data_1VFP # _model_server_result.job_id I3151LtsgkDkPq1invlpsg _model_server_result.datetime_utc '2024-11-21 13:58:33' _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 1vfp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1001}' # _entry.id 1VFP # _exptl.entry_id 1VFP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 107.21 _cell.angle_gamma 90 _cell.entry_id 1VFP _cell.length_a 90.92 _cell.length_b 123.62 _cell.length_c 151.82 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VFP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 J 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 876 A CYS 876 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 B SG CYS 876 B CYS 876 1_555 B SG CYS 888 B CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc1 A O VAL 304 A VAL 304 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.759 ? metalc ? metalc2 A O ALA 305 A ALA 305 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.288 ? metalc ? metalc3 A O ILE 307 A ILE 307 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? metalc ? metalc4 A OE1 GLU 309 A GLU 309 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.995 ? metalc ? metalc5 A OE2 GLU 309 A GLU 309 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? metalc ? metalc6 A OD2 ASP 351 A ASP 351 1_555 E MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.399 ? metalc ? metalc7 A O THR 353 A THR 353 1_555 E MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc8 A OD1 ASP 703 A ASP 703 1_555 E MG MG . A MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc9 A OD1 ASN 768 A ASN 768 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc10 A OE2 GLU 771 A GLU 771 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc11 A OD1 ASN 796 A ASN 796 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc12 A OG1 THR 799 A THR 799 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc13 A OD2 ASP 800 A ASP 800 1_555 C CA CA . A CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc14 A OD1 ASP 800 A ASP 800 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc15 A OE2 GLU 908 A GLU 908 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.509 ? metalc ? metalc16 A OE1 GLU 908 A GLU 908 1_555 D CA CA . A CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.198 ? metalc ? metalc17 D CA CA . A CA 996 1_555 K O HOH . A HOH 1013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc18 D CA CA . A CA 996 1_555 K O HOH . A HOH 1014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc19 E MG MG . A MG 997 1_555 F O2G ACP . A ACP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc20 E MG MG . A MG 997 1_555 K O HOH . A HOH 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc21 E MG MG . A MG 997 1_555 K O HOH . A HOH 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc22 B O VAL 304 B VAL 304 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc23 B O ALA 305 B ALA 305 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.212 ? metalc ? metalc24 B O ILE 307 B ILE 307 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? metalc ? metalc25 B OE2 GLU 309 B GLU 309 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? metalc ? metalc26 B OE1 GLU 309 B GLU 309 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.078 ? metalc ? metalc27 B OD2 ASP 351 B ASP 351 1_555 I MG MG . B MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc28 B O THR 353 B THR 353 1_555 I MG MG . B MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc29 B OD1 ASP 703 B ASP 703 1_555 I MG MG . B MG 997 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc30 B OD1 ASN 768 B ASN 768 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? metalc ? metalc31 B OE2 GLU 771 B GLU 771 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.373 ? metalc ? metalc32 B OD1 ASN 796 B ASN 796 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.363 ? metalc ? metalc33 B OG1 THR 799 B THR 799 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc34 B OD2 ASP 800 B ASP 800 1_555 G CA CA . B CA 995 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc35 B OD1 ASP 800 B ASP 800 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc36 B OE2 GLU 908 B GLU 908 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc37 B OE1 GLU 908 B GLU 908 1_555 H CA CA . B CA 996 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.203 ? metalc ? metalc38 H CA CA . B CA 996 1_555 L O HOH . B HOH 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc39 H CA CA . B CA 996 1_555 L O HOH . B HOH 2014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? metalc ? metalc40 I MG MG . B MG 997 1_555 J O2G ACP . B ACP 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc41 I MG MG . B MG 997 1_555 L O HOH . B HOH 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc42 I MG MG . B MG 997 1_555 L O HOH . B HOH 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.961 ? # _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 1VFP _atom_sites.fract_transf_matrix[1][1] 0.010999 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003407 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008089 _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] 0.006895 _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 CA A 1 995 995 CA CA . D 2 CA A 1 996 996 CA CA . E 3 MG A 1 997 997 MG MG . F 4 ACP A 1 1001 1001 ACP ACP . G 2 CA B 1 995 995 CA CA . H 2 CA B 1 996 996 CA CA . I 3 MG B 1 997 997 MG MG . J 4 ACP B 1 2001 2001 ACP ACP . K 5 HOH A 1 1011 1011 HOH HOH . K 5 HOH A 2 1012 1012 HOH HOH . K 5 HOH A 3 1013 1013 HOH HOH . K 5 HOH A 4 1014 1014 HOH HOH . L 5 HOH B 1 2011 2011 HOH HOH . L 5 HOH B 2 2012 2012 HOH HOH . L 5 HOH B 3 2013 2013 HOH HOH . L 5 HOH B 4 2014 2014 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 . . . F 4 17.682 -3.038 54.982 1 37.51 ? PG ACP 1001 A 1 HETATM 2 O O1G ACP . . . F 4 16.204 -2.75 55.213 1 33.19 ? O1G ACP 1001 A 1 HETATM 3 O O2G ACP . . . F 4 17.96 -3.527 53.601 1 34.21 ? O2G ACP 1001 A 1 HETATM 4 O O3G ACP . . . F 4 18.615 -1.891 55.338 1 40.72 ? O3G ACP 1001 A 1 HETATM 5 P PB ACP . . . F 4 17.774 -4.435 57.682 1 35.75 ? PB ACP 1001 A 1 HETATM 6 O O1B ACP . . . F 4 18.305 -5.801 57.973 1 35.92 ? O1B ACP 1001 A 1 HETATM 7 O O2B ACP . . . F 4 18.234 -3.396 58.614 1 37.94 ? O2B ACP 1001 A 1 HETATM 8 C C3B ACP . . . F 4 18.204 -4.335 56.001 1 38.97 ? C3B ACP 1001 A 1 HETATM 9 P PA ACP . . . F 4 15.287 -5.869 58.386 1 39.89 ? PA ACP 1001 A 1 HETATM 10 O O1A ACP . . . F 4 15.703 -7.047 57.493 1 37.73 ? O1A ACP 1001 A 1 HETATM 11 O O2A ACP . . . F 4 13.85 -5.5 58.333 1 39.91 ? O2A ACP 1001 A 1 HETATM 12 O O3A ACP . . . F 4 16.18 -4.596 58.069 1 38.26 ? O3A ACP 1001 A 1 HETATM 13 O O5' ACP . . . F 4 15.872 -6.268 59.799 1 38.74 ? O5' ACP 1001 A 1 HETATM 14 C C5' ACP . . . F 4 15.624 -5.299 60.813 1 41.08 ? C5' ACP 1001 A 1 HETATM 15 C C4' ACP . . . F 4 16.372 -5.2 62.153 1 43.61 ? C4' ACP 1001 A 1 HETATM 16 O O4' ACP . . . F 4 16.491 -6.505 62.675 1 45.96 ? O4' ACP 1001 A 1 HETATM 17 C C3' ACP . . . F 4 17.742 -4.969 61.569 1 43.89 ? C3' ACP 1001 A 1 HETATM 18 O O3' ACP . . . F 4 17.974 -3.624 61.231 1 49.37 ? O3' ACP 1001 A 1 HETATM 19 C C2' ACP . . . F 4 18.654 -5.587 62.63 1 42.96 ? C2' ACP 1001 A 1 HETATM 20 O O2' ACP . . . F 4 18.849 -4.656 63.675 1 45.16 ? O2' ACP 1001 A 1 HETATM 21 C C1' ACP . . . F 4 17.858 -6.761 62.974 1 41.93 ? C1' ACP 1001 A 1 HETATM 22 N N9 ACP . . . F 4 18.354 -8.037 62.283 1 38.62 ? N9 ACP 1001 A 1 HETATM 23 C C8 ACP . . . F 4 18.709 -8.297 61.009 1 37.8 ? C8 ACP 1001 A 1 HETATM 24 N N7 ACP . . . F 4 19.113 -9.542 60.76 1 40.18 ? N7 ACP 1001 A 1 HETATM 25 C C5 ACP . . . F 4 19.007 -10.106 61.951 1 37.81 ? C5 ACP 1001 A 1 HETATM 26 C C6 ACP . . . F 4 19.267 -11.429 62.466 1 37.56 ? C6 ACP 1001 A 1 HETATM 27 N N6 ACP . . . F 4 19.731 -12.417 61.651 1 39.17 ? N6 ACP 1001 A 1 HETATM 28 N N1 ACP . . . F 4 19.055 -11.735 63.812 1 37.35 ? N1 ACP 1001 A 1 HETATM 29 C C2 ACP . . . F 4 18.596 -10.764 64.658 1 38.69 ? C2 ACP 1001 A 1 HETATM 30 N N3 ACP . . . F 4 18.324 -9.478 64.259 1 38.68 ? N3 ACP 1001 A 1 HETATM 31 C C4 ACP . . . F 4 18.541 -9.209 62.926 1 37.73 ? C4 ACP 1001 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 348 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #