data_6EDR # _model_server_result.job_id aUF7e25ApPDh3KOOcc1gYw _model_server_result.datetime_utc '2024-11-08 18:15:05' _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":"C","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 . . . C 2 -17.634 -0.787 -1.646 1 73.56 ? N01 ZNA 401 A 1 HETATM 2 C C02 ZNA . . . C 2 -16.549 -0.012 -1.822 1 89.59 ? C02 ZNA 401 A 1 HETATM 3 O O03 ZNA . . . C 2 -16.462 1.083 -1.26 1 90.33 ? O03 ZNA 401 A 1 HETATM 4 C C04 ZNA . . . C 2 -15.493 -0.477 -2.644 1 97.06 ? C04 ZNA 401 A 1 HETATM 5 C C44 ZNA . . . C 2 -15.331 -1.827 -3.004 1 100 ? C44 ZNA 401 A 1 HETATM 6 C C05 ZNA . . . C 2 -14.533 0.431 -3.13 1 96.64 ? C05 ZNA 401 A 1 HETATM 7 C C06 ZNA . . . C 2 -13.466 0.008 -3.931 1 99.61 ? C06 ZNA 401 A 1 HETATM 8 C C07 ZNA . . . C 2 -13.323 -1.332 -4.284 1 95.96 ? C07 ZNA 401 A 1 HETATM 9 N N08 ZNA . . . C 2 -14.268 -2.256 -3.832 1 107.5 ? N08 ZNA 401 A 1 HETATM 10 C C09 ZNA . . . C 2 -14.204 -3.716 -4.127 1 121.8 ? C09 ZNA 401 A 1 HETATM 11 S S10 ZNA . . . C 2 -13.417 -4.399 -2.643 1 155.51 ? S10 ZNA 401 A 1 HETATM 12 C C42 ZNA . . . C 2 -13.289 -4.268 -5.274 1 117.93 ? C42 ZNA 401 A 1 HETATM 13 O O43 ZNA . . . C 2 -13.908 -5.453 -5.793 1 105.17 ? O43 ZNA 401 A 1 HETATM 14 C C40 ZNA . . . C 2 -11.903 -4.676 -4.705 1 120.73 ? C40 ZNA 401 A 1 HETATM 15 O O41 ZNA . . . C 2 -11.194 -5.499 -5.658 1 95.2 ? O41 ZNA 401 A 1 HETATM 16 C C11 ZNA . . . C 2 -12.208 -5.496 -3.449 1 138.85 ? C11 ZNA 401 A 1 HETATM 17 C C12 ZNA . . . C 2 -10.982 -5.704 -2.555 1 146.25 ? C12 ZNA 401 A 1 HETATM 18 O O13 ZNA . . . C 2 -11.049 -4.944 -1.333 1 154.99 ? O13 ZNA 401 A 1 HETATM 19 P P14 ZNA . . . C 2 -11.447 -5.586 0.108 1 151.68 ? P14 ZNA 401 A 1 HETATM 20 O O15 ZNA . . . C 2 -10.42 -5.151 1.075 1 149.83 ? O15 ZNA 401 A 1 HETATM 21 O O16 ZNA . . . C 2 -11.764 -7.032 -0.014 1 123.18 ? O16 ZNA 401 A 1 HETATM 22 O O17 ZNA . . . C 2 -12.852 -4.831 0.415 1 138.75 ? O17 ZNA 401 A 1 HETATM 23 P P18 ZNA . . . C 2 -13.044 -3.502 1.308 1 130.38 ? P18 ZNA 401 A 1 HETATM 24 O O19 ZNA . . . C 2 -12.361 -3.688 2.604 1 128.97 ? O19 ZNA 401 A 1 HETATM 25 O O20 ZNA . . . C 2 -14.489 -3.194 1.299 1 123.43 ? O20 ZNA 401 A 1 HETATM 26 O O21 ZNA . . . C 2 -12.224 -2.326 0.498 1 151.81 ? O21 ZNA 401 A 1 HETATM 27 C C22 ZNA . . . C 2 -12.795 -1.529 -0.561 1 151.93 ? C22 ZNA 401 A 1 HETATM 28 C C23 ZNA . . . C 2 -12.435 -0.029 -0.435 1 149.85 ? C23 ZNA 401 A 1 HETATM 29 O O24 ZNA . . . C 2 -12.544 0.527 0.894 1 151.59 ? O24 ZNA 401 A 1 HETATM 30 C C38 ZNA . . . C 2 -10.975 0.228 -0.776 1 140.52 ? C38 ZNA 401 A 1 HETATM 31 O O39 ZNA . . . C 2 -10.71 0.046 -2.188 1 110.35 ? O39 ZNA 401 A 1 HETATM 32 C C36 ZNA . . . C 2 -10.869 1.688 -0.37 1 142.34 ? C36 ZNA 401 A 1 HETATM 33 O O37 ZNA . . . C 2 -11.315 2.544 -1.442 1 125.07 ? O37 ZNA 401 A 1 HETATM 34 C C25 ZNA . . . C 2 -11.829 1.8 0.836 1 155.86 ? C25 ZNA 401 A 1 HETATM 35 N N26 ZNA . . . C 2 -11.085 2.046 2.118 1 169.43 ? N26 ZNA 401 A 1 HETATM 36 C C27 ZNA . . . C 2 -10.391 1.107 2.757 1 169.35 ? C27 ZNA 401 A 1 HETATM 37 N N28 ZNA . . . C 2 -9.858 1.649 3.848 1 172.31 ? N28 ZNA 401 A 1 HETATM 38 C C29 ZNA . . . C 2 -10.215 2.931 3.9 1 169.34 ? C29 ZNA 401 A 1 HETATM 39 C C35 ZNA . . . C 2 -10.982 3.18 2.821 1 166.61 ? C35 ZNA 401 A 1 HETATM 40 N N34 ZNA . . . C 2 -11.49 4.415 2.614 1 150.98 ? N34 ZNA 401 A 1 HETATM 41 C C33 ZNA . . . C 2 -11.217 5.448 3.533 1 142.3 ? C33 ZNA 401 A 1 HETATM 42 N N32 ZNA . . . C 2 -10.412 5.154 4.649 1 150.14 ? N32 ZNA 401 A 1 HETATM 43 C C30 ZNA . . . C 2 -9.939 3.9 4.793 1 152.79 ? C30 ZNA 401 A 1 HETATM 44 N N31 ZNA . . . C 2 -9.171 3.564 5.831 1 118.69 ? N31 ZNA 401 A 1 # _model_server_stats.io_time_ms 66 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 44 #