data_8ALK # _model_server_result.job_id eBxOLCZFa3byKka481jnpA _model_server_result.datetime_utc '2025-02-05 10:01:10' _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 8alk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":203}' # _entry.id 8ALK # _exptl.entry_id 8ALK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 608.881 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium _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 8ALK _cell.length_a 119.332 _cell.length_b 119.332 _cell.length_c 79.058 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8ALK _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall 'P 61' _symmetry.space_group_name_H-M 'P 61' # _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 _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 H _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 covale ? covale1 A SG CYS 374 A CYS 391 1_555 H C37 OJU . B OJU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.766 ? covale ? covale2 B OG1 THR 77 B THR 76 1_555 H P OJU . B OJU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc1 A OD1 ASP 88 A ASP 105 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? metalc ? metalc2 A OD2 ASP 88 A ASP 105 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc3 A OD1 ASP 88 A ASP 105 1_555 D CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? metalc ? metalc4 A O GLY 89 A GLY 106 1_555 D CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc5 A OD2 ASP 173 A ASP 190 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc6 A OD1 ASP 237 A ASP 254 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc7 A OD2 ASP 237 A ASP 254 1_555 E CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc8 A OD2 ASP 377 A ASP 394 1_555 C CA CA . A CA 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc9 C CA CA . A CA 501 1_555 I O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.394 ? metalc ? metalc10 C CA CA . A CA 501 1_555 I O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc11 C CA CA . A CA 501 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc12 D CA CA . A CA 502 1_555 I O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.391 ? metalc ? metalc13 D CA CA . A CA 502 1_555 I O HOH . A HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc14 D CA CA . A CA 502 1_555 I O HOH . A HOH 616 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.488 ? metalc ? metalc15 D CA CA . A CA 502 1_555 H O3 OJU . B OJU 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc16 E CA CA . A CA 503 1_555 I O HOH . A HOH 618 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc17 E CA CA . A CA 503 1_555 I O HOH . A HOH 621 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc18 E CA CA . A CA 503 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc19 B OG SER 23 B SER 22 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc20 B OD1 ASP 45 B ASP 44 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc21 B OD2 ASP 64 B ASP 63 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc22 F O1B GDP . B GDP 201 1_555 G CA CA . B CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc23 G CA CA . B CA 202 1_555 J O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc24 G CA CA . B CA 202 1_555 J O HOH . B HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc25 G CA CA . B CA 202 1_555 J O HOH . B HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? # _chem_comp.formula 'C18 H33 Cl N5 O12 P2 1' _chem_comp.formula_weight 608.881 _chem_comp.id OJU _chem_comp.mon_nstd_flag . _chem_comp.name 2-[[[5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxyethyl-[3-(2-chloranylethanoylamino)propyl]-dimethyl-azanium _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Cytidine-diphosphate with a thiol-reactive chloroacetamide (cross-linker)' # 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 C37 C32 OJU sing 282 n n C32 O36 OJU doub 283 n n C32 N31 OJU sing 284 n n N31 C29 OJU sing 285 n n C29 C25 OJU sing 286 n n C25 C04 OJU sing 287 n n C04 N02 OJU sing 288 n n C03 N02 OJU sing 289 n n N02 C01 OJU sing 290 n n N02 C05 OJU sing 291 n n C05 C06 OJU sing 292 n n C06 O2 OJU sing 293 n n O2 P OJU sing 294 n n P O1 OJU doub 295 n n P O3 OJU sing 296 n n C25 H1 OJU sing 297 n n C25 H2 OJU sing 298 n n O3 H3 OJU sing 299 n n C01 H5 OJU sing 300 n n C01 H6 OJU sing 301 n n C01 H7 OJU sing 302 n n C03 H8 OJU sing 303 n n C03 H9 OJU sing 304 n n C03 H10 OJU sing 305 n n C04 H11 OJU sing 306 n n C04 H12 OJU sing 307 n n C05 H13 OJU sing 308 n n C05 H14 OJU sing 309 n n C06 H15 OJU sing 310 n n C06 H16 OJU sing 311 n n C29 H17 OJU sing 312 n n C29 H18 OJU sing 313 n n C37 H19 OJU sing 314 n n C37 CL1 OJU sing 315 n n C37 H21 OJU sing 316 n n N31 H22 OJU sing 317 n n P O4 OJU sing 318 n n O4 P1 OJU sing 319 n n P1 O5 OJU doub 320 n n P1 O6 OJU sing 321 n n P1 O7 OJU sing 322 n n O6 C1 OJU sing 323 n n O7 H20 OJU sing 324 n n C1 C2 OJU sing 325 n n C2 C3 OJU sing 326 n n C3 C4 OJU sing 327 n n C4 C5 OJU sing 328 n n C5 O8 OJU sing 329 n n O8 C2 OJU sing 330 n n C1 H4 OJU sing 331 n n C1 H23 OJU sing 332 n n C2 H24 OJU sing 333 n n C3 H25 OJU sing 334 n n C3 O9 OJU sing 335 n n C4 H27 OJU sing 336 n n C4 O10 OJU sing 337 n n C5 H29 OJU sing 338 n n C5 N1 OJU sing 339 n n N1 C8 OJU sing 340 n n C8 N2 OJU sing 341 n n N2 C9 OJU doub 342 n n C9 C10 OJU sing 343 n n C10 C11 OJU doub 344 n n C11 N1 OJU sing 345 n n C9 N3 OJU sing 346 n n C8 O11 OJU doub 347 n n O9 H26 OJU sing 348 n n O10 H28 OJU sing 349 n n C10 H30 OJU sing 350 n n C11 H31 OJU sing 351 n n N3 H32 OJU sing 352 n n N3 H33 OJU sing 353 n n # _atom_sites.entry_id 8ALK _atom_sites.fract_transf_matrix[1][1] 0.00838 _atom_sites.fract_transf_matrix[1][2] 0.004838 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009676 _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] 0.012649 _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 CA A 1 501 1 CA CA . D 3 CA A 1 502 8 CA CA . E 3 CA A 1 503 9 CA CA . F 4 GDP B 1 201 201 GDP GDP . G 3 CA B 1 202 6 CA CA . H 5 OJU B 1 203 502 OJU PCX . I 6 HOH A 1 601 82 HOH HOH . I 6 HOH A 2 602 1 HOH HOH . I 6 HOH A 3 603 23 HOH HOH . I 6 HOH A 4 604 61 HOH HOH . I 6 HOH A 5 605 73 HOH HOH . I 6 HOH A 6 606 70 HOH HOH . I 6 HOH A 7 607 60 HOH HOH . I 6 HOH A 8 608 9 HOH HOH . I 6 HOH A 9 609 17 HOH HOH . I 6 HOH A 10 610 3 HOH HOH . I 6 HOH A 11 611 4 HOH HOH . I 6 HOH A 12 612 57 HOH HOH . I 6 HOH A 13 613 43 HOH HOH . I 6 HOH A 14 614 79 HOH HOH . I 6 HOH A 15 615 15 HOH HOH . I 6 HOH A 16 616 18 HOH HOH . I 6 HOH A 17 617 44 HOH HOH . I 6 HOH A 18 618 84 HOH HOH . I 6 HOH A 19 619 85 HOH HOH . I 6 HOH A 20 620 26 HOH HOH . I 6 HOH A 21 621 81 HOH HOH . I 6 HOH A 22 622 41 HOH HOH . I 6 HOH A 23 623 7 HOH HOH . I 6 HOH A 24 624 59 HOH HOH . I 6 HOH A 25 625 62 HOH HOH . I 6 HOH A 26 626 5 HOH HOH . I 6 HOH A 27 627 20 HOH HOH . I 6 HOH A 28 628 63 HOH HOH . I 6 HOH A 29 629 8 HOH HOH . I 6 HOH A 30 630 78 HOH HOH . I 6 HOH A 31 631 29 HOH HOH . I 6 HOH A 32 632 10 HOH HOH . I 6 HOH A 33 633 38 HOH HOH . I 6 HOH A 34 634 13 HOH HOH . I 6 HOH A 35 635 19 HOH HOH . I 6 HOH A 36 636 2 HOH HOH . I 6 HOH A 37 637 51 HOH HOH . I 6 HOH A 38 638 11 HOH HOH . I 6 HOH A 39 639 12 HOH HOH . I 6 HOH A 40 640 16 HOH HOH . I 6 HOH A 41 641 36 HOH HOH . I 6 HOH A 42 642 28 HOH HOH . I 6 HOH A 43 643 66 HOH HOH . I 6 HOH A 44 644 47 HOH HOH . I 6 HOH A 45 645 34 HOH HOH . I 6 HOH A 46 646 32 HOH HOH . I 6 HOH A 47 647 54 HOH HOH . I 6 HOH A 48 648 64 HOH HOH . I 6 HOH A 49 649 22 HOH HOH . I 6 HOH A 50 650 14 HOH HOH . I 6 HOH A 51 651 67 HOH HOH . I 6 HOH A 52 652 48 HOH HOH . I 6 HOH A 53 653 25 HOH HOH . I 6 HOH A 54 654 45 HOH HOH . I 6 HOH A 55 655 31 HOH HOH . I 6 HOH A 56 656 21 HOH HOH . I 6 HOH A 57 657 33 HOH HOH . I 6 HOH A 58 658 50 HOH HOH . I 6 HOH A 59 659 30 HOH HOH . I 6 HOH A 60 660 68 HOH HOH . I 6 HOH A 61 661 80 HOH HOH . J 6 HOH B 1 301 83 HOH HOH . J 6 HOH B 2 302 27 HOH HOH . J 6 HOH B 3 303 42 HOH HOH . J 6 HOH B 4 304 6 HOH HOH . J 6 HOH B 5 305 65 HOH HOH . J 6 HOH B 6 306 35 HOH HOH . J 6 HOH B 7 307 56 HOH HOH . J 6 HOH B 8 308 72 HOH HOH . J 6 HOH B 9 309 69 HOH HOH . J 6 HOH B 10 310 40 HOH HOH . J 6 HOH B 11 311 58 HOH HOH . J 6 HOH B 12 312 24 HOH HOH . J 6 HOH B 13 313 74 HOH HOH . J 6 HOH B 14 314 46 HOH HOH . J 6 HOH B 15 315 49 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 C25 OJU . . . H 5 -38.663 -13.717 -7.382 1 99.05 ? C25 OJU 203 B 1 HETATM 2 P P OJU . . . H 5 -40.634 -12.762 -1.98 1 76.5 ? P OJU 203 B 1 HETATM 3 O O1 OJU . . . H 5 -40.328 -14.155 -1.587 1 75.8 ? O1 OJU 203 B 1 HETATM 4 O O2 OJU . . . H 5 -39.961 -12.452 -3.409 1 83.9 ? O2 OJU 203 B 1 HETATM 5 O O3 OJU . . . H 5 -40.063 -11.748 -0.875 1 87.18 ? O3 OJU 203 B 1 HETATM 6 C C01 OJU . . . H 5 -36.98 -13.906 -5.284 1 86.76 ? C01 OJU 203 B 1 HETATM 7 C C03 OJU . . . H 5 -36.249 -11.98 -6.441 1 92.31 ? C03 OJU 203 B 1 HETATM 8 C C04 OJU . . . H 5 -38.556 -12.501 -6.444 1 96.79 ? C04 OJU 203 B 1 HETATM 9 C C05 OJU . . . H 5 -37.492 -11.738 -4.445 1 83.68 ? C05 OJU 203 B 1 HETATM 10 C C06 OJU . . . H 5 -38.602 -12.333 -3.567 1 88.07 ? C06 OJU 203 B 1 HETATM 11 C C29 OJU . . . H 5 -38.735 -13.216 -8.828 1 101.2 ? C29 OJU 203 B 1 HETATM 12 C C32 OJU . . . H 5 -36.571 -13.234 -10.123 1 87.89 ? C32 OJU 203 B 1 HETATM 13 C C37 OJU . . . H 5 -35.54 -13.983 -10.972 1 74.42 ? C37 OJU 203 B 1 HETATM 14 N N02 OJU . . . H 5 -37.324 -12.545 -5.65 1 101.1 ? N02 OJU 203 B 1 HETATM 15 N N31 OJU . . . H 5 -37.755 -13.934 -9.633 1 96.79 ? N31 OJU 203 B 1 HETATM 16 O O36 OJU . . . H 5 -36.407 -12.091 -9.861 1 87.15 ? O36 OJU 203 B 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #