data_8CLG # _model_server_result.job_id 7q192cIijf0JdTH9oOO_kw _model_server_result.datetime_utc '2024-11-05 08:37:09' _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 8clg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":401}' # _entry.id 8CLG # _exptl.entry_id 8CLG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 11 _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 8CLG _cell.length_a 106.76 _cell.length_b 160.76 _cell.length_c 180.96 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8CLG _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,X,Y,Z,AA,BA _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 11 _struct_asym.id V _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc4 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? metalc ? metalc5 A OE1 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc7 G O2G GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc8 G O1B GTP . A GTP 501 1_555 H MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? metalc ? metalc9 H MG MG . A MG 502 1_555 W O HOH . A HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc10 H MG MG . A MG 502 1_555 W O HOH . A HOH 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc11 B OE1 GLN 11 B GLN 11 1_555 O MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc12 B OE2 GLU 111 B GLU 113 1_555 K CA CA . B CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc13 K CA CA . B CA 502 1_555 Y O HOH . C HOH 618 4_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? metalc ? metalc14 N O1A GDP . B GDP 505 1_555 O MG MG . B MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc15 O MG MG . B MG 506 1_555 X O HOH . B HOH 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc16 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc17 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc18 C O THR 41 C THR 41 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc19 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc22 C OD2 ASP 69 C ASP 69 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.871 ? metalc ? metalc23 P O1B GTP . C GTP 501 1_555 Q MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc24 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? metalc ? metalc25 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc26 Q MG MG . C MG 502 1_555 Y O HOH . C HOH 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc27 D OE1 GLN 11 D GLN 11 1_555 U MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? metalc ? metalc28 T O1A GDP . D GDP 502 1_555 U MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? # _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 8CLG _atom_sites.fract_transf_matrix[1][1] 0.009367 _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] 0.00622 _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 7 CA B 1 501 504 CA CA . K 7 CA B 1 502 505 CA CA . L 8 EP B 1 503 506 EP EPA . M 9 LOC B 1 504 507 LOC COL . N 10 GDP B 1 505 508 GDP GDP . O 6 MG B 1 506 509 MG MG . P 5 GTP C 1 501 510 GTP GTP . Q 6 MG C 1 502 511 MG MG . R 7 CA C 1 503 516 CA CA . S 8 EP D 1 501 512 EP EPA . T 10 GDP D 1 502 513 GDP GDP . U 6 MG D 1 503 514 MG MG . V 11 ACP F 1 401 515 ACP ACP . W 12 HOH A 1 601 6 HOH HOH . W 12 HOH A 2 602 10 HOH HOH . W 12 HOH A 3 603 23 HOH HOH . W 12 HOH A 4 604 66 HOH HOH . W 12 HOH A 5 605 50 HOH HOH . W 12 HOH A 6 606 30 HOH HOH . W 12 HOH A 7 607 4 HOH HOH . W 12 HOH A 8 608 47 HOH HOH . X 12 HOH B 1 601 36 HOH HOH . X 12 HOH B 2 602 13 HOH HOH . X 12 HOH B 3 603 22 HOH HOH . X 12 HOH B 4 604 48 HOH HOH . X 12 HOH B 5 605 14 HOH HOH . X 12 HOH B 6 606 69 HOH HOH . X 12 HOH B 7 607 44 HOH HOH . X 12 HOH B 8 608 37 HOH HOH . X 12 HOH B 9 609 51 HOH HOH . Y 12 HOH C 1 601 61 HOH HOH . Y 12 HOH C 2 602 2 HOH HOH . Y 12 HOH C 3 603 3 HOH HOH . Y 12 HOH C 4 604 24 HOH HOH . Y 12 HOH C 5 605 32 HOH HOH . Y 12 HOH C 6 606 64 HOH HOH . Y 12 HOH C 7 607 60 HOH HOH . Y 12 HOH C 8 608 54 HOH HOH . Y 12 HOH C 9 609 49 HOH HOH . Y 12 HOH C 10 610 46 HOH HOH . Y 12 HOH C 11 611 73 HOH HOH . Y 12 HOH C 12 612 41 HOH HOH . Y 12 HOH C 13 613 65 HOH HOH . Y 12 HOH C 14 614 25 HOH HOH . Y 12 HOH C 15 615 16 HOH HOH . Y 12 HOH C 16 616 38 HOH HOH . Y 12 HOH C 17 617 12 HOH HOH . Y 12 HOH C 18 618 19 HOH HOH . Y 12 HOH C 19 619 45 HOH HOH . Y 12 HOH C 20 620 21 HOH HOH . Y 12 HOH C 21 621 43 HOH HOH . Z 12 HOH D 1 601 71 HOH HOH . Z 12 HOH D 2 602 39 HOH HOH . Z 12 HOH D 3 603 79 HOH HOH . Z 12 HOH D 4 604 26 HOH HOH . AA 12 HOH E 1 201 72 HOH HOH . BA 12 HOH F 1 501 40 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 . . . V 11 10.002 50.087 95.139 1 178.14 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . V 11 9.39 49.812 96.483 1 174.59 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . V 11 10.028 48.862 94.266 1 169.85 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . V 11 9.348 51.251 94.453 1 158.64 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . V 11 11.888 52.259 96.027 1 158.83 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . V 11 12.1 53.159 94.842 1 147.27 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . V 11 12.952 52.291 97.089 1 157.13 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . V 11 11.719 50.555 95.421 1 146.18 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . V 11 10.081 53.023 98.162 1 137.23 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . V 11 10.896 52.237 99.132 1 141.87 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . V 11 10.116 54.511 98.232 1 108.03 -1 O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . V 11 10.481 52.586 96.678 1 142.5 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . V 11 8.563 52.523 98.214 1 140.03 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . V 11 7.824 52.766 99.431 1 134.97 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . V 11 7.787 51.504 100.254 1 122.79 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . V 11 8.788 51.584 101.297 1 112.62 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . V 11 6.476 51.24 100.997 1 123.27 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . V 11 6.285 49.853 101.22 1 123.24 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . V 11 6.678 51.99 102.314 1 123.05 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . V 11 5.999 51.372 103.383 1 129.18 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . V 11 8.19 51.933 102.524 1 115.08 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . V 11 8.748 53.206 102.963 1 116.93 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . V 11 9.603 54.018 102.262 1 111.78 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . V 11 9.931 55.107 102.91 1 96.05 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . V 11 9.247 55.011 104.112 1 104.57 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . V 11 9.181 55.858 105.235 1 100.32 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . V 11 9.835 57.012 105.331 1 91.11 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . V 11 8.404 55.464 106.27 1 100.2 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . V 11 7.745 54.304 106.167 1 102.91 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . V 11 7.731 53.43 105.167 1 107.76 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . V 11 8.511 53.844 104.156 1 110.88 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 46 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 31 #