data_7SSI # _model_server_result.job_id QLcT8CNe-uv09GSzTN4bhg _model_server_result.datetime_utc '2024-11-27 22:32:44' _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 7ssi # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":401}' # _entry.id 7SSI # _exptl.entry_id 7SSI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.74 _cell.angle_gamma 90 _cell.entry_id 7SSI _cell.length_a 88.067 _cell.length_b 115.634 _cell.length_c 91.374 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7SSI _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,G,H,I,J,K,Q,R 1 1 D,E,F,L,M,N,O,P,S,T,U 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 ? 3 G N N ? 3 I N N ? 3 L N N ? 3 N 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 OE2 GLU 137 A GLU 289 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.268 ? metalc ? metalc2 A OD1 ASN 141 A ASN 293 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc3 G O3G ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.282 ? metalc ? metalc4 G O2B ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc5 G O1A ACP . A ACP 401 1_555 H MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc6 B OE2 GLU 137 B GLU 289 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc7 B OD1 ASN 141 B ASN 293 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc8 I O3G ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc9 I O2B ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc10 I O1A ACP . B ACP 401 1_555 J MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? metalc ? metalc11 J MG MG . B MG 402 1_555 Q O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.945 ? metalc ? metalc12 C OD2 ASP 58 C ASP 54 1_555 K MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc13 C O GLU 60 C GLU 56 1_555 K MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc14 K MG MG . C MG 201 1_555 R O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc15 D OE2 GLU 137 D GLU 289 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc16 D OD1 ASN 141 D ASN 293 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc17 L O3G ACP . D ACP 401 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc18 L O2B ACP . D ACP 401 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc19 L O1A ACP . D ACP 401 1_555 M MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc20 M MG MG . D MG 402 1_555 S O HOH . D HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc21 E OE2 GLU 137 E GLU 289 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc22 E OD1 ASN 141 E ASN 293 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc23 N O3G ACP . E ACP 401 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc24 N O2B ACP . E ACP 401 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc25 N O1A ACP . E ACP 401 1_555 O MG MG . E MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc26 O MG MG . E MG 402 1_555 T O HOH . E HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.942 ? # _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 7SSI _atom_sites.fract_transf_matrix[1][1] 0.011355 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005721 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008648 _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] 0.012255 _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 3 ACP A 1 401 401 ACP ACP . H 4 MG A 1 402 402 MG MG . I 3 ACP B 1 401 401 ACP ACP . J 4 MG B 1 402 402 MG MG . K 4 MG C 1 201 201 MG MG . L 3 ACP D 1 401 401 ACP ACP . M 4 MG D 1 402 402 MG MG . N 3 ACP E 1 401 401 ACP ACP . O 4 MG E 1 402 402 MG MG . P 4 MG F 1 201 201 MG MG . Q 5 HOH B 1 501 501 HOH HOH . Q 5 HOH B 2 502 6 HOH HOH . R 5 HOH C 1 301 3 HOH HOH . R 5 HOH C 2 302 1 HOH HOH . R 5 HOH C 3 303 4 HOH HOH . S 5 HOH D 1 501 501 HOH HOH . S 5 HOH D 2 502 5 HOH HOH . T 5 HOH E 1 501 501 HOH HOH . T 5 HOH E 2 502 7 HOH HOH . U 5 HOH F 1 301 2 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 . . . N 3 -80.394 -4.693 49.583 1 118.26 ? PG ACP 401 E 1 HETATM 2 O O1G ACP . . . N 3 -80.062 -3.734 50.682 1 118.18 ? O1G ACP 401 E 1 HETATM 3 O O2G ACP . . . N 3 -79.335 -4.665 48.459 1 118.4 ? O2G ACP 401 E 1 HETATM 4 O O3G ACP . . . N 3 -81.765 -4.383 48.948 1 118.02 ? O3G ACP 401 E 1 HETATM 5 P PB ACP . . . N 3 -81.76 -7.45 49.452 1 118.68 ? PB ACP 401 E 1 HETATM 6 O O1B ACP . . . N 3 -81.826 -8.914 49.853 1 118.81 ? O1B ACP 401 E 1 HETATM 7 O O2B ACP . . . N 3 -81.588 -7.384 47.907 1 118.74 ? O2B ACP 401 E 1 HETATM 8 C C3B ACP . . . N 3 -80.465 -6.404 50.138 1 118.55 ? C3B ACP 401 E 1 HETATM 9 P PA ACP . . . N 3 -84.452 -6.441 48.961 1 118.47 ? PA ACP 401 E 1 HETATM 10 O O1A ACP . . . N 3 -84.01 -5.696 47.76 1 118.59 ? O1A ACP 401 E 1 HETATM 11 O O2A ACP . . . N 3 -85.436 -5.595 49.763 1 117.97 ? O2A ACP 401 E 1 HETATM 12 O O3A ACP . . . N 3 -83.152 -6.742 49.829 1 118.53 ? O3A ACP 401 E 1 HETATM 13 O O5' ACP . . . N 3 -85.163 -7.851 48.565 1 119.35 ? O5' ACP 401 E 1 HETATM 14 C C5' ACP . . . N 3 -85.82 -8.687 49.537 1 120.33 ? C5' ACP 401 E 1 HETATM 15 C C4' ACP . . . N 3 -85.766 -10.134 49.11 1 121.39 ? C4' ACP 401 E 1 HETATM 16 O O4' ACP . . . N 3 -86.651 -10.357 47.989 1 122.21 ? O4' ACP 401 E 1 HETATM 17 C C3' ACP . . . N 3 -84.407 -10.626 48.638 1 121.76 ? C3' ACP 401 E 1 HETATM 18 O O3' ACP . . . N 3 -83.572 -10.992 49.733 1 121.56 ? O3' ACP 401 E 1 HETATM 19 C C2' ACP . . . N 3 -84.787 -11.818 47.756 1 122.44 ? C2' ACP 401 E 1 HETATM 20 O O2' ACP . . . N 3 -85.019 -12.977 48.548 1 122.53 ? O2' ACP 401 E 1 HETATM 21 C C1' ACP . . . N 3 -86.103 -11.34 47.123 1 122.96 ? C1' ACP 401 E 1 HETATM 22 N N9 ACP . . . N 3 -85.976 -10.775 45.774 1 124.1 ? N9 ACP 401 E 1 HETATM 23 C C8 ACP . . . N 3 -85.96 -9.445 45.44 1 124.56 ? C8 ACP 401 E 1 HETATM 24 N N7 ACP . . . N 3 -85.868 -9.215 44.152 1 124.75 ? N7 ACP 401 E 1 HETATM 25 C C5 ACP . . . N 3 -85.815 -10.484 43.595 1 124.96 ? C5 ACP 401 E 1 HETATM 26 C C6 ACP . . . N 3 -85.706 -10.935 42.262 1 125.33 ? C6 ACP 401 E 1 HETATM 27 N N6 ACP . . . N 3 -85.618 -10.124 41.2 1 125.58 ? N6 ACP 401 E 1 HETATM 28 N N1 ACP . . . N 3 -85.68 -12.269 42.05 1 125.23 ? N1 ACP 401 E 1 HETATM 29 C C2 ACP . . . N 3 -85.751 -13.087 43.104 1 125.02 ? C2 ACP 401 E 1 HETATM 30 N N3 ACP . . . N 3 -85.851 -12.782 44.402 1 124.8 ? N3 ACP 401 E 1 HETATM 31 C C4 ACP . . . N 3 -85.881 -11.457 44.583 1 124.63 ? C4 ACP 401 E 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #