data_8CLF # _model_server_result.job_id 9vZIz1DbEI-3-BcF8CvbGg _model_server_result.datetime_utc '2024-11-05 11:03:48' _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 8clf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":401}' # _entry.id 8CLF # _exptl.entry_id 8CLF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 90 _cell.entry_id 8CLF _cell.length_a 106.65 _cell.length_b 160.33 _cell.length_c 180.95 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLF _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 _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,K,L,M,N,O,P,Q,R,S,T,U,V,W _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 10 _struct_asym.id R _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 metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.635 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc6 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc7 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc8 G O1G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.872 ? metalc ? metalc9 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc10 H MG MG . A MG 502 1_555 S O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? metalc ? metalc11 J O1A GDP . B GDP 501 1_555 K MG MG . B MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc12 K MG MG . B MG 502 1_555 T O HOH . B HOH 606 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.746 ? metalc ? metalc13 C OD1 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc14 C OD2 ASP 39 C ASP 39 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc15 C O THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc16 C OG1 THR 41 C THR 41 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc17 C O GLY 44 C GLY 44 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc18 C OE1 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc19 C OE2 GLU 55 C GLU 55 1_555 O CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc20 C OD2 ASP 69 C ASP 69 1_555 N MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc21 N MG MG . C MG 502 1_555 U O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc22 N MG MG . C MG 502 1_555 U O HOH . C HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.617 ? metalc ? metalc23 N MG MG . C MG 502 1_555 U O HOH . C HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? metalc ? metalc24 D OE1 GLN 11 D GLN 11 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.964 ? metalc ? metalc25 D OD2 ASP 177 D ASP 179 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.828 ? metalc ? metalc26 P O1A GDP . D GDP 501 1_555 Q MG MG . D MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 PG O1G ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 8CLF _atom_sites.fract_transf_matrix[1][1] 0.009376 _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] 0.006237 _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] 0.005526 _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 G 5 GTP A 1 501 501 GTP GTP . H 6 MG A 1 502 502 MG MG . I 7 CA A 1 503 503 CA CA . J 8 GDP B 1 501 504 GDP GDP . K 6 MG B 1 502 505 MG MG . L 9 V1O B 1 503 506 V1O SQB . M 5 GTP C 1 501 507 GTP GTP . N 6 MG C 1 502 508 MG MG . O 7 CA C 1 503 512 CA CA . P 8 GDP D 1 501 509 GDP GDP . Q 6 MG D 1 502 510 MG MG . R 10 ACP F 1 401 511 ACP ACP . S 11 HOH A 1 601 66 HOH HOH . S 11 HOH A 2 602 29 HOH HOH . S 11 HOH A 3 603 42 HOH HOH . S 11 HOH A 4 604 8 HOH HOH . T 11 HOH B 1 601 65 HOH HOH . T 11 HOH B 2 602 3 HOH HOH . T 11 HOH B 3 603 14 HOH HOH . T 11 HOH B 4 604 1 HOH HOH . T 11 HOH B 5 605 5 HOH HOH . T 11 HOH B 6 606 30 HOH HOH . U 11 HOH C 1 601 13 HOH HOH . U 11 HOH C 2 602 27 HOH HOH . U 11 HOH C 3 603 48 HOH HOH . U 11 HOH C 4 604 11 HOH HOH . U 11 HOH C 5 605 68 HOH HOH . U 11 HOH C 6 606 36 HOH HOH . U 11 HOH C 7 607 43 HOH HOH . U 11 HOH C 8 608 25 HOH HOH . U 11 HOH C 9 609 44 HOH HOH . U 11 HOH C 10 610 63 HOH HOH . U 11 HOH C 11 611 17 HOH HOH . U 11 HOH C 12 612 2 HOH HOH . U 11 HOH C 13 613 28 HOH HOH . U 11 HOH C 14 614 46 HOH HOH . U 11 HOH C 15 615 49 HOH HOH . U 11 HOH C 16 616 72 HOH HOH . U 11 HOH C 17 617 4 HOH HOH . U 11 HOH C 18 618 45 HOH HOH . V 11 HOH D 1 601 58 HOH HOH . W 11 HOH F 1 501 19 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 P PG ACP . . . R 10 8.734 51.469 95.022 1 159.06 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . R 10 9.151 50.071 94.673 1 163.76 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . R 10 8.092 52.165 93.857 1 143.56 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . R 10 7.865 51.51 96.247 1 126.65 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . R 10 11.33 51.572 96.637 1 159.19 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . R 10 12.699 51.465 96.028 1 146.22 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . R 10 10.683 50.278 97.035 1 158.36 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . R 10 10.248 52.363 95.413 1 140.49 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . R 10 10.298 52.918 99.016 1 137.79 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . R 10 10.789 54.129 99.735 1 124.2 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . R 10 8.957 52.969 98.366 1 133.95 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . R 10 11.381 52.53 97.902 1 143.89 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . R 10 10.365 51.654 100 1 139.89 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . R 10 9.443 50.554 99.788 1 139.75 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . R 10 8.634 50.31 101.038 1 141.11 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . R 10 9.377 50.754 102.199 1 129.9 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . R 10 7.303 51.058 101.131 1 152.29 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . R 10 6.283 50.335 100.456 1 180.04 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . R 10 7.072 51.108 102.643 1 135.5 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . R 10 6.433 49.95 103.134 1 144.54 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . R 10 8.493 51.228 103.191 1 132.12 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . R 10 8.879 52.591 103.536 1 122.46 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . R 10 9.607 53.458 102.762 1 120.24 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . R 10 9.809 54.618 103.333 1 117.2 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . R 10 9.179 54.511 104.563 1 121.33 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . R 10 9.037 55.412 105.636 1 117.43 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . R 10 9.539 56.642 105.64 1 98.57 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . R 10 8.346 54.989 106.72 1 115.48 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . R 10 7.84 53.751 106.709 1 114.79 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . R 10 7.915 52.819 105.764 1 119.19 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . R 10 8.602 53.265 104.701 1 122.54 ? C4 ACP 401 F 1 HETATM 32 H H3B1 ACP . . . R 10 10.009 53.245 95.738 1 140.49 ? H3B1 ACP 401 F 1 HETATM 33 H H3B2 ACP . . . R 10 10.751 52.489 94.593 1 140.49 ? H3B2 ACP 401 F 1 HETATM 34 H "H5'1" ACP . . . R 10 9.934 49.752 99.55 1 139.75 ? "H5'1" ACP 401 F 1 HETATM 35 H "H5'2" ACP . . . R 10 8.852 50.756 99.046 1 139.75 ? "H5'2" ACP 401 F 1 HETATM 36 H H4' ACP . . . R 10 8.456 49.357 101.004 1 141.11 ? H4' ACP 401 F 1 HETATM 37 H H3' ACP . . . R 10 7.302 51.936 100.72 1 152.29 ? H3' ACP 401 F 1 HETATM 38 H HO3' ACP . . . R 10 5.619 50.835 100.334 1 180.04 ? HO3' ACP 401 F 1 HETATM 39 H H2' ACP . . . R 10 6.484 51.833 102.906 1 135.5 ? H2' ACP 401 F 1 HETATM 40 H HO2' ACP . . . R 10 5.673 49.879 102.784 1 144.54 ? HO2' ACP 401 F 1 HETATM 41 H H1' ACP . . . R 10 8.532 50.711 104.011 1 132.12 ? H1' ACP 401 F 1 HETATM 42 H H8 ACP . . . R 10 9.939 53.234 101.879 1 120.24 ? H8 ACP 401 F 1 HETATM 43 H HN61 ACP . . . R 10 9.98 56.929 104.96 1 98.57 ? HN61 ACP 401 F 1 HETATM 44 H HN62 ACP . . . R 10 9.423 57.152 106.323 1 98.57 ? HN62 ACP 401 F 1 HETATM 45 H H2 ACP . . . R 10 7.347 53.497 107.505 1 114.79 ? H2 ACP 401 F 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 45 #