data_6QCH # _model_server_result.job_id XNLKGFF7y8cCWjjgD_W5Ng _model_server_result.datetime_utc '2024-11-24 17:34:25' _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 6qch # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6QCH # _exptl.entry_id 6QCH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] 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 90 _cell.angle_gamma 120 _cell.entry_id 6QCH _cell.length_a 91.387 _cell.length_b 91.387 _cell.length_c 143.806 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QCH _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,D,E,F,G,H,I,J,K,L,W 1 1 B,M,N,O,P,Q,R,S,T,U,V,X 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 M 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 SG CYS 135 A CYS 141 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc2 A SG CYS 160 A CYS 166 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc3 A SG CYS 171 A CYS 177 1_555 D ZN ZN . A ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.537 ? metalc ? metalc4 B SG CYS 135 B CYS 141 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc5 B SG CYS 138 B CYS 144 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc6 B SG CYS 160 B CYS 166 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.6 ? metalc ? metalc7 B SG CYS 171 B CYS 177 1_555 N ZN ZN . B ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id AR6 _chem_comp.mon_nstd_flag . _chem_comp.name '[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Adenosine-5-Diphosphoribose # 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 N1 C2 AR6 doub 13 n y N1 C6 AR6 sing 14 n y C2 N3 AR6 sing 15 n y N3 C4 AR6 doub 16 n y C4 C5 AR6 sing 17 n y C4 N9 AR6 sing 18 n y C5 C6 AR6 doub 19 n y C5 N7 AR6 sing 20 n y C6 N6 AR6 sing 21 n n N7 C8 AR6 doub 22 n y C8 N9 AR6 sing 23 n y N9 C1' AR6 sing 24 n n PA O1A AR6 sing 25 n n PA O2A AR6 doub 26 n n PA O3A AR6 sing 27 n n PA O5' AR6 sing 28 n n PB O1B AR6 sing 29 n n PB O2B AR6 doub 30 n n PB O3A AR6 sing 31 n n PB O5D AR6 sing 32 n n C1' C2' AR6 sing 33 n n C1' O4' AR6 sing 34 n n C1D O1D AR6 sing 35 n n C1D C2D AR6 sing 36 n n C1D O4D AR6 sing 37 n n C2' O2' AR6 sing 38 n n C2' C3' AR6 sing 39 n n C2D O2D AR6 sing 40 n n C2D C3D AR6 sing 41 n n C3' O3' AR6 sing 42 n n C3' C4' AR6 sing 43 n n C3D O3D AR6 sing 44 n n C3D C4D AR6 sing 45 n n C4' O4' AR6 sing 46 n n C4' C5' AR6 sing 47 n n C4D O4D AR6 sing 48 n n C4D C5D AR6 sing 49 n n C5' O5' AR6 sing 50 n n C5D O5D AR6 sing 51 n n C2 H2 AR6 sing 52 n n N6 HN6 AR6 sing 53 n n N6 HN6A AR6 sing 54 n n C8 H8 AR6 sing 55 n n C1' H1' AR6 sing 56 n n C1D H1D AR6 sing 57 n n C2' H2' AR6 sing 58 n n O2' HO2' AR6 sing 59 n n C2D H2D AR6 sing 60 n n O2D HO2D AR6 sing 61 n n C3' H3' AR6 sing 62 n n O3' HO3' AR6 sing 63 n n C3D H3D AR6 sing 64 n n O3D HO3D AR6 sing 65 n n C4' H4' AR6 sing 66 n n C4D H4D AR6 sing 67 n n C5' H5' AR6 sing 68 n n C5' "H5'A" AR6 sing 69 n n C5D H5D AR6 sing 70 n n C5D H5DA AR6 sing 71 n n O1A H1A AR6 sing 72 n n O1B H1B AR6 sing 73 n n O1D HD1 AR6 sing 74 n n # _atom_sites.entry_id 6QCH _atom_sites.fract_transf_matrix[1][1] 0.010942 _atom_sites.fract_transf_matrix[1][2] 0.006318 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012635 _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] 0.006954 _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 AR6 A 1 401 500 AR6 AR6 . D 3 ZN A 1 402 501 ZN ZN . E 4 EDO A 1 403 601 EDO EDO . F 4 EDO A 1 404 701 EDO EDO . G 4 EDO A 1 405 601 EDO EDO . H 5 SO4 A 1 406 4 SO4 SO4 . I 5 SO4 A 1 407 6 SO4 SO4 . J 5 SO4 A 1 408 8 SO4 SO4 . K 5 SO4 A 1 409 9 SO4 SO4 . L 6 HWB A 1 410 1 HWB CYA . M 2 AR6 B 1 401 500 AR6 AR6 . N 3 ZN B 1 402 501 ZN ZN . O 4 EDO B 1 403 701 EDO EDO . P 5 SO4 B 1 404 1 SO4 SO4 . Q 5 SO4 B 1 405 3 SO4 SO4 . R 5 SO4 B 1 406 5 SO4 SO4 . S 5 SO4 B 1 407 7 SO4 SO4 . T 5 SO4 B 1 408 10 SO4 SO4 . U 5 SO4 B 1 409 11 SO4 SO4 . V 6 HWB B 1 410 2 HWB CYA . W 7 HOH A 1 501 94 HOH HOH . W 7 HOH A 2 502 57 HOH HOH . W 7 HOH A 3 503 19 HOH HOH . W 7 HOH A 4 504 95 HOH HOH . W 7 HOH A 5 505 1 HOH HOH . W 7 HOH A 6 506 7 HOH HOH . W 7 HOH A 7 507 33 HOH HOH . W 7 HOH A 8 508 102 HOH HOH . W 7 HOH A 9 509 85 HOH HOH . W 7 HOH A 10 510 103 HOH HOH . W 7 HOH A 11 511 55 HOH HOH . W 7 HOH A 12 512 41 HOH HOH . W 7 HOH A 13 513 81 HOH HOH . W 7 HOH A 14 514 49 HOH HOH . W 7 HOH A 15 515 18 HOH HOH . W 7 HOH A 16 516 2 HOH HOH . W 7 HOH A 17 517 69 HOH HOH . W 7 HOH A 18 518 36 HOH HOH . W 7 HOH A 19 519 96 HOH HOH . W 7 HOH A 20 520 14 HOH HOH . W 7 HOH A 21 521 108 HOH HOH . W 7 HOH A 22 522 116 HOH HOH . W 7 HOH A 23 523 66 HOH HOH . W 7 HOH A 24 524 16 HOH HOH . W 7 HOH A 25 525 56 HOH HOH . W 7 HOH A 26 526 46 HOH HOH . W 7 HOH A 27 527 100 HOH HOH . W 7 HOH A 28 528 13 HOH HOH . W 7 HOH A 29 529 48 HOH HOH . W 7 HOH A 30 530 47 HOH HOH . W 7 HOH A 31 531 26 HOH HOH . W 7 HOH A 32 532 25 HOH HOH . W 7 HOH A 33 533 45 HOH HOH . W 7 HOH A 34 534 32 HOH HOH . W 7 HOH A 35 535 15 HOH HOH . W 7 HOH A 36 536 9 HOH HOH . W 7 HOH A 37 537 11 HOH HOH . W 7 HOH A 38 538 62 HOH HOH . W 7 HOH A 39 539 74 HOH HOH . W 7 HOH A 40 540 22 HOH HOH . W 7 HOH A 41 541 37 HOH HOH . W 7 HOH A 42 542 44 HOH HOH . W 7 HOH A 43 543 59 HOH HOH . W 7 HOH A 44 544 76 HOH HOH . W 7 HOH A 45 545 107 HOH HOH . W 7 HOH A 46 546 89 HOH HOH . W 7 HOH A 47 547 80 HOH HOH . W 7 HOH A 48 548 73 HOH HOH . W 7 HOH A 49 549 5 HOH HOH . W 7 HOH A 50 550 117 HOH HOH . W 7 HOH A 51 551 61 HOH HOH . W 7 HOH A 52 552 88 HOH HOH . W 7 HOH A 53 553 51 HOH HOH . W 7 HOH A 54 554 31 HOH HOH . W 7 HOH A 55 555 71 HOH HOH . W 7 HOH A 56 556 109 HOH HOH . W 7 HOH A 57 557 97 HOH HOH . W 7 HOH A 58 558 38 HOH HOH . W 7 HOH A 59 559 77 HOH HOH . W 7 HOH A 60 560 60 HOH HOH . W 7 HOH A 61 561 113 HOH HOH . W 7 HOH A 62 562 54 HOH HOH . W 7 HOH A 63 563 65 HOH HOH . W 7 HOH A 64 564 53 HOH HOH . W 7 HOH A 65 565 72 HOH HOH . X 7 HOH B 1 501 58 HOH HOH . X 7 HOH B 2 502 83 HOH HOH . X 7 HOH B 3 503 3 HOH HOH . X 7 HOH B 4 504 52 HOH HOH . X 7 HOH B 5 505 93 HOH HOH . X 7 HOH B 6 506 6 HOH HOH . X 7 HOH B 7 507 27 HOH HOH . X 7 HOH B 8 508 70 HOH HOH . X 7 HOH B 9 509 114 HOH HOH . X 7 HOH B 10 510 42 HOH HOH . X 7 HOH B 11 511 92 HOH HOH . X 7 HOH B 12 512 104 HOH HOH . X 7 HOH B 13 513 43 HOH HOH . X 7 HOH B 14 514 24 HOH HOH . X 7 HOH B 15 515 75 HOH HOH . X 7 HOH B 16 516 84 HOH HOH . X 7 HOH B 17 517 79 HOH HOH . X 7 HOH B 18 518 78 HOH HOH . X 7 HOH B 19 519 4 HOH HOH . X 7 HOH B 20 520 28 HOH HOH . X 7 HOH B 21 521 111 HOH HOH . X 7 HOH B 22 522 10 HOH HOH . X 7 HOH B 23 523 101 HOH HOH . X 7 HOH B 24 524 12 HOH HOH . X 7 HOH B 25 525 50 HOH HOH . X 7 HOH B 26 526 68 HOH HOH . X 7 HOH B 27 527 35 HOH HOH . X 7 HOH B 28 528 99 HOH HOH . X 7 HOH B 29 529 39 HOH HOH . X 7 HOH B 30 530 40 HOH HOH . X 7 HOH B 31 531 17 HOH HOH . X 7 HOH B 32 532 8 HOH HOH . X 7 HOH B 33 533 20 HOH HOH . X 7 HOH B 34 534 82 HOH HOH . X 7 HOH B 35 535 30 HOH HOH . X 7 HOH B 36 536 112 HOH HOH . X 7 HOH B 37 537 63 HOH HOH . X 7 HOH B 38 538 67 HOH HOH . X 7 HOH B 39 539 23 HOH HOH . X 7 HOH B 40 540 105 HOH HOH . X 7 HOH B 41 541 90 HOH HOH . X 7 HOH B 42 542 64 HOH HOH . X 7 HOH B 43 543 91 HOH HOH . X 7 HOH B 44 544 115 HOH HOH . X 7 HOH B 45 545 29 HOH HOH . X 7 HOH B 46 546 34 HOH HOH . X 7 HOH B 47 547 86 HOH HOH . X 7 HOH B 48 548 98 HOH HOH . X 7 HOH B 49 549 87 HOH HOH . X 7 HOH B 50 550 106 HOH HOH . X 7 HOH B 51 551 21 HOH HOH . X 7 HOH B 52 552 110 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 N1 AR6 . . . C 2 -29.85 9.52 24.402 1 38.29 ? N1 AR6 401 A 1 HETATM 2 C C2 AR6 . . . C 2 -30.667 9.354 23.342 1 34.08 ? C2 AR6 401 A 1 HETATM 3 N N3 AR6 . . . C 2 -31.344 10.282 22.648 1 38.88 ? N3 AR6 401 A 1 HETATM 4 C C4 AR6 . . . C 2 -31.014 11.523 23.016 1 37.51 ? C4 AR6 401 A 1 HETATM 5 C C5 AR6 . . . C 2 -30.224 11.858 24.103 1 33.11 ? C5 AR6 401 A 1 HETATM 6 C C6 AR6 . . . C 2 -29.599 10.797 24.815 1 32.15 ? C6 AR6 401 A 1 HETATM 7 N N6 AR6 . . . C 2 -28.742 10.956 25.836 1 39.82 ? N6 AR6 401 A 1 HETATM 8 N N7 AR6 . . . C 2 -30.178 13.251 24.19 1 33.69 ? N7 AR6 401 A 1 HETATM 9 C C8 AR6 . . . C 2 -30.871 13.697 23.168 1 33.55 ? C8 AR6 401 A 1 HETATM 10 N N9 AR6 . . . C 2 -31.503 12.694 22.488 1 33.98 ? N9 AR6 401 A 1 HETATM 11 P PA AR6 . . . C 2 -31.953 17.127 17.117 1 42.53 ? PA AR6 401 A 1 HETATM 12 P PB AR6 . . . C 2 -29.834 16.748 15.073 1 34.76 ? PB AR6 401 A 1 HETATM 13 C C1' AR6 . . . C 2 -32.389 12.831 21.285 1 31.93 ? C1' AR6 401 A 1 HETATM 14 O O1A AR6 . . . C 2 -32.98 17.28 16.031 1 43.9 ? O1A AR6 401 A 1 HETATM 15 O O1B AR6 . . . C 2 -28.405 16.379 15.248 1 43.5 ? O1B AR6 401 A 1 HETATM 16 C C1D AR6 . . . C 2 -29.694 21.776 13.519 1 40.63 ? C1D AR6 401 A 1 HETATM 17 O O1D AR6 . . . C 2 -30.392 22.821 12.958 1 40.96 ? O1D AR6 401 A 1 HETATM 18 C C2' AR6 . . . C 2 -33.478 13.883 21.281 1 27.39 ? C2' AR6 401 A 1 HETATM 19 O O2' AR6 . . . C 2 -34.658 13.297 21.718 1 25.06 ? O2' AR6 401 A 1 HETATM 20 O O2A AR6 . . . C 2 -31.987 18.035 18.321 1 37.48 ? O2A AR6 401 A 1 HETATM 21 O O2B AR6 . . . C 2 -30.818 15.776 14.503 1 40.21 ? O2B AR6 401 A 1 HETATM 22 C C2D AR6 . . . C 2 -28.184 21.709 13.286 1 36.77 ? C2D AR6 401 A 1 HETATM 23 O O2D AR6 . . . C 2 -27.751 21.989 11.966 1 44.74 ? O2D AR6 401 A 1 HETATM 24 C C3' AR6 . . . C 2 -33.595 14.319 19.787 1 28.01 ? C3' AR6 401 A 1 HETATM 25 O O3' AR6 . . . C 2 -34.699 13.699 19.151 1 32.02 ? O3' AR6 401 A 1 HETATM 26 O O3A AR6 . . . C 2 -30.466 17.264 16.498 1 40.2 ? O3A AR6 401 A 1 HETATM 27 C C3D AR6 . . . C 2 -27.942 20.215 13.518 1 41.29 ? C3D AR6 401 A 1 HETATM 28 O O3D AR6 . . . C 2 -26.767 19.715 12.898 1 39.67 ? O3D AR6 401 A 1 HETATM 29 C C4' AR6 . . . C 2 -32.262 13.884 19.178 1 28.23 ? C4' AR6 401 A 1 HETATM 30 O O4' AR6 . . . C 2 -31.536 13.227 20.243 1 30.01 ? O4' AR6 401 A 1 HETATM 31 C C4D AR6 . . . C 2 -29.112 19.639 12.72 1 38.67 ? C4D AR6 401 A 1 HETATM 32 O O4D AR6 . . . C 2 -30.178 20.571 12.911 1 38.91 ? O4D AR6 401 A 1 HETATM 33 C C5' AR6 . . . C 2 -31.348 14.906 18.574 1 32.48 ? C5' AR6 401 A 1 HETATM 34 O O5' AR6 . . . C 2 -32.045 15.601 17.493 1 39.54 ? O5' AR6 401 A 1 HETATM 35 C C5D AR6 . . . C 2 -29.609 18.256 13.012 1 41.46 ? C5D AR6 401 A 1 HETATM 36 O O5D AR6 . . . C 2 -29.942 18.182 14.404 1 36.36 ? O5D AR6 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 36 #