data_7D8V
#
_model_server_result.job_id            0UXPiorAo4sGR1rGV-LYTA 
_model_server_result.datetime_utc      '2024-11-05 04:38:28' 
_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          7d8v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":502}' 
#
_entry.id    7D8V 
#
_exptl.entry_id    7D8V 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          3 
_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            7D8V 
_cell.length_a            87.51 
_cell.length_b            87.51 
_cell.length_c            97.5 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7D8V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
_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 
_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' 5_554 x-y,-y,-z-2/3 1 0 0 0 -1 0 0 0 -1 0 0 -65 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_struct_asym.id                             C 
_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 110 A SER 110 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
metalc ? metalc2 C O1B ADP . A ADP 502 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc3 D MG MG . A MG 503 1_555 E O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc4 D MG MG . A MG 503 1_555 E O HOH . A HOH 654 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc5 D MG MG . A MG 503 1_555 E O HOH . A HOH 666 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? 
metalc ? metalc6 D MG MG . A MG 503 1_555 E O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? 
#
_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                     7D8V 
_atom_sites.fract_transf_matrix[1][1]    0.011427 
_atom_sites.fract_transf_matrix[1][2]    0.006598 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013195 
_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]    0.010256 
_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 TRS A 1 501 401 TRS TRS . 
C 3 ADP A 1 502 501 ADP ADP . 
D 4 MG A 1 503 1 MG MG . 
E 5 HOH A 1 601 103 HOH HOH . 
E 5 HOH A 2 602 91 HOH HOH . 
E 5 HOH A 3 603 81 HOH HOH . 
E 5 HOH A 4 604 110 HOH HOH . 
E 5 HOH A 5 605 46 HOH HOH . 
E 5 HOH A 6 606 29 HOH HOH . 
E 5 HOH A 7 607 51 HOH HOH . 
E 5 HOH A 8 608 62 HOH HOH . 
E 5 HOH A 9 609 73 HOH HOH . 
E 5 HOH A 10 610 7 HOH HOH . 
E 5 HOH A 11 611 11 HOH HOH . 
E 5 HOH A 12 612 95 HOH HOH . 
E 5 HOH A 13 613 14 HOH HOH . 
E 5 HOH A 14 614 112 HOH HOH . 
E 5 HOH A 15 615 30 HOH HOH . 
E 5 HOH A 16 616 52 HOH HOH . 
E 5 HOH A 17 617 33 HOH HOH . 
E 5 HOH A 18 618 102 HOH HOH . 
E 5 HOH A 19 619 17 HOH HOH . 
E 5 HOH A 20 620 1 HOH HOH . 
E 5 HOH A 21 621 61 HOH HOH . 
E 5 HOH A 22 622 69 HOH HOH . 
E 5 HOH A 23 623 34 HOH HOH . 
E 5 HOH A 24 624 49 HOH HOH . 
E 5 HOH A 25 625 96 HOH HOH . 
E 5 HOH A 26 626 4 HOH HOH . 
E 5 HOH A 27 627 93 HOH HOH . 
E 5 HOH A 28 628 63 HOH HOH . 
E 5 HOH A 29 629 25 HOH HOH . 
E 5 HOH A 30 630 9 HOH HOH . 
E 5 HOH A 31 631 108 HOH HOH . 
E 5 HOH A 32 632 21 HOH HOH . 
E 5 HOH A 33 633 2 HOH HOH . 
E 5 HOH A 34 634 86 HOH HOH . 
E 5 HOH A 35 635 16 HOH HOH . 
E 5 HOH A 36 636 104 HOH HOH . 
E 5 HOH A 37 637 18 HOH HOH . 
E 5 HOH A 38 638 90 HOH HOH . 
E 5 HOH A 39 639 76 HOH HOH . 
E 5 HOH A 40 640 89 HOH HOH . 
E 5 HOH A 41 641 27 HOH HOH . 
E 5 HOH A 42 642 45 HOH HOH . 
E 5 HOH A 43 643 31 HOH HOH . 
E 5 HOH A 44 644 26 HOH HOH . 
E 5 HOH A 45 645 92 HOH HOH . 
E 5 HOH A 46 646 43 HOH HOH . 
E 5 HOH A 47 647 56 HOH HOH . 
E 5 HOH A 48 648 66 HOH HOH . 
E 5 HOH A 49 649 94 HOH HOH . 
E 5 HOH A 50 650 28 HOH HOH . 
E 5 HOH A 51 651 20 HOH HOH . 
E 5 HOH A 52 652 24 HOH HOH . 
E 5 HOH A 53 653 111 HOH HOH . 
E 5 HOH A 54 654 19 HOH HOH . 
E 5 HOH A 55 655 53 HOH HOH . 
E 5 HOH A 56 656 36 HOH HOH . 
E 5 HOH A 57 657 38 HOH HOH . 
E 5 HOH A 58 658 101 HOH HOH . 
E 5 HOH A 59 659 15 HOH HOH . 
E 5 HOH A 60 660 77 HOH HOH . 
E 5 HOH A 61 661 10 HOH HOH . 
E 5 HOH A 62 662 48 HOH HOH . 
E 5 HOH A 63 663 57 HOH HOH . 
E 5 HOH A 64 664 8 HOH HOH . 
E 5 HOH A 65 665 5 HOH HOH . 
E 5 HOH A 66 666 97 HOH HOH . 
E 5 HOH A 67 667 75 HOH HOH . 
E 5 HOH A 68 668 44 HOH HOH . 
E 5 HOH A 69 669 35 HOH HOH . 
E 5 HOH A 70 670 23 HOH HOH . 
E 5 HOH A 71 671 64 HOH HOH . 
E 5 HOH A 72 672 47 HOH HOH . 
E 5 HOH A 73 673 60 HOH HOH . 
E 5 HOH A 74 674 85 HOH HOH . 
E 5 HOH A 75 675 13 HOH HOH . 
E 5 HOH A 76 676 87 HOH HOH . 
E 5 HOH A 77 677 71 HOH HOH . 
E 5 HOH A 78 678 59 HOH HOH . 
E 5 HOH A 79 679 83 HOH HOH . 
E 5 HOH A 80 680 105 HOH HOH . 
E 5 HOH A 81 681 3 HOH HOH . 
E 5 HOH A 82 682 72 HOH HOH . 
E 5 HOH A 83 683 67 HOH HOH . 
E 5 HOH A 84 684 68 HOH HOH . 
E 5 HOH A 85 685 42 HOH HOH . 
E 5 HOH A 86 686 70 HOH HOH . 
E 5 HOH A 87 687 55 HOH HOH . 
E 5 HOH A 88 688 78 HOH HOH . 
E 5 HOH A 89 689 58 HOH HOH . 
E 5 HOH A 90 690 39 HOH HOH . 
E 5 HOH A 91 691 40 HOH HOH . 
E 5 HOH A 92 692 54 HOH HOH . 
E 5 HOH A 93 693 32 HOH HOH . 
E 5 HOH A 94 694 6 HOH HOH . 
E 5 HOH A 95 695 22 HOH HOH . 
E 5 HOH A 96 696 12 HOH HOH . 
E 5 HOH A 97 697 50 HOH HOH . 
E 5 HOH A 98 698 98 HOH HOH . 
E 5 HOH A 99 699 113 HOH HOH . 
E 5 HOH A 100 700 65 HOH HOH . 
E 5 HOH A 101 701 37 HOH HOH . 
E 5 HOH A 102 702 107 HOH HOH . 
E 5 HOH A 103 703 99 HOH HOH . 
E 5 HOH A 104 704 84 HOH HOH . 
E 5 HOH A 105 705 41 HOH HOH . 
E 5 HOH A 106 706 82 HOH HOH . 
E 5 HOH A 107 707 74 HOH HOH . 
E 5 HOH A 108 708 80 HOH HOH . 
E 5 HOH A 109 709 106 HOH HOH . 
E 5 HOH A 110 710 88 HOH HOH . 
E 5 HOH A 111 711 109 HOH HOH . 
E 5 HOH A 112 712 100 HOH HOH . 
E 5 HOH A 113 713 79 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 . . . C 3 -39.212 13.644 -5.058 1 31.48 ? PB ADP 502 A 1 
HETATM 2 O O1B ADP . . . C 3 -39.047 12.957 -6.397 1 31.18 ? O1B ADP 502 A 1 
HETATM 3 O O2B ADP . . . C 3 -39.994 12.829 -4.05 1 43.07 ? O2B ADP 502 A 1 
HETATM 4 O O3B ADP . . . C 3 -37.928 14.215 -4.489 1 35.68 ? O3B ADP 502 A 1 
HETATM 5 P PA ADP . . . C 3 -40.935 15.264 -6.665 1 36.88 ? PA ADP 502 A 1 
HETATM 6 O O1A ADP . . . C 3 -40.007 15.725 -7.763 1 56.46 ? O1A ADP 502 A 1 
HETATM 7 O O2A ADP . . . C 3 -41.846 14.077 -6.882 1 47.41 ? O2A ADP 502 A 1 
HETATM 8 O O3A ADP . . . C 3 -40.065 14.986 -5.33 1 39.4 ? O3A ADP 502 A 1 
HETATM 9 O O5' ADP . . . C 3 -41.81 16.529 -6.179 1 42.04 ? O5' ADP 502 A 1 
HETATM 10 C C5' ADP . . . C 3 -43.04 16.342 -5.479 1 52.8 ? C5' ADP 502 A 1 
HETATM 11 C C4' ADP . . . C 3 -44.079 17.286 -6.063 1 67.34 ? C4' ADP 502 A 1 
HETATM 12 O O4' ADP . . . C 3 -43.645 18.638 -5.92 1 53.62 ? O4' ADP 502 A 1 
HETATM 13 C C3' ADP . . . C 3 -44.257 17.01 -7.546 1 79.79 ? C3' ADP 502 A 1 
HETATM 14 O O3' ADP . . . C 3 -45.642 16.815 -7.832 1 88.13 ? O3' ADP 502 A 1 
HETATM 15 C C2' ADP . . . C 3 -43.758 18.249 -8.254 1 71.63 ? C2' ADP 502 A 1 
HETATM 16 O O2' ADP . . . C 3 -44.659 18.623 -9.296 1 81.21 ? O2' ADP 502 A 1 
HETATM 17 C C1' ADP . . . C 3 -43.683 19.319 -7.177 1 51.55 ? C1' ADP 502 A 1 
HETATM 18 N N9 ADP . . . C 3 -42.422 20.072 -7.328 1 38.72 ? N9 ADP 502 A 1 
HETATM 19 C C8 ADP . . . C 3 -41.219 19.625 -6.917 1 32.17 ? C8 ADP 502 A 1 
HETATM 20 N N7 ADP . . . C 3 -40.245 20.533 -7.186 1 29.2 ? N7 ADP 502 A 1 
HETATM 21 C C5 ADP . . . C 3 -40.824 21.584 -7.787 1 24.2 ? C5 ADP 502 A 1 
HETATM 22 C C6 ADP . . . C 3 -40.36 22.884 -8.325 1 30.41 ? C6 ADP 502 A 1 
HETATM 23 N N6 ADP . . . C 3 -39.05 23.239 -8.273 1 34.56 ? N6 ADP 502 A 1 
HETATM 24 N N1 ADP . . . C 3 -41.287 23.698 -8.867 1 31.01 ? N1 ADP 502 A 1 
HETATM 25 C C2 ADP . . . C 3 -42.587 23.36 -8.916 1 27.26 ? C2 ADP 502 A 1 
HETATM 26 N N3 ADP . . . C 3 -43.069 22.2 -8.446 1 32.59 ? N3 ADP 502 A 1 
HETATM 27 C C4 ADP . . . C 3 -42.259 21.283 -7.874 1 29.38 ? C4 ADP 502 A 1 
#
_model_server_stats.io_time_ms              114 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           286 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           27 
#