data_6E2V # _model_server_result.job_id lZLs8CPvxzkbqWtVcw4Yew _model_server_result.datetime_utc '2024-10-19 02:16:36' _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 6e2v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 6E2V # _exptl.entry_id 6E2V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 6E2V _cell.length_a 79.636 _cell.length_b 98.599 _cell.length_c 45.632 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E2V _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,D,E,F,G _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 5 _struct_asym.id F _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 OG SER 130 A SER 106 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc2 B MG MG . A MG 401 1_555 D O2A DP6 . A DP6 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc3 B MG MG . A MG 401 1_555 F O1B ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc4 B MG MG . A MG 401 1_555 F O1A ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? metalc ? metalc5 B MG MG . A MG 401 1_555 G O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc6 C MG MG . A MG 402 1_555 D O3A DP6 . A DP6 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc7 C MG MG . A MG 402 1_555 D O2 DP6 . A DP6 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc8 C MG MG . A MG 402 1_555 G O HOH . A HOH 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.659 ? metalc ? metalc9 C MG MG . A MG 402 1_555 G O HOH . A HOH 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc10 E BE BEF . A BEF 404 1_555 F O2B ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? # _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 6E2V _atom_sites.fract_transf_matrix[1][1] 0.012557 _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] 0.010142 _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] 0.021914 _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 MG A 1 401 401 MG MG . C 2 MG A 1 402 402 MG MG . D 3 DP6 A 1 403 403 DP6 DP6 . E 4 BEF A 1 404 404 BEF BEF . F 5 ADP A 1 405 405 ADP ADP . G 6 HOH A 1 501 501 HOH HOH . G 6 HOH A 2 502 502 HOH HOH . G 6 HOH A 3 503 503 HOH HOH . G 6 HOH A 4 504 504 HOH HOH . G 6 HOH A 5 505 505 HOH HOH . G 6 HOH A 6 506 506 HOH HOH . G 6 HOH A 7 507 507 HOH HOH . G 6 HOH A 8 508 508 HOH HOH . G 6 HOH A 9 509 509 HOH HOH . G 6 HOH A 10 510 510 HOH HOH . G 6 HOH A 11 511 511 HOH HOH . G 6 HOH A 12 512 512 HOH HOH . G 6 HOH A 13 513 513 HOH HOH . G 6 HOH A 14 514 514 HOH HOH . G 6 HOH A 15 515 515 HOH HOH . G 6 HOH A 16 516 516 HOH HOH . G 6 HOH A 17 517 517 HOH HOH . G 6 HOH A 18 518 518 HOH HOH . G 6 HOH A 19 519 519 HOH HOH . G 6 HOH A 20 520 520 HOH HOH . G 6 HOH A 21 521 521 HOH HOH . G 6 HOH A 22 522 522 HOH HOH . G 6 HOH A 23 523 523 HOH HOH . G 6 HOH A 24 524 524 HOH HOH . G 6 HOH A 25 525 525 HOH HOH . G 6 HOH A 26 526 526 HOH HOH . G 6 HOH A 27 527 527 HOH HOH . G 6 HOH A 28 528 528 HOH HOH . G 6 HOH A 29 529 529 HOH HOH . G 6 HOH A 30 530 530 HOH HOH . G 6 HOH A 31 531 531 HOH HOH . G 6 HOH A 32 532 532 HOH HOH . G 6 HOH A 33 533 533 HOH HOH . G 6 HOH A 34 534 534 HOH HOH . G 6 HOH A 35 535 535 HOH HOH . G 6 HOH A 36 536 536 HOH HOH . G 6 HOH A 37 537 537 HOH HOH . G 6 HOH A 38 538 538 HOH HOH . G 6 HOH A 39 539 539 HOH HOH . G 6 HOH A 40 540 540 HOH HOH . G 6 HOH A 41 541 541 HOH HOH . G 6 HOH A 42 542 542 HOH HOH . G 6 HOH A 43 543 543 HOH HOH . G 6 HOH A 44 544 544 HOH HOH . G 6 HOH A 45 545 545 HOH HOH . G 6 HOH A 46 546 546 HOH HOH . G 6 HOH A 47 547 547 HOH HOH . G 6 HOH A 48 548 548 HOH HOH . G 6 HOH A 49 549 549 HOH HOH . G 6 HOH A 50 550 550 HOH HOH . G 6 HOH A 51 551 551 HOH HOH . G 6 HOH A 52 552 552 HOH HOH . G 6 HOH A 53 553 553 HOH HOH . G 6 HOH A 54 554 554 HOH HOH . G 6 HOH A 55 555 555 HOH HOH . G 6 HOH A 56 556 556 HOH HOH . G 6 HOH A 57 557 557 HOH HOH . G 6 HOH A 58 558 558 HOH HOH . G 6 HOH A 59 559 559 HOH HOH . G 6 HOH A 60 560 560 HOH HOH . G 6 HOH A 61 561 561 HOH HOH . G 6 HOH A 62 562 562 HOH HOH . G 6 HOH A 63 563 563 HOH HOH . G 6 HOH A 64 564 564 HOH HOH . G 6 HOH A 65 565 565 HOH HOH . G 6 HOH A 66 566 566 HOH HOH . G 6 HOH A 67 567 567 HOH HOH . G 6 HOH A 68 568 568 HOH HOH . G 6 HOH A 69 569 569 HOH HOH . G 6 HOH A 70 570 570 HOH HOH . G 6 HOH A 71 571 571 HOH HOH . G 6 HOH A 72 572 572 HOH HOH . G 6 HOH A 73 573 573 HOH HOH . G 6 HOH A 74 574 574 HOH HOH . G 6 HOH A 75 575 575 HOH HOH . G 6 HOH A 76 576 576 HOH HOH . G 6 HOH A 77 577 577 HOH HOH . G 6 HOH A 78 578 578 HOH HOH . G 6 HOH A 79 579 579 HOH HOH . G 6 HOH A 80 580 580 HOH HOH . G 6 HOH A 81 581 581 HOH HOH . G 6 HOH A 82 582 582 HOH HOH . G 6 HOH A 83 583 583 HOH HOH . G 6 HOH A 84 584 584 HOH HOH . G 6 HOH A 85 585 585 HOH HOH . G 6 HOH A 86 586 586 HOH HOH . G 6 HOH A 87 587 587 HOH HOH . G 6 HOH A 88 588 588 HOH HOH . G 6 HOH A 89 589 589 HOH HOH . G 6 HOH A 90 590 590 HOH HOH . G 6 HOH A 91 591 591 HOH HOH . G 6 HOH A 92 592 592 HOH HOH . G 6 HOH A 93 593 593 HOH HOH . G 6 HOH A 94 594 594 HOH HOH . G 6 HOH A 95 595 595 HOH HOH . G 6 HOH A 96 596 596 HOH HOH . G 6 HOH A 97 597 597 HOH HOH . G 6 HOH A 98 598 598 HOH HOH . G 6 HOH A 99 599 599 HOH HOH . G 6 HOH A 100 600 600 HOH HOH . G 6 HOH A 101 601 601 HOH HOH . G 6 HOH A 102 602 602 HOH HOH . G 6 HOH A 103 603 603 HOH HOH . G 6 HOH A 104 604 604 HOH HOH . G 6 HOH A 105 605 605 HOH HOH . G 6 HOH A 106 606 606 HOH HOH . G 6 HOH A 107 607 607 HOH HOH . G 6 HOH A 108 608 608 HOH HOH . G 6 HOH A 109 609 609 HOH HOH . G 6 HOH A 110 610 610 HOH HOH . G 6 HOH A 111 611 611 HOH HOH . G 6 HOH A 112 612 612 HOH HOH . G 6 HOH A 113 613 613 HOH HOH . G 6 HOH A 114 614 614 HOH HOH . G 6 HOH A 115 615 615 HOH HOH . G 6 HOH A 116 616 616 HOH HOH . G 6 HOH A 117 617 617 HOH HOH . G 6 HOH A 118 618 618 HOH HOH . G 6 HOH A 119 619 619 HOH HOH . G 6 HOH A 120 620 620 HOH HOH . G 6 HOH A 121 621 621 HOH HOH . G 6 HOH A 122 622 622 HOH HOH . G 6 HOH A 123 623 623 HOH HOH . G 6 HOH A 124 624 624 HOH HOH . G 6 HOH A 125 625 625 HOH HOH . G 6 HOH A 126 626 626 HOH HOH . G 6 HOH A 127 627 627 HOH HOH . G 6 HOH A 128 628 628 HOH HOH . G 6 HOH A 129 629 629 HOH HOH . G 6 HOH A 130 630 630 HOH HOH . G 6 HOH A 131 631 631 HOH HOH . G 6 HOH A 132 632 632 HOH HOH . G 6 HOH A 133 633 633 HOH HOH . G 6 HOH A 134 634 634 HOH HOH . G 6 HOH A 135 635 635 HOH HOH . G 6 HOH A 136 636 636 HOH HOH . G 6 HOH A 137 637 637 HOH HOH . G 6 HOH A 138 638 638 HOH HOH . G 6 HOH A 139 639 639 HOH HOH . G 6 HOH A 140 640 640 HOH HOH . G 6 HOH A 141 641 641 HOH HOH . G 6 HOH A 142 642 642 HOH HOH . G 6 HOH A 143 643 643 HOH HOH . G 6 HOH A 144 644 644 HOH HOH . G 6 HOH A 145 645 645 HOH HOH . G 6 HOH A 146 646 646 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 . . . F 5 -15.076 12.952 -33.863 1 25.46 ? PB ADP 405 A 1 HETATM 2 O O1B ADP . . . F 5 -16.081 13.077 -34.999 1 21.31 ? O1B ADP 405 A 1 HETATM 3 O O2B ADP . . . F 5 -14.394 11.616 -33.854 1 30.48 ? O2B ADP 405 A 1 HETATM 4 O O3B ADP . . . F 5 -15.677 13.33 -32.519 1 27.57 ? O3B ADP 405 A 1 HETATM 5 P PA ADP . . . F 5 -13.685 14.842 -35.605 1 22.07 ? PA ADP 405 A 1 HETATM 6 O O1A ADP . . . F 5 -14.252 14.232 -36.85 1 18.34 ? O1A ADP 405 A 1 HETATM 7 O O2A ADP . . . F 5 -12.221 15.219 -35.593 1 20.62 ? O2A ADP 405 A 1 HETATM 8 O O3A ADP . . . F 5 -13.994 14.103 -34.23 1 21.72 ? O3A ADP 405 A 1 HETATM 9 O O5' ADP . . . F 5 -14.489 16.182 -35.376 1 22.25 ? O5' ADP 405 A 1 HETATM 10 C C5' ADP . . . F 5 -14.464 16.893 -34.116 1 27.67 ? C5' ADP 405 A 1 HETATM 11 C C4' ADP . . . F 5 -15.013 18.296 -34.422 1 22.67 ? C4' ADP 405 A 1 HETATM 12 O O4' ADP . . . F 5 -16.386 18.182 -34.753 1 24.41 ? O4' ADP 405 A 1 HETATM 13 C C3' ADP . . . F 5 -15.033 19.2 -33.179 1 25.01 ? C3' ADP 405 A 1 HETATM 14 O O3' ADP . . . F 5 -13.728 19.702 -32.903 1 29.28 ? O3' ADP 405 A 1 HETATM 15 C C2' ADP . . . F 5 -15.973 20.301 -33.699 1 16.43 ? C2' ADP 405 A 1 HETATM 16 O O2' ADP . . . F 5 -15.351 21.169 -34.637 1 26.95 ? O2' ADP 405 A 1 HETATM 17 C C1' ADP . . . F 5 -17.006 19.449 -34.48 1 19.16 ? C1' ADP 405 A 1 HETATM 18 N N9 ADP . . . F 5 -18.189 19.2 -33.632 1 23.62 ? N9 ADP 405 A 1 HETATM 19 C C8 ADP . . . F 5 -18.379 18.206 -32.683 1 32.91 ? C8 ADP 405 A 1 HETATM 20 N N7 ADP . . . F 5 -19.567 18.264 -32.092 1 29.4 ? N7 ADP 405 A 1 HETATM 21 C C5 ADP . . . F 5 -20.194 19.358 -32.68 1 27.97 ? C5 ADP 405 A 1 HETATM 22 C C6 ADP . . . F 5 -21.452 19.947 -32.502 1 28.93 ? C6 ADP 405 A 1 HETATM 23 N N6 ADP . . . F 5 -22.364 19.467 -31.603 1 19.66 ? N6 ADP 405 A 1 HETATM 24 N N1 ADP . . . F 5 -21.782 21.027 -33.24 1 20.42 ? N1 ADP 405 A 1 HETATM 25 C C2 ADP . . . F 5 -20.887 21.48 -34.108 1 23.34 ? C2 ADP 405 A 1 HETATM 26 N N3 ADP . . . F 5 -19.65 21.045 -34.409 1 25.58 ? N3 ADP 405 A 1 HETATM 27 C C4 ADP . . . F 5 -19.344 19.952 -33.646 1 24.64 ? C4 ADP 405 A 1 HETATM 28 H "H5'1" ADP . . . F 5 -13.555 17.06 -33.823 1 33.21 ? "H5'1" ADP 405 A 1 HETATM 29 H "H5'2" ADP . . . F 5 -14.887 16.403 -33.394 1 33.21 ? "H5'2" ADP 405 A 1 HETATM 30 H H4' ADP . . . F 5 -14.517 18.673 -35.165 1 27.2 ? H4' ADP 405 A 1 HETATM 31 H H3' ADP . . . F 5 -15.433 18.726 -32.433 1 30.01 ? H3' ADP 405 A 1 HETATM 32 H HO3' ADP . . . F 5 -13.752 19.974 -32.098 1 35.13 ? HO3' ADP 405 A 1 HETATM 33 H H2' ADP . . . F 5 -16.398 20.786 -32.974 1 19.72 ? H2' ADP 405 A 1 HETATM 34 H HO2' ADP . . . F 5 -15.347 20.743 -35.373 1 32.34 ? HO2' ADP 405 A 1 HETATM 35 H H1' ADP . . . F 5 -17.312 19.875 -35.296 1 22.99 ? H1' ADP 405 A 1 HETATM 36 H H8 ADP . . . F 5 -17.714 17.578 -32.512 1 39.5 ? H8 ADP 405 A 1 HETATM 37 H HN61 ADP . . . F 5 -23.083 19.914 -31.452 1 23.59 ? HN61 ADP 405 A 1 HETATM 38 H HN62 ADP . . . F 5 -22.207 18.723 -31.201 1 23.59 ? HN62 ADP 405 A 1 HETATM 39 H H2 ADP . . . F 5 -21.166 22.225 -34.589 1 28.01 ? H2 ADP 405 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #