data_8EGF # _model_server_result.job_id e0SzdG-ooDwF5bkOHk9uZw _model_server_result.datetime_utc '2025-04-16 01:57:15' _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 8egf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8EGF # _exptl.entry_id 8EGF _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 8EGF _cell.length_a 111.401 _cell.length_b 111.401 _cell.length_c 140.547 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EGF _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 _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 1 167.1015 96.476096 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 O VAL 298 A VAL 298 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc2 A O ASP 300 A ASP 300 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.863 ? metalc ? metalc3 A O PHE 303 A PHE 303 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.727 ? metalc ? metalc4 A O GLY 337 A GLY 337 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc5 B O2A ADP . A ADP 401 1_555 C K K . A K 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? # _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 8EGF _atom_sites.fract_transf_matrix[1][1] 0.008977 _atom_sites.fract_transf_matrix[1][2] 0.005183 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010365 _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] 0.007115 _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 K A 1 402 403 K K . D 4 SO4 A 1 403 404 SO4 SO4 . E 4 SO4 A 1 404 405 SO4 SO4 . F 5 WIK A 1 405 4000 WIK PFE . G 5 WIK A 1 406 4001 WIK PFE . H 4 SO4 A 1 407 1 SO4 SO4 . I 6 HOH A 1 501 16 HOH HOH . I 6 HOH A 2 502 23 HOH HOH . I 6 HOH A 3 503 35 HOH HOH . I 6 HOH A 4 504 43 HOH HOH . I 6 HOH A 5 505 77 HOH HOH . I 6 HOH A 6 506 33 HOH HOH . I 6 HOH A 7 507 37 HOH HOH . I 6 HOH A 8 508 70 HOH HOH . I 6 HOH A 9 509 67 HOH HOH . I 6 HOH A 10 510 74 HOH HOH . I 6 HOH A 11 511 9 HOH HOH . I 6 HOH A 12 512 72 HOH HOH . I 6 HOH A 13 513 20 HOH HOH . I 6 HOH A 14 514 65 HOH HOH . I 6 HOH A 15 515 78 HOH HOH . I 6 HOH A 16 516 60 HOH HOH . I 6 HOH A 17 517 27 HOH HOH . I 6 HOH A 18 518 69 HOH HOH . I 6 HOH A 19 519 14 HOH HOH . I 6 HOH A 20 520 44 HOH HOH . I 6 HOH A 21 521 45 HOH HOH . I 6 HOH A 22 522 1 HOH HOH . I 6 HOH A 23 523 17 HOH HOH . I 6 HOH A 24 524 28 HOH HOH . I 6 HOH A 25 525 32 HOH HOH . I 6 HOH A 26 526 62 HOH HOH . I 6 HOH A 27 527 64 HOH HOH . I 6 HOH A 28 528 88 HOH HOH . I 6 HOH A 29 529 90 HOH HOH . I 6 HOH A 30 530 83 HOH HOH . I 6 HOH A 31 531 11 HOH HOH . I 6 HOH A 32 532 4 HOH HOH . I 6 HOH A 33 533 36 HOH HOH . I 6 HOH A 34 534 48 HOH HOH . I 6 HOH A 35 535 18 HOH HOH . I 6 HOH A 36 536 29 HOH HOH . I 6 HOH A 37 537 61 HOH HOH . I 6 HOH A 38 538 73 HOH HOH . I 6 HOH A 39 539 79 HOH HOH . I 6 HOH A 40 540 26 HOH HOH . I 6 HOH A 41 541 10 HOH HOH . I 6 HOH A 42 542 80 HOH HOH . I 6 HOH A 43 543 12 HOH HOH . I 6 HOH A 44 544 66 HOH HOH . I 6 HOH A 45 545 57 HOH HOH . I 6 HOH A 46 546 5 HOH HOH . I 6 HOH A 47 547 56 HOH HOH . I 6 HOH A 48 548 58 HOH HOH . I 6 HOH A 49 549 87 HOH HOH . I 6 HOH A 50 550 25 HOH HOH . I 6 HOH A 51 551 2 HOH HOH . I 6 HOH A 52 552 13 HOH HOH . I 6 HOH A 53 553 21 HOH HOH . I 6 HOH A 54 554 39 HOH HOH . I 6 HOH A 55 555 24 HOH HOH . I 6 HOH A 56 556 19 HOH HOH . I 6 HOH A 57 557 86 HOH HOH . I 6 HOH A 58 558 49 HOH HOH . I 6 HOH A 59 559 55 HOH HOH . I 6 HOH A 60 560 6 HOH HOH . I 6 HOH A 61 561 38 HOH HOH . I 6 HOH A 62 562 89 HOH HOH . I 6 HOH A 63 563 54 HOH HOH . I 6 HOH A 64 564 47 HOH HOH . I 6 HOH A 65 565 30 HOH HOH . I 6 HOH A 66 566 15 HOH HOH . I 6 HOH A 67 567 46 HOH HOH . I 6 HOH A 68 568 52 HOH HOH . I 6 HOH A 69 569 42 HOH HOH . I 6 HOH A 70 570 71 HOH HOH . I 6 HOH A 71 571 51 HOH HOH . I 6 HOH A 72 572 41 HOH HOH . I 6 HOH A 73 573 81 HOH HOH . I 6 HOH A 74 574 68 HOH HOH . I 6 HOH A 75 575 3 HOH HOH . I 6 HOH A 76 576 8 HOH HOH . I 6 HOH A 77 577 76 HOH HOH . I 6 HOH A 78 578 7 HOH HOH . I 6 HOH A 79 579 84 HOH HOH . I 6 HOH A 80 580 22 HOH HOH . I 6 HOH A 81 581 40 HOH HOH . I 6 HOH A 82 582 63 HOH HOH . I 6 HOH A 83 583 75 HOH HOH . I 6 HOH A 84 584 50 HOH HOH . I 6 HOH A 85 585 34 HOH HOH . I 6 HOH A 86 586 82 HOH HOH . I 6 HOH A 87 587 53 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 89.139 28.646 17.681 1 39.13 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 89.662 29.401 16.462 1 36.63 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 90.131 27.562 18.051 1 41.75 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 87.753 28.164 17.528 1 39.28 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 89.072 31.31 18.927 1 36.92 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 89.951 31.971 17.939 1 37.27 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 89.374 31.691 20.382 1 34.71 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 89.21 29.717 18.864 1 38.55 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 87.53 31.615 18.637 1 35.72 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 86.468 31.141 19.493 1 38.53 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 85.179 31.084 18.71 1 39.67 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 84.755 32.427 18.396 1 38.25 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 85.202 30.39 17.356 1 40.27 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 85.168 28.969 17.386 1 41.58 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 83.954 30.97 16.699 1 40.46 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 82.767 30.356 17.19 1 42.12 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 83.985 32.415 17.208 1 38.02 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 84.564 33.36 16.262 1 35.87 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 85.805 33.942 16.307 1 34.98 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 86.031 34.793 15.336 1 35.09 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 84.857 34.768 14.597 1 33.2 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 84.43 35.494 13.469 1 31.55 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 85.195 36.361 12.816 1 30.25 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 83.169 35.279 13.023 1 33.35 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 82.407 34.374 13.647 1 32.72 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 82.708 33.624 14.709 1 33.9 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 83.949 33.881 15.149 1 33.86 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #