K VK3 . . . H 4 37.62 15.439 32.522 1 36.35 ? C6K VK3 236 B 1 HETATM 9 C C7K VK3 . . . H 4 38.159 14.745 33.569 1 37.62 ? C7K VK3 236 B 1 HETATM 10 C C8K VK3 . . . H 4 37.373 14.145 34.51 1 35.64 ? C8K VK3 236 B 1 HETATM 11 C C9K VK3 . . . H 4 36.015 14.221 34.421 1 34.1 ? C9K VK3 236 B 1 HETATM 12 C C10 VK3 . . . H 4 35.444 14.908 33.377 1 36.16 ? C10 VK3 236 B 1 HETATM 13 C C11 VK3 . . . H 4 33.589 17.3 30.166 1 34.41 ? C11 VK3 236 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 13 #