data_4CVL # _model_server_result.job_id IEHbVFWwHIlLpXuNk820kw _model_server_result.datetime_utc '2025-01-22 03:06:08' _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 4cvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1452}' # _entry.id 4CVL # _exptl.entry_id 4CVL _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _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 4CVL _cell.length_a 58.58 _cell.length_b 87.38 _cell.length_c 91.52 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4CVL _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _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 OG1 THR 114 A THR 114 1_555 C MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc2 A OD1 ASN 140 A ASN 140 1_555 C MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc3 A OE2 GLU 164 A GLU 164 1_555 C MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc4 B O3G ACP . A ACP 1452 1_555 C MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc5 B O2B ACP . A ACP 1452 1_555 C MG MG . A MG 1453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc6 B O3G ACP . A ACP 1452 1_555 D MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc7 B O2B ACP . A ACP 1452 1_555 D MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc8 B O1A ACP . A ACP 1452 1_555 D MG MG . A MG 1454 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? # _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 4CVL _atom_sites.fract_transf_matrix[1][1] 0.017071 _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] 0.011444 _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] 0.010927 _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 B 2 ACP A 1 1452 1452 ACP ACP . C 3 MG A 1 1453 1453 MG MG . D 3 MG A 1 1454 1454 MG MG . # 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 . . . B 2 18.571 -28.453 -13.946 1 70.31 ? PG ACP 1452 A 1 HETATM 2 O O1G ACP . . . B 2 18.333 -26.854 -13.927 1 65.4 ? O1G ACP 1452 A 1 HETATM 3 O O2G ACP . . . B 2 19.586 -28.874 -15.109 1 71.44 ? O2G ACP 1452 A 1 HETATM 4 O O3G ACP . . . B 2 17.3 -29.188 -14.18 1 76.7 ? O3G ACP 1452 A 1 HETATM 5 P PB ACP . . . B 2 18.208 -29.558 -11.194 1 52.46 ? PB ACP 1452 A 1 HETATM 6 O O1B ACP . . . B 2 17.872 -28.497 -10.222 1 50.55 ? O1B ACP 1452 A 1 HETATM 7 O O2B ACP . . . B 2 16.895 -30.208 -11.859 1 48.99 ? O2B ACP 1452 A 1 HETATM 8 C C3B ACP . . . B 2 19.381 -28.922 -12.404 1 61.44 ? C3B ACP 1452 A 1 HETATM 9 P PA ACP . . . B 2 18.58 -32.143 -10.354 1 62.74 ? PA ACP 1452 A 1 HETATM 10 O O1A ACP . . . B 2 18.407 -32.598 -11.793 1 65.36 ? O1A ACP 1452 A 1 HETATM 11 O O2A ACP . . . B 2 17.462 -32.303 -9.337 1 56.51 ? O2A ACP 1452 A 1 HETATM 12 O O3A ACP . . . B 2 19.039 -30.621 -10.371 1 55.73 ? O3A ACP 1452 A 1 HETATM 13 O O5' ACP . . . B 2 19.976 -32.753 -9.812 1 62.4 ? O5' ACP 1452 A 1 HETATM 14 C C5' ACP . . . B 2 21.046 -32.893 -10.744 1 58.31 ? C5' ACP 1452 A 1 HETATM 15 C C4' ACP . . . B 2 22.403 -32.802 -10.072 1 57.38 ? C4' ACP 1452 A 1 HETATM 16 O O4' ACP . . . B 2 22.49 -31.664 -9.213 1 54.95 ? O4' ACP 1452 A 1 HETATM 17 C C3' ACP . . . B 2 22.713 -34.063 -9.271 1 57.03 ? C3' ACP 1452 A 1 HETATM 18 O O3' ACP . . . B 2 23.737 -34.835 -9.908 1 60.71 ? O3' ACP 1452 A 1 HETATM 19 C C2' ACP . . . B 2 23.218 -33.588 -7.935 1 58.45 ? C2' ACP 1452 A 1 HETATM 20 O O2' ACP . . . B 2 24.598 -33.896 -7.716 1 59.56 ? O2' ACP 1452 A 1 HETATM 21 C C1' ACP . . . B 2 23.05 -32.078 -7.956 1 59.14 ? C1' ACP 1452 A 1 HETATM 22 N N9 ACP . . . B 2 22.154 -31.745 -6.83 1 57.12 ? N9 ACP 1452 A 1 HETATM 23 C C8 ACP . . . B 2 20.894 -32.198 -6.664 1 55.95 ? C8 ACP 1452 A 1 HETATM 24 N N7 ACP . . . B 2 20.375 -31.693 -5.522 1 56.57 ? N7 ACP 1452 A 1 HETATM 25 C C5 ACP . . . B 2 21.317 -30.914 -4.953 1 53.32 ? C5 ACP 1452 A 1 HETATM 26 C C6 ACP . . . B 2 21.418 -30.072 -3.742 1 51.3 ? C6 ACP 1452 A 1 HETATM 27 N N6 ACP . . . B 2 20.356 -30 -2.91 1 51.75 ? N6 ACP 1452 A 1 HETATM 28 N N1 ACP . . . B 2 22.578 -29.411 -3.49 1 48.9 ? N1 ACP 1452 A 1 HETATM 29 C C2 ACP . . . B 2 23.62 -29.503 -4.334 1 51.93 ? C2 ACP 1452 A 1 HETATM 30 N N3 ACP . . . B 2 23.585 -30.247 -5.467 1 52.47 ? N3 ACP 1452 A 1 HETATM 31 C C4 ACP . . . B 2 22.491 -30.963 -5.814 1 53.01 ? C4 ACP 1452 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #