data_3KZB # _model_server_result.job_id 55EXLdkcAu_mA5lloHCDfg _model_server_result.datetime_utc '2024-10-20 07:37:31' _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 3kzb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1760}' # _entry.id 3KZB # _exptl.entry_id 3KZB _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 90 _cell.entry_id 3KZB _cell.length_a 71.893 _cell.length_b 159.799 _cell.length_c 47.336 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KZB _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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 _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' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 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 disulf ? disulf1 A SG CYS 356 A CYS 354 1_555 A SG CYS 394 A CYS 392 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A C GLN 82 A GLN 80 1_555 A N MSE 83 A MSE 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A C MSE 83 A MSE 81 1_555 A N GLN 84 A GLN 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 A C PRO 130 A PRO 128 1_555 A N MSE 131 A MSE 129 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale4 A C MSE 131 A MSE 129 1_555 A N THR 132 A THR 130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale5 A C LEU 207 A LEU 205 1_555 A N MSE 208 A MSE 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale6 A C MSE 208 A MSE 206 1_555 A N PRO 209 A PRO 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? covale ? covale7 A C ASP 280 A ASP 278 1_555 A N MSE 281 A MSE 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale8 A C MSE 281 A MSE 279 1_555 A N PRO 282 A PRO 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale9 A C HIS 330 A HIS 328 1_555 A N MSE 331 A MSE 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 A C MSE 331 A MSE 329 1_555 A N ALA 332 A ALA 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale11 A C GLY 399 A GLY 397 1_555 A N MSE 400 A MSE 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale12 A C MSE 400 A MSE 398 1_555 A N GLU 401 A GLU 399 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale13 A C ARG 420 A ARG 418 1_555 A N MSE 421 A MSE 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale14 A C MSE 421 A MSE 419 1_555 A N ILE 422 A ILE 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _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 3KZB _atom_sites.fract_transf_matrix[1][1] 0.01391 _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] 0.006258 _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] 0.021126 _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 1760 1760 ADP ADP . C 3 HOH A 1 510 1 HOH HOH . C 3 HOH A 2 511 3 HOH HOH . C 3 HOH A 3 512 4 HOH HOH . C 3 HOH A 4 513 5 HOH HOH . C 3 HOH A 5 514 6 HOH HOH . C 3 HOH A 6 515 7 HOH HOH . C 3 HOH A 7 516 8 HOH HOH . C 3 HOH A 8 517 9 HOH HOH . C 3 HOH A 9 518 10 HOH HOH . C 3 HOH A 10 519 11 HOH HOH . C 3 HOH A 11 520 12 HOH HOH . C 3 HOH A 12 521 14 HOH HOH . C 3 HOH A 13 522 15 HOH HOH . C 3 HOH A 14 523 16 HOH HOH . C 3 HOH A 15 524 17 HOH HOH . C 3 HOH A 16 525 18 HOH HOH . C 3 HOH A 17 526 19 HOH HOH . C 3 HOH A 18 527 20 HOH HOH . C 3 HOH A 19 528 21 HOH HOH . C 3 HOH A 20 529 22 HOH HOH . C 3 HOH A 21 530 23 HOH HOH . C 3 HOH A 22 531 24 HOH HOH . C 3 HOH A 23 532 25 HOH HOH . C 3 HOH A 24 533 26 HOH HOH . C 3 HOH A 25 534 27 HOH HOH . C 3 HOH A 26 535 28 HOH HOH . C 3 HOH A 27 536 29 HOH HOH . C 3 HOH A 28 537 30 HOH HOH . C 3 HOH A 29 538 31 HOH HOH . C 3 HOH A 30 539 32 HOH HOH . C 3 HOH A 31 540 33 HOH HOH . C 3 HOH A 32 541 34 HOH HOH . C 3 HOH A 33 542 35 HOH HOH . C 3 HOH A 34 543 36 HOH HOH . C 3 HOH A 35 544 37 HOH HOH . C 3 HOH A 36 545 38 HOH HOH . C 3 HOH A 37 546 39 HOH HOH . C 3 HOH A 38 547 40 HOH HOH . C 3 HOH A 39 548 41 HOH HOH . C 3 HOH A 40 549 42 HOH HOH . C 3 HOH A 41 550 43 HOH HOH . C 3 HOH A 42 551 44 HOH HOH . C 3 HOH A 43 552 45 HOH HOH . C 3 HOH A 44 553 46 HOH HOH . C 3 HOH A 45 554 47 HOH HOH . C 3 HOH A 46 555 48 HOH HOH . C 3 HOH A 47 556 49 HOH HOH . C 3 HOH A 48 557 50 HOH HOH . C 3 HOH A 49 558 51 HOH HOH . C 3 HOH A 50 559 52 HOH HOH . C 3 HOH A 51 560 53 HOH HOH . C 3 HOH A 52 561 54 HOH HOH . C 3 HOH A 53 562 55 HOH HOH . C 3 HOH A 54 563 56 HOH HOH . C 3 HOH A 55 564 57 HOH HOH . C 3 HOH A 56 565 58 HOH HOH . C 3 HOH A 57 566 59 HOH HOH . C 3 HOH A 58 567 60 HOH HOH . C 3 HOH A 59 568 61 HOH HOH . C 3 HOH A 60 569 62 HOH HOH . C 3 HOH A 61 570 63 HOH HOH . C 3 HOH A 62 571 64 HOH HOH . C 3 HOH A 63 572 65 HOH HOH . C 3 HOH A 64 573 66 HOH HOH . C 3 HOH A 65 574 67 HOH HOH . C 3 HOH A 66 575 68 HOH HOH . C 3 HOH A 67 576 69 HOH HOH . C 3 HOH A 68 577 70 HOH HOH . C 3 HOH A 69 578 71 HOH HOH . C 3 HOH A 70 579 73 HOH HOH . C 3 HOH A 71 580 74 HOH HOH . C 3 HOH A 72 581 75 HOH HOH . C 3 HOH A 73 582 76 HOH HOH . C 3 HOH A 74 583 77 HOH HOH . C 3 HOH A 75 584 78 HOH HOH . C 3 HOH A 76 585 79 HOH HOH . C 3 HOH A 77 586 80 HOH HOH . C 3 HOH A 78 587 83 HOH HOH . C 3 HOH A 79 588 85 HOH HOH . C 3 HOH A 80 589 86 HOH HOH . C 3 HOH A 81 590 87 HOH HOH . C 3 HOH A 82 591 88 HOH HOH . C 3 HOH A 83 592 89 HOH HOH . C 3 HOH A 84 593 90 HOH HOH . C 3 HOH A 85 594 91 HOH HOH . C 3 HOH A 86 595 92 HOH HOH . C 3 HOH A 87 596 96 HOH HOH . C 3 HOH A 88 597 99 HOH HOH . C 3 HOH A 89 598 102 HOH HOH . C 3 HOH A 90 599 109 HOH HOH . C 3 HOH A 91 600 112 HOH HOH . C 3 HOH A 92 601 132 HOH HOH . C 3 HOH A 93 602 133 HOH HOH . C 3 HOH A 94 603 135 HOH HOH . C 3 HOH A 95 604 136 HOH HOH . C 3 HOH A 96 605 137 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 19.906 14.195 1.363 1 44.08 ? PB ADP 1760 A 1 HETATM 2 O O1B ADP . . . B 2 21.196 14.89 0.72 1 40.59 ? O1B ADP 1760 A 1 HETATM 3 O O2B ADP . . . B 2 19.743 12.702 0.846 1 34.37 ? O2B ADP 1760 A 1 HETATM 4 O O3B ADP . . . B 2 20.103 14.132 2.763 1 38.22 ? O3B ADP 1760 A 1 HETATM 5 P PA ADP . . . B 2 17.943 15.569 -0.158 1 35.67 ? PA ADP 1760 A 1 HETATM 6 O O1A ADP . . . B 2 18.878 15.12 -1.348 1 36.43 ? O1A ADP 1760 A 1 HETATM 7 O O2A ADP . . . B 2 17.8 16.951 -0.148 1 33.4 ? O2A ADP 1760 A 1 HETATM 8 O O3A ADP . . . B 2 18.582 15.098 1.22 1 31.55 ? O3A ADP 1760 A 1 HETATM 9 O O5' ADP . . . B 2 16.498 14.989 -0.322 1 31.35 ? O5' ADP 1760 A 1 HETATM 10 C C5' ADP . . . B 2 16.246 13.691 0.046 1 29.52 ? C5' ADP 1760 A 1 HETATM 11 C C4' ADP . . . B 2 14.755 13.471 0.041 1 29.92 ? C4' ADP 1760 A 1 HETATM 12 O O4' ADP . . . B 2 14.201 14.013 -1.095 1 31.65 ? O4' ADP 1760 A 1 HETATM 13 C C3' ADP . . . B 2 14.181 12.045 0.01 1 29.37 ? C3' ADP 1760 A 1 HETATM 14 O O3' ADP . . . B 2 14.231 11.33 1.177 1 30.61 ? O3' ADP 1760 A 1 HETATM 15 C C2' ADP . . . B 2 12.804 12.254 -0.649 1 29.84 ? C2' ADP 1760 A 1 HETATM 16 O O2' ADP . . . B 2 11.761 12.138 0.182 1 35.07 ? O2' ADP 1760 A 1 HETATM 17 C C1' ADP . . . B 2 12.915 13.602 -1.182 1 30.94 ? C1' ADP 1760 A 1 HETATM 18 N N9 ADP . . . B 2 12.606 13.587 -2.58 1 32.96 ? N9 ADP 1760 A 1 HETATM 19 C C8 ADP . . . B 2 13.434 13.305 -3.594 1 34.46 ? C8 ADP 1760 A 1 HETATM 20 N N7 ADP . . . B 2 12.687 13.339 -4.771 1 32.84 ? N7 ADP 1760 A 1 HETATM 21 C C5 ADP . . . B 2 11.432 13.76 -4.43 1 31.6 ? C5 ADP 1760 A 1 HETATM 22 C C6 ADP . . . B 2 10.383 14.113 -5.174 1 32.33 ? C6 ADP 1760 A 1 HETATM 23 N N6 ADP . . . B 2 10.419 13.967 -6.581 1 36.17 ? N6 ADP 1760 A 1 HETATM 24 N N1 ADP . . . B 2 9.238 14.385 -4.585 1 34.02 ? N1 ADP 1760 A 1 HETATM 25 C C2 ADP . . . B 2 9.141 14.382 -3.243 1 32.72 ? C2 ADP 1760 A 1 HETATM 26 N N3 ADP . . . B 2 10.244 14.245 -2.485 1 29.55 ? N3 ADP 1760 A 1 HETATM 27 C C4 ADP . . . B 2 11.378 13.974 -3.111 1 31.03 ? C4 ADP 1760 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #