data_6EDR # _model_server_result.job_id QLjessgNxtrqX8CQt4IzaA _model_server_result.datetime_utc '2024-11-08 18:19:03' _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 6edr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 6EDR # _exptl.entry_id 6EDR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 680.499 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate' _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 96.89 _cell.angle_gamma 90 _cell.entry_id 6EDR _cell.length_a 57.742 _cell.length_b 51.106 _cell.length_c 100.674 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EDR _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E 1 1 B,D,F 2 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 ? 2 C N N ? 2 D 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 disulf ? disulf1 A SG CYS 24 A CYS 67 1_555 A SG CYS 39 A CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? disulf ? disulf2 A SG CYS 56 A CYS 99 1_555 A SG CYS 137 A CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf3 A SG CYS 76 A CYS 119 1_555 A SG CYS 158 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? disulf ? disulf4 A SG CYS 117 A CYS 160 1_555 A SG CYS 130 A CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? disulf ? disulf5 A SG CYS 211 A CYS 254 1_555 A SG CYS 232 A CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf6 B SG CYS 24 B CYS 67 1_555 B SG CYS 39 B CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? disulf ? disulf7 B SG CYS 56 B CYS 99 1_555 B SG CYS 137 B CYS 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf8 B SG CYS 76 B CYS 119 1_555 B SG CYS 158 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? disulf ? disulf9 B SG CYS 117 B CYS 160 1_555 B SG CYS 130 B CYS 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? disulf ? disulf10 B SG CYS 211 B CYS 254 1_555 B SG CYS 232 B CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? # _chem_comp.formula 'C21 H28 N7 O13 P2 S 1' _chem_comp.formula_weight 680.499 _chem_comp.id ZNA _chem_comp.mon_nstd_flag . _chem_comp.name '[[(2~{R},3~{S},4~{R},5~{R})-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-bis(oxidanyl)thiolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen 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 O43 C42 ZNA sing 376 n n O41 C40 ZNA sing 377 n n C42 C40 ZNA sing 378 n n C42 C09 ZNA sing 379 n n C40 C11 ZNA sing 380 n n C07 C06 ZNA doub 381 n y C07 N08 ZNA sing 382 n y C09 N08 ZNA sing 383 n n C09 S10 ZNA sing 384 n n C06 C05 ZNA sing 385 n y N08 C44 ZNA doub 386 n y C11 S10 ZNA sing 387 n n C11 C12 ZNA sing 388 n n C05 C04 ZNA doub 389 n y C44 C04 ZNA sing 390 n y C04 C02 ZNA sing 391 n n C12 O13 ZNA sing 392 n n O39 C38 ZNA sing 393 n n C02 N01 ZNA sing 394 n n C02 O03 ZNA doub 395 n n O37 C36 ZNA sing 396 n n O13 P14 ZNA sing 397 n n C38 C23 ZNA sing 398 n n C38 C36 ZNA sing 399 n n C22 C23 ZNA sing 400 n n C22 O21 ZNA sing 401 n n C23 O24 ZNA sing 402 n n C36 C25 ZNA sing 403 n n O16 P14 ZNA doub 404 n n P14 O17 ZNA sing 405 n n P14 O15 ZNA sing 406 n n O17 P18 ZNA sing 407 n n O21 P18 ZNA sing 408 n n C25 O24 ZNA sing 409 n n C25 N26 ZNA sing 410 n n O20 P18 ZNA doub 411 n n P18 O19 ZNA sing 412 n n N26 C27 ZNA sing 413 n y N26 C35 ZNA sing 414 n y N34 C35 ZNA doub 415 n y N34 C33 ZNA sing 416 n y C27 N28 ZNA doub 417 n y C35 C29 ZNA sing 418 n y C33 N32 ZNA doub 419 n y N28 C29 ZNA sing 420 n y C29 C30 ZNA doub 421 n y N32 C30 ZNA sing 422 n y C30 N31 ZNA sing 423 n n N01 H1 ZNA sing 424 n n N01 H2 ZNA sing 425 n n C44 H3 ZNA sing 426 n n C05 H4 ZNA sing 427 n n C06 H5 ZNA sing 428 n n C07 H6 ZNA sing 429 n n C09 H7 ZNA sing 430 n n C42 H8 ZNA sing 431 n n O43 H9 ZNA sing 432 n n C40 H10 ZNA sing 433 n n O41 H11 ZNA sing 434 n n C11 H12 ZNA sing 435 n n C12 H13 ZNA sing 436 n n C12 H14 ZNA sing 437 n n O15 H15 ZNA sing 438 n n O19 H16 ZNA sing 439 n n C22 H17 ZNA sing 440 n n C22 H18 ZNA sing 441 n n C23 H19 ZNA sing 442 n n C38 H20 ZNA sing 443 n n O39 H21 ZNA sing 444 n n C36 H22 ZNA sing 445 n n O37 H23 ZNA sing 446 n n C25 H24 ZNA sing 447 n n C27 H25 ZNA sing 448 n n C33 H26 ZNA sing 449 n n N31 H27 ZNA sing 450 n n N31 H28 ZNA sing 451 n n # _atom_sites.entry_id 6EDR _atom_sites.fract_transf_matrix[1][1] 0.017319 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002091 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019567 _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] 0.010005 _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 ZNA A 1 401 300 ZNA ZNA . D 2 ZNA B 1 401 300 ZNA ZNA . E 3 HOH A 1 501 68 HOH HOH . E 3 HOH A 2 502 19 HOH HOH . E 3 HOH A 3 503 36 HOH HOH . E 3 HOH A 4 504 1 HOH HOH . E 3 HOH A 5 505 18 HOH HOH . E 3 HOH A 6 506 21 HOH HOH . E 3 HOH A 7 507 16 HOH HOH . E 3 HOH A 8 508 51 HOH HOH . E 3 HOH A 9 509 44 HOH HOH . E 3 HOH A 10 510 46 HOH HOH . E 3 HOH A 11 511 42 HOH HOH . E 3 HOH A 12 512 30 HOH HOH . E 3 HOH A 13 513 35 HOH HOH . E 3 HOH A 14 514 85 HOH HOH . E 3 HOH A 15 515 17 HOH HOH . E 3 HOH A 16 516 12 HOH HOH . E 3 HOH A 17 517 69 HOH HOH . E 3 HOH A 18 518 54 HOH HOH . E 3 HOH A 19 519 38 HOH HOH . E 3 HOH A 20 520 3 HOH HOH . E 3 HOH A 21 521 61 HOH HOH . E 3 HOH A 22 522 58 HOH HOH . E 3 HOH A 23 523 43 HOH HOH . E 3 HOH A 24 524 24 HOH HOH . E 3 HOH A 25 525 47 HOH HOH . E 3 HOH A 26 526 73 HOH HOH . E 3 HOH A 27 527 76 HOH HOH . E 3 HOH A 28 528 10 HOH HOH . E 3 HOH A 29 529 71 HOH HOH . E 3 HOH A 30 530 9 HOH HOH . E 3 HOH A 31 531 27 HOH HOH . E 3 HOH A 32 532 8 HOH HOH . E 3 HOH A 33 533 75 HOH HOH . E 3 HOH A 34 534 57 HOH HOH . E 3 HOH A 35 535 59 HOH HOH . E 3 HOH A 36 536 79 HOH HOH . E 3 HOH A 37 537 22 HOH HOH . E 3 HOH A 38 538 87 HOH HOH . E 3 HOH A 39 539 41 HOH HOH . E 3 HOH A 40 540 67 HOH HOH . E 3 HOH A 41 541 70 HOH HOH . E 3 HOH A 42 542 45 HOH HOH . E 3 HOH A 43 543 84 HOH HOH . E 3 HOH A 44 544 23 HOH HOH . E 3 HOH A 45 545 80 HOH HOH . E 3 HOH A 46 546 55 HOH HOH . E 3 HOH A 47 547 72 HOH HOH . E 3 HOH A 48 548 39 HOH HOH . E 3 HOH A 49 549 56 HOH HOH . F 3 HOH B 1 501 86 HOH HOH . F 3 HOH B 2 502 4 HOH HOH . F 3 HOH B 3 503 48 HOH HOH . F 3 HOH B 4 504 82 HOH HOH . F 3 HOH B 5 505 32 HOH HOH . F 3 HOH B 6 506 53 HOH HOH . F 3 HOH B 7 507 11 HOH HOH . F 3 HOH B 8 508 13 HOH HOH . F 3 HOH B 9 509 7 HOH HOH . F 3 HOH B 10 510 2 HOH HOH . F 3 HOH B 11 511 81 HOH HOH . F 3 HOH B 12 512 77 HOH HOH . F 3 HOH B 13 513 78 HOH HOH . F 3 HOH B 14 514 26 HOH HOH . F 3 HOH B 15 515 33 HOH HOH . F 3 HOH B 16 516 83 HOH HOH . F 3 HOH B 17 517 52 HOH HOH . F 3 HOH B 18 518 5 HOH HOH . F 3 HOH B 19 519 66 HOH HOH . F 3 HOH B 20 520 29 HOH HOH . F 3 HOH B 21 521 50 HOH HOH . F 3 HOH B 22 522 6 HOH HOH . F 3 HOH B 23 523 74 HOH HOH . F 3 HOH B 24 524 62 HOH HOH . F 3 HOH B 25 525 15 HOH HOH . F 3 HOH B 26 526 20 HOH HOH . F 3 HOH B 27 527 65 HOH HOH . F 3 HOH B 28 528 34 HOH HOH . F 3 HOH B 29 529 60 HOH HOH . F 3 HOH B 30 530 28 HOH HOH . F 3 HOH B 31 531 64 HOH HOH . F 3 HOH B 32 532 14 HOH HOH . F 3 HOH B 33 533 40 HOH HOH . F 3 HOH B 34 534 63 HOH HOH . F 3 HOH B 35 535 31 HOH HOH . F 3 HOH B 36 536 25 HOH HOH . F 3 HOH B 37 537 49 HOH HOH . F 3 HOH B 38 538 37 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 N01 ZNA . . . D 2 -10.88 -29.253 -45.963 1 69.91 ? N01 ZNA 401 B 1 HETATM 2 C C02 ZNA . . . D 2 -10.923 -29.969 -44.836 1 79.18 ? C02 ZNA 401 B 1 HETATM 3 O O03 ZNA . . . D 2 -11.558 -31.018 -44.757 1 83.53 ? O03 ZNA 401 B 1 HETATM 4 C C04 ZNA . . . D 2 -10.199 -29.486 -43.739 1 86.76 ? C04 ZNA 401 B 1 HETATM 5 C C44 ZNA . . . D 2 -10.172 -28.125 -43.45 1 87.27 ? C44 ZNA 401 B 1 HETATM 6 C C05 ZNA . . . D 2 -9.509 -30.366 -42.896 1 93.77 ? C05 ZNA 401 B 1 HETATM 7 C C06 ZNA . . . D 2 -8.785 -29.893 -41.797 1 94.16 ? C06 ZNA 401 B 1 HETATM 8 C C07 ZNA . . . D 2 -8.748 -28.527 -41.513 1 99.89 ? C07 ZNA 401 B 1 HETATM 9 N N08 ZNA . . . D 2 -9.459 -27.631 -42.349 1 96.31 ? N08 ZNA 401 B 1 HETATM 10 C C09 ZNA . . . D 2 -9.504 -26.15 -42.193 1 88.05 ? C09 ZNA 401 B 1 HETATM 11 S S10 ZNA . . . D 2 -8.427 -25.522 -43.524 1 93.25 ? S10 ZNA 401 B 1 HETATM 12 C C42 ZNA . . . D 2 -8.87 -25.485 -40.946 1 80.19 ? C42 ZNA 401 B 1 HETATM 13 O O43 ZNA . . . D 2 -9.526 -24.22 -40.764 1 71.72 ? O43 ZNA 401 B 1 HETATM 14 C C40 ZNA . . . D 2 -7.353 -25.248 -41.22 1 77.28 ? C40 ZNA 401 B 1 HETATM 15 O O41 ZNA . . . D 2 -6.76 -24.472 -40.17 1 61.35 ? O41 ZNA 401 B 1 HETATM 16 C C11 ZNA . . . D 2 -7.3 -24.478 -42.541 1 89.48 ? C11 ZNA 401 B 1 HETATM 17 C C12 ZNA . . . D 2 -5.886 -24.423 -43.14 1 94.34 ? C12 ZNA 401 B 1 HETATM 18 O O13 ZNA . . . D 2 -5.767 -25.154 -44.367 1 97.86 ? O13 ZNA 401 B 1 HETATM 19 P P14 ZNA . . . D 2 -5.67 -24.481 -45.838 1 81.92 ? P14 ZNA 401 B 1 HETATM 20 O O15 ZNA . . . D 2 -4.364 -24.895 -46.406 1 80.32 ? O15 ZNA 401 B 1 HETATM 21 O O16 ZNA . . . D 2 -6.039 -23.046 -45.813 1 72.14 ? O16 ZNA 401 B 1 HETATM 22 O O17 ZNA . . . D 2 -6.903 -25.24 -46.578 1 85.07 ? O17 ZNA 401 B 1 HETATM 23 P P18 ZNA . . . D 2 -6.761 -26.495 -47.588 1 73.6 ? P18 ZNA 401 B 1 HETATM 24 O O19 ZNA . . . D 2 -5.661 -26.262 -48.55 1 68.8 ? O19 ZNA 401 B 1 HETATM 25 O O20 ZNA . . . D 2 -8.127 -26.763 -48.084 1 71.59 ? O20 ZNA 401 B 1 HETATM 26 O O21 ZNA . . . D 2 -6.291 -27.737 -46.647 1 92.52 ? O21 ZNA 401 B 1 HETATM 27 C C22 ZNA . . . D 2 -7.018 -28.112 -45.469 1 107.71 ? C22 ZNA 401 B 1 HETATM 28 C C23 ZNA . . . D 2 -6.836 -29.6 -45.122 1 118.43 ? C23 ZNA 401 B 1 HETATM 29 O O24 ZNA . . . D 2 -7.226 -30.498 -46.194 1 115.87 ? O24 ZNA 401 B 1 HETATM 30 C C38 ZNA . . . D 2 -5.38 -29.939 -44.84 1 121.5 ? C38 ZNA 401 B 1 HETATM 31 O O39 ZNA . . . D 2 -4.994 -29.503 -43.525 1 112.74 ? O39 ZNA 401 B 1 HETATM 32 C C36 ZNA . . . D 2 -5.445 -31.442 -44.908 1 126.3 ? C36 ZNA 401 B 1 HETATM 33 O O37 ZNA . . . D 2 -6.056 -31.998 -43.72 1 117.31 ? O37 ZNA 401 B 1 HETATM 34 C C25 ZNA . . . D 2 -6.347 -31.653 -46.12 1 131.31 ? C25 ZNA 401 B 1 HETATM 35 N N26 ZNA . . . D 2 -5.529 -31.773 -47.359 1 150.38 ? N26 ZNA 401 B 1 HETATM 36 C C27 ZNA . . . D 2 -5.108 -30.814 -48.183 1 150.98 ? C27 ZNA 401 B 1 HETATM 37 N N28 ZNA . . . D 2 -4.402 -31.385 -49.157 1 156.7 ? N28 ZNA 401 B 1 HETATM 38 C C29 ZNA . . . D 2 -4.377 -32.701 -48.942 1 163.41 ? C29 ZNA 401 B 1 HETATM 39 C C35 ZNA . . . D 2 -5.078 -32.933 -47.821 1 160.93 ? C35 ZNA 401 B 1 HETATM 40 N N34 ZNA . . . D 2 -5.232 -34.182 -47.346 1 155.1 ? N34 ZNA 401 B 1 HETATM 41 C C33 ZNA . . . D 2 -4.653 -35.256 -48.029 1 147.9 ? C33 ZNA 401 B 1 HETATM 42 N N32 ZNA . . . D 2 -3.921 -34.997 -49.201 1 147.98 ? N32 ZNA 401 B 1 HETATM 43 C C30 ZNA . . . D 2 -3.809 -33.719 -49.615 1 154.93 ? C30 ZNA 401 B 1 HETATM 44 N N31 ZNA . . . D 2 -3.13 -33.408 -50.717 1 145 ? N31 ZNA 401 B 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #