data_8EGD # _model_server_result.job_id '_jPmzkjxL_6knnQfiSnlmQ' _model_server_result.datetime_utc '2024-11-15 03:48:25' _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 8egd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8EGD # _exptl.entry_id 8EGD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 8EGD _cell.length_a 111.96 _cell.length_b 111.96 _cell.length_c 137.18 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EGD _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_765 -x+2,-y+1,z -1 0 0 0 -1 0 0 0 1 167.94 96.960204 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 OE1 GLU 245 A GLU 245 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc2 A OD1 ASN 249 A ASN 249 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.985 ? metalc ? metalc3 A O VAL 298 A VAL 298 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc4 A O ASP 300 A ASP 300 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.963 ? metalc ? metalc5 A O PHE 303 A PHE 303 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.791 ? metalc ? metalc6 A O GLY 337 A GLY 337 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.111 ? metalc ? metalc7 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? metalc ? metalc8 B O2A ADP . A ADP 401 1_555 D K K . A K 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 8EGD _atom_sites.fract_transf_matrix[1][1] 0.008932 _atom_sites.fract_transf_matrix[1][2] 0.005157 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010314 _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] 0.00729 _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 ADP A 1 401 401 ADP ADP . C 3 MG A 1 402 402 MG MG . D 4 K A 1 403 403 K K . E 5 SO4 A 1 404 1 SO4 SO4 . F 5 SO4 A 1 405 2 SO4 SO4 . G 5 SO4 A 1 406 3 SO4 SO4 . H 6 WIH A 1 407 4000 WIH PFE . I 6 WIH A 1 408 4001 WIH PFE . J 6 WIH A 1 409 4002 WIH PFE . K 7 HOH A 1 501 19 HOH HOH . K 7 HOH A 2 502 40 HOH HOH . K 7 HOH A 3 503 5 HOH HOH . K 7 HOH A 4 504 22 HOH HOH . K 7 HOH A 5 505 10 HOH HOH . K 7 HOH A 6 506 15 HOH HOH . K 7 HOH A 7 507 16 HOH HOH . K 7 HOH A 8 508 13 HOH HOH . K 7 HOH A 9 509 14 HOH HOH . K 7 HOH A 10 510 25 HOH HOH . K 7 HOH A 11 511 26 HOH HOH . K 7 HOH A 12 512 23 HOH HOH . K 7 HOH A 13 513 30 HOH HOH . K 7 HOH A 14 514 36 HOH HOH . K 7 HOH A 15 515 20 HOH HOH . K 7 HOH A 16 516 4 HOH HOH . K 7 HOH A 17 517 17 HOH HOH . K 7 HOH A 18 518 9 HOH HOH . K 7 HOH A 19 519 6 HOH HOH . K 7 HOH A 20 520 21 HOH HOH . K 7 HOH A 21 521 44 HOH HOH . K 7 HOH A 22 522 29 HOH HOH . K 7 HOH A 23 523 39 HOH HOH . K 7 HOH A 24 524 48 HOH HOH . K 7 HOH A 25 525 11 HOH HOH . K 7 HOH A 26 526 24 HOH HOH . K 7 HOH A 27 527 47 HOH HOH . K 7 HOH A 28 528 34 HOH HOH . K 7 HOH A 29 529 28 HOH HOH . K 7 HOH A 30 530 43 HOH HOH . K 7 HOH A 31 531 49 HOH HOH . K 7 HOH A 32 532 1 HOH HOH . K 7 HOH A 33 533 2 HOH HOH . K 7 HOH A 34 534 12 HOH HOH . K 7 HOH A 35 535 32 HOH HOH . K 7 HOH A 36 536 45 HOH HOH . K 7 HOH A 37 537 31 HOH HOH . K 7 HOH A 38 538 18 HOH HOH . K 7 HOH A 39 539 3 HOH HOH . K 7 HOH A 40 540 7 HOH HOH . K 7 HOH A 41 541 33 HOH HOH . K 7 HOH A 42 542 42 HOH HOH . K 7 HOH A 43 543 8 HOH HOH . K 7 HOH A 44 544 27 HOH HOH . K 7 HOH A 45 545 37 HOH HOH . K 7 HOH A 46 546 46 HOH HOH . K 7 HOH A 47 547 41 HOH HOH . K 7 HOH A 48 548 38 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 PB ADP . . . B 2 90.154 28.96 18.406 1 65.05 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 90.536 29.738 17.186 1 64.88 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 88.699 28.41 18.365 1 65.21 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 91.151 27.793 18.67 1 65.47 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 89.889 31.539 19.716 1 61.41 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 90.81 32.245 18.794 1 61.32 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 90.109 31.968 21.155 1 61.28 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 90.17 29.968 19.644 1 63.59 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 88.336 31.81 19.375 1 59.95 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 87.266 31.442 20.269 1 58.76 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 85.973 31.379 19.498 1 57.77 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 85.546 32.709 19.133 1 57.33 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 86.024 30.629 18.172 1 57.33 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 86.004 29.213 18.341 1 56.54 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 84.787 31.181 17.461 1 57.5 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 83.601 30.563 17.959 1 57.89 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 84.797 32.649 17.926 1 56.94 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 85.35 33.6 16.961 1 55.89 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 86.591 34.186 16.976 1 55.36 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 86.779 35.063 16.018 1 54.73 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 85.582 35.049 15.318 1 54.53 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 85.132 35.764 14.189 1 53.64 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 85.905 36.587 13.473 1 52.53 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 83.863 35.542 13.773 1 54.16 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 83.119 34.638 14.42 1 54.4 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 83.443 33.889 15.476 1 54.69 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 84.693 34.149 15.885 1 55.15 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #