data_6Y4M # _model_server_result.job_id xtvQuDdDyqjN1_phY4r9uQ _model_server_result.datetime_utc '2024-11-28 16:22:32' _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 6y4m # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":401}' # _entry.id 6Y4M # _exptl.entry_id 6Y4M _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 15 _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 6Y4M _cell.length_a 103.961 _cell.length_b 152.59 _cell.length_c 185.989 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y4M _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 15 _struct_asym.id W _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 covale ? covale1 M C31 O9B . B O9B 1004 1_555 T N VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale2 N C5 O9H . B O9H 1005 1_555 O NBI OH5 . B OH5 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale3 N N3 O9H . B O9H 1005 1_555 T C VAL . C VAL 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? metalc ? metalc1 A OD1 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc2 A OD2 ASP 39 A ASP 39 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc3 A O THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc4 A OG1 THR 41 A THR 41 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc5 A O GLY 44 A GLY 44 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.585 ? metalc ? metalc6 A OE2 GLU 55 A GLU 55 1_555 I CA CA . A CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc7 G O1G GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc8 G O1B GTP . A GTP 1001 1_555 H MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc9 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc10 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc11 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc12 H MG MG . A MG 1002 1_555 X O HOH . A HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc13 K MG MG . B MG 1002 1_555 Y O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc14 K MG MG . B MG 1002 1_555 Z O HOH . C HOH 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc15 C OD1 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.783 ? metalc ? metalc16 C OD2 ASP 39 C ASP 39 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc17 C O THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc18 C OG1 THR 41 C THR 41 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.36 ? metalc ? metalc19 C O GLY 44 C GLY 44 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? metalc ? metalc20 C OE1 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.006 ? metalc ? metalc21 C OE2 GLU 55 C GLU 55 1_555 R CA CA . C CA 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc22 P O1G GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? metalc ? metalc23 P O1B GTP . C GTP 1001 1_555 Q MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc24 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc26 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc27 Q MG MG . C MG 1002 1_555 Z O HOH . C HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc28 U O1G GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.789 ? metalc ? metalc29 U O1B GTP . D GTP 1001 1_555 V MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc30 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc31 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc32 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc33 V MG MG . D MG 1002 1_555 AA O HOH . D HOH 1105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? # _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 6Y4M _atom_sites.fract_transf_matrix[1][1] 0.009619 _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] 0.006554 _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] 0.005377 _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 1001 1001 GTP GTP . H 6 MG A 1 1002 1002 MG MO6 . I 7 CA A 1 1003 1003 CA CA . J 8 GDP B 1 1001 1001 GDP GDP . K 6 MG B 1 1002 1002 MG MG . L 9 MES B 1 1003 1004 MES MES . M 10 O9B B 1 1004 2001 O9B ABB . N 11 O9H B 1 1005 2001 O9H ABB . O 12 OH5 B 1 1006 2001 OH5 ABB . P 5 GTP C 1 1001 1001 GTP GTP . Q 6 MG C 1 1002 1002 MG MO6 . R 7 CA C 1 1003 1003 CA CA . S 13 PGE C 1 1004 1004 PGE PGE . T 14 VAL C 1 1005 2001 VAL ABB . U 5 GTP D 1 1001 1001 GTP GTP . V 6 MG D 1 1002 1002 MG MO6 . W 15 ACP F 1 401 401 ACP ACP . X 16 HOH A 1 1101 1002 HOH MO6 . X 16 HOH A 2 1102 1002 HOH MO6 . X 16 HOH A 3 1103 1002 HOH MO6 . X 16 HOH A 4 1104 11 HOH HOH . X 16 HOH A 5 1105 1002 HOH MO6 . X 16 HOH A 6 1106 8 HOH HOH . X 16 HOH A 7 1107 10 HOH HOH . X 16 HOH A 8 1108 13 HOH HOH . X 16 HOH A 9 1109 7 HOH HOH . Y 16 HOH B 1 1101 20 HOH HOH . Y 16 HOH B 2 1102 18 HOH HOH . Y 16 HOH B 3 1103 5 HOH HOH . Y 16 HOH B 4 1104 16 HOH HOH . Y 16 HOH B 5 1105 4 HOH HOH . Y 16 HOH B 6 1106 14 HOH HOH . Y 16 HOH B 7 1107 6 HOH HOH . Y 16 HOH B 8 1108 21 HOH HOH . Y 16 HOH B 9 1109 1 HOH HOH . Y 16 HOH B 10 1110 9 HOH HOH . Y 16 HOH B 11 1111 19 HOH HOH . Z 16 HOH C 1 1101 1002 HOH MO6 . Z 16 HOH C 2 1102 1002 HOH MO6 . Z 16 HOH C 3 1103 1002 HOH MO6 . Z 16 HOH C 4 1104 15 HOH HOH . Z 16 HOH C 5 1105 1002 HOH MO6 . Z 16 HOH C 6 1106 2 HOH HOH . Z 16 HOH C 7 1107 3 HOH HOH . AA 16 HOH D 1 1101 1002 HOH MO6 . AA 16 HOH D 2 1102 17 HOH HOH . AA 16 HOH D 3 1103 1002 HOH MO6 . AA 16 HOH D 4 1104 1002 HOH MO6 . AA 16 HOH D 5 1105 1002 HOH MO6 . BA 16 HOH E 1 201 12 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 . . . W 15 -8.7 30.438 93.819 1 128.99 ? PG ACP 401 F 1 HETATM 2 O O1G ACP . . . W 15 -9.676 29.985 92.799 1 127.69 ? O1G ACP 401 F 1 HETATM 3 O O2G ACP . . . W 15 -7.448 31.124 93.075 1 129.56 ? O2G ACP 401 F 1 HETATM 4 O O3G ACP . . . W 15 -8.158 29.182 94.664 1 127.88 ? O3G ACP 401 F 1 HETATM 5 P PB ACP . . . W 15 -11.135 31.125 95.45 1 129.34 ? PB ACP 401 F 1 HETATM 6 O O1B ACP . . . W 15 -11.536 29.894 94.733 1 126.67 ? O1B ACP 401 F 1 HETATM 7 O O2B ACP . . . W 15 -12.141 32.319 95.051 1 131.54 ? O2B ACP 401 F 1 HETATM 8 C C3B ACP . . . W 15 -9.46 31.628 94.962 1 130.13 ? C3B ACP 401 F 1 HETATM 9 P PA ACP . . . W 15 -10.454 29.712 97.853 1 123.09 ? PA ACP 401 F 1 HETATM 10 O O1A ACP . . . W 15 -9.143 29.414 97.166 1 120.08 ? O1A ACP 401 F 1 HETATM 11 O O2A ACP . . . W 15 -11.401 28.581 98.172 1 122.21 ? O2A ACP 401 F 1 HETATM 12 O O3A ACP . . . W 15 -11.24 30.874 97.045 1 127.81 ? O3A ACP 401 F 1 HETATM 13 O O5' ACP . . . W 15 -10.124 30.466 99.234 1 122.99 ? O5' ACP 401 F 1 HETATM 14 C C5' ACP . . . W 15 -9.589 31.786 99.19 1 121.96 ? C5' ACP 401 F 1 HETATM 15 C C4' ACP . . . W 15 -8.862 32.15 100.482 1 121.19 ? C4' ACP 401 F 1 HETATM 16 O O4' ACP . . . W 15 -9.564 31.657 101.624 1 121.45 ? O4' ACP 401 F 1 HETATM 17 C C3' ACP . . . W 15 -7.453 31.576 100.534 1 117.41 ? C3' ACP 401 F 1 HETATM 18 O O3' ACP . . . W 15 -6.494 32.574 100.175 1 117.05 ? O3' ACP 401 F 1 HETATM 19 C C2' ACP . . . W 15 -7.27 31.078 101.957 1 117.47 ? C2' ACP 401 F 1 HETATM 20 O O2' ACP . . . W 15 -6.378 31.899 102.718 1 118.44 ? O2' ACP 401 F 1 HETATM 21 C C1' ACP . . . W 15 -8.654 31.116 102.582 1 119.64 ? C1' ACP 401 F 1 HETATM 22 N N9 ACP . . . W 15 -9.081 29.75 102.955 1 118.02 ? N9 ACP 401 F 1 HETATM 23 C C8 ACP . . . W 15 -9.692 28.851 102.158 1 116.39 ? C8 ACP 401 F 1 HETATM 24 N N7 ACP . . . W 15 -9.941 27.701 102.834 1 116.02 ? N7 ACP 401 F 1 HETATM 25 C C5 ACP . . . W 15 -9.482 27.865 104.086 1 117.64 ? C5 ACP 401 F 1 HETATM 26 C C6 ACP . . . W 15 -9.424 27.046 105.317 1 118.58 ? C6 ACP 401 F 1 HETATM 27 N N6 ACP . . . W 15 -9.924 25.789 105.329 1 117.59 ? N6 ACP 401 F 1 HETATM 28 N N1 ACP . . . W 15 -8.857 27.604 106.413 1 120.4 ? N1 ACP 401 F 1 HETATM 29 C C2 ACP . . . W 15 -8.354 28.856 106.411 1 121.06 ? C2 ACP 401 F 1 HETATM 30 N N3 ACP . . . W 15 -8.376 29.653 105.325 1 120.28 ? N3 ACP 401 F 1 HETATM 31 C C4 ACP . . . W 15 -8.915 29.22 104.16 1 118.66 ? C4 ACP 401 F 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #