data_5ZO8
#
_model_server_result.job_id            OK7cxmzkM1GOyWxyaw0s7g 
_model_server_result.datetime_utc      '2024-10-22 03:26:57' 
_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          5zo8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":600}' 
#
_entry.id    5ZO8 
#
_exptl.entry_id    5ZO8 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          112.99 
_cell.angle_gamma         90 
_cell.entry_id            5ZO8 
_cell.length_a            95.293 
_cell.length_b            50.724 
_cell.length_c            83.355 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5ZO8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,O 1 1 
B,I,J,K,L,M,N,P 2 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 I N 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 OG1 THR 103 A THR 112 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc2 A OE1 GLU 158 A GLU 167 1_555 H NA NA . A NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.806 ? 
metalc ? metalc3 C O1B ADP . A ADP 600 1_555 D MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc4 D MG MG . A MG 601 1_555 O O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? 
metalc ? metalc5 D MG MG . A MG 601 1_555 O O HOH . A HOH 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? 
metalc ? metalc6 D MG MG . A MG 601 1_555 O O HOH . A HOH 714 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? 
metalc ? metalc7 D MG MG . A MG 601 1_555 O O HOH . A HOH 749 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? 
metalc ? metalc8 G O1 SO4 . A SO4 604 1_555 H NA NA . A NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.74 ? 
metalc ? metalc9 H NA NA . A NA 605 1_555 O O HOH . A HOH 759 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc10 B OG1 THR 103 B THR 112 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc11 B OE1 GLU 158 B GLU 167 1_555 N NA NA . B NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.826 ? 
metalc ? metalc12 I O3B ADP . B ADP 600 1_555 J MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? 
metalc ? metalc13 J MG MG . B MG 601 1_555 P O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc14 J MG MG . B MG 601 1_555 P O HOH . B HOH 711 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? 
metalc ? metalc15 J MG MG . B MG 601 1_555 P O HOH . B HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.23 ? 
metalc ? metalc16 J MG MG . B MG 601 1_555 P O HOH . B HOH 745 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? 
metalc ? metalc17 M O4 SO4 . B SO4 604 1_555 N NA NA . B NA 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.562 ? 
#
_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 54 n n 
PB O2B ADP sing 55 n n 
PB O3B ADP sing 56 n n 
PB O3A ADP sing 57 n n 
O2B HOB2 ADP sing 58 n n 
O3B HOB3 ADP sing 59 n n 
PA O1A ADP doub 60 n n 
PA O2A ADP sing 61 n n 
PA O3A ADP sing 62 n n 
PA O5' ADP sing 63 n n 
O2A HOA2 ADP sing 64 n n 
O5' C5' ADP sing 65 n n 
C5' C4' ADP sing 66 n n 
C5' "H5'1" ADP sing 67 n n 
C5' "H5'2" ADP sing 68 n n 
C4' O4' ADP sing 69 n n 
C4' C3' ADP sing 70 n n 
C4' H4' ADP sing 71 n n 
O4' C1' ADP sing 72 n n 
C3' O3' ADP sing 73 n n 
C3' C2' ADP sing 74 n n 
C3' H3' ADP sing 75 n n 
O3' HO3' ADP sing 76 n n 
C2' O2' ADP sing 77 n n 
C2' C1' ADP sing 78 n n 
C2' H2' ADP sing 79 n n 
O2' HO2' ADP sing 80 n n 
C1' N9 ADP sing 81 n n 
C1' H1' ADP sing 82 n n 
N9 C8 ADP sing 83 n y 
N9 C4 ADP sing 84 n y 
C8 N7 ADP doub 85 n y 
C8 H8 ADP sing 86 n n 
N7 C5 ADP sing 87 n y 
C5 C6 ADP sing 88 n y 
C5 C4 ADP doub 89 n y 
C6 N6 ADP sing 90 n n 
C6 N1 ADP doub 91 n y 
N6 HN61 ADP sing 92 n n 
N6 HN62 ADP sing 93 n n 
N1 C2 ADP sing 94 n y 
C2 N3 ADP doub 95 n y 
C2 H2 ADP sing 96 n n 
N3 C4 ADP sing 97 n y 
#
_atom_sites.entry_id                     5ZO8 
_atom_sites.fract_transf_matrix[1][1]    0.010494 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.004452 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.019715 
_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]    0.013032 
_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
C 2 ADP A 1 600 600 ADP ADP . 
D 3 MG A 1 601 601 MG MG . 
E 4 4C5 A 1 602 602 4C5 4C5 . 
F 5 SO4 A 1 603 603 SO4 SO4 . 
G 5 SO4 A 1 604 604 SO4 SO4 . 
H 6 NA A 1 605 605 NA NA . 
I 2 ADP B 1 600 600 ADP ADP . 
J 3 MG B 1 601 601 MG MG . 
K 4 4C5 B 1 602 602 4C5 4C5 . 
L 5 SO4 B 1 603 603 SO4 SO4 . 
M 5 SO4 B 1 604 604 SO4 SO4 . 
N 6 NA B 1 605 605 NA NA . 
O 7 HOH A 1 701 41 HOH HOH . 
O 7 HOH A 2 702 16 HOH HOH . 
O 7 HOH A 3 703 49 HOH HOH . 
O 7 HOH A 4 704 58 HOH HOH . 
O 7 HOH A 5 705 78 HOH HOH . 
O 7 HOH A 6 706 102 HOH HOH . 
O 7 HOH A 7 707 38 HOH HOH . 
O 7 HOH A 8 708 53 HOH HOH . 
O 7 HOH A 9 709 66 HOH HOH . 
O 7 HOH A 10 710 5 HOH HOH . 
O 7 HOH A 11 711 13 HOH HOH . 
O 7 HOH A 12 712 106 HOH HOH . 
O 7 HOH A 13 713 57 HOH HOH . 
O 7 HOH A 14 714 21 HOH HOH . 
O 7 HOH A 15 715 48 HOH HOH . 
O 7 HOH A 16 716 91 HOH HOH . 
O 7 HOH A 17 717 2 HOH HOH . 
O 7 HOH A 18 718 8 HOH HOH . 
O 7 HOH A 19 719 3 HOH HOH . 
O 7 HOH A 20 720 83 HOH HOH . 
O 7 HOH A 21 721 31 HOH HOH . 
O 7 HOH A 22 722 82 HOH HOH . 
O 7 HOH A 23 723 11 HOH HOH . 
O 7 HOH A 24 724 7 HOH HOH . 
O 7 HOH A 25 725 6 HOH HOH . 
O 7 HOH A 26 726 75 HOH HOH . 
O 7 HOH A 27 727 39 HOH HOH . 
O 7 HOH A 28 728 62 HOH HOH . 
O 7 HOH A 29 729 79 HOH HOH . 
O 7 HOH A 30 730 45 HOH HOH . 
O 7 HOH A 31 731 27 HOH HOH . 
O 7 HOH A 32 732 107 HOH HOH . 
O 7 HOH A 33 733 100 HOH HOH . 
O 7 HOH A 34 734 101 HOH HOH . 
O 7 HOH A 35 735 18 HOH HOH . 
O 7 HOH A 36 736 56 HOH HOH . 
O 7 HOH A 37 737 55 HOH HOH . 
O 7 HOH A 38 738 28 HOH HOH . 
O 7 HOH A 39 739 94 HOH HOH . 
O 7 HOH A 40 740 105 HOH HOH . 
O 7 HOH A 41 741 96 HOH HOH . 
O 7 HOH A 42 742 93 HOH HOH . 
O 7 HOH A 43 743 61 HOH HOH . 
O 7 HOH A 44 744 85 HOH HOH . 
O 7 HOH A 45 745 20 HOH HOH . 
O 7 HOH A 46 746 10 HOH HOH . 
O 7 HOH A 47 747 97 HOH HOH . 
O 7 HOH A 48 748 98 HOH HOH . 
O 7 HOH A 49 749 54 HOH HOH . 
O 7 HOH A 50 750 92 HOH HOH . 
O 7 HOH A 51 751 1 HOH HOH . 
O 7 HOH A 52 752 47 HOH HOH . 
O 7 HOH A 53 753 74 HOH HOH . 
O 7 HOH A 54 754 15 HOH HOH . 
O 7 HOH A 55 755 29 HOH HOH . 
O 7 HOH A 56 756 36 HOH HOH . 
O 7 HOH A 57 757 24 HOH HOH . 
O 7 HOH A 58 758 67 HOH HOH . 
O 7 HOH A 59 759 70 HOH HOH . 
P 7 HOH B 1 701 72 HOH HOH . 
P 7 HOH B 2 702 64 HOH HOH . 
P 7 HOH B 3 703 26 HOH HOH . 
P 7 HOH B 4 704 77 HOH HOH . 
P 7 HOH B 5 705 84 HOH HOH . 
P 7 HOH B 6 706 42 HOH HOH . 
P 7 HOH B 7 707 12 HOH HOH . 
P 7 HOH B 8 708 25 HOH HOH . 
P 7 HOH B 9 709 86 HOH HOH . 
P 7 HOH B 10 710 88 HOH HOH . 
P 7 HOH B 11 711 22 HOH HOH . 
P 7 HOH B 12 712 68 HOH HOH . 
P 7 HOH B 13 713 95 HOH HOH . 
P 7 HOH B 14 714 35 HOH HOH . 
P 7 HOH B 15 715 87 HOH HOH . 
P 7 HOH B 16 716 60 HOH HOH . 
P 7 HOH B 17 717 104 HOH HOH . 
P 7 HOH B 18 718 80 HOH HOH . 
P 7 HOH B 19 719 90 HOH HOH . 
P 7 HOH B 20 720 73 HOH HOH . 
P 7 HOH B 21 721 50 HOH HOH . 
P 7 HOH B 22 722 103 HOH HOH . 
P 7 HOH B 23 723 71 HOH HOH . 
P 7 HOH B 24 724 17 HOH HOH . 
P 7 HOH B 25 725 51 HOH HOH . 
P 7 HOH B 26 726 89 HOH HOH . 
P 7 HOH B 27 727 43 HOH HOH . 
P 7 HOH B 28 728 32 HOH HOH . 
P 7 HOH B 29 729 59 HOH HOH . 
P 7 HOH B 30 730 4 HOH HOH . 
P 7 HOH B 31 731 37 HOH HOH . 
P 7 HOH B 32 732 40 HOH HOH . 
P 7 HOH B 33 733 44 HOH HOH . 
P 7 HOH B 34 734 52 HOH HOH . 
P 7 HOH B 35 735 81 HOH HOH . 
P 7 HOH B 36 736 65 HOH HOH . 
P 7 HOH B 37 737 33 HOH HOH . 
P 7 HOH B 38 738 76 HOH HOH . 
P 7 HOH B 39 739 23 HOH HOH . 
P 7 HOH B 40 740 46 HOH HOH . 
P 7 HOH B 41 741 14 HOH HOH . 
P 7 HOH B 42 742 30 HOH HOH . 
P 7 HOH B 43 743 9 HOH HOH . 
P 7 HOH B 44 744 19 HOH HOH . 
P 7 HOH B 45 745 69 HOH HOH . 
P 7 HOH B 46 746 34 HOH HOH . 
P 7 HOH B 47 747 63 HOH HOH . 
P 7 HOH B 48 748 99 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 . . . I 2 -13.879 -12.657 48.575 1 20.34 ? PB ADP 600 B 1 
HETATM 2 O O1B ADP . . . I 2 -14.005 -12.87 47.069 1 19.76 ? O1B ADP 600 B 1 
HETATM 3 O O2B ADP . . . I 2 -12.409 -12.465 48.866 1 20.96 ? O2B ADP 600 B 1 
HETATM 4 O O3B ADP . . . I 2 -14.774 -11.611 49.19 1 19.8 ? O3B ADP 600 B 1 
HETATM 5 P PA ADP . . . I 2 -15.61 -14.535 49.867 1 20.63 ? PA ADP 600 B 1 
HETATM 6 O O1A ADP . . . I 2 -16.621 -14.164 48.885 1 20.33 ? O1A ADP 600 B 1 
HETATM 7 O O2A ADP . . . I 2 -15.596 -14.013 51.266 1 23.36 ? O2A ADP 600 B 1 
HETATM 8 O O3A ADP . . . I 2 -14.179 -14.069 49.31 1 21.77 ? O3A ADP 600 B 1 
HETATM 9 O O5' ADP . . . I 2 -15.515 -16.148 50.053 1 21.85 ? O5' ADP 600 B 1 
HETATM 10 C C5' ADP . . . I 2 -15.515 -17.078 48.961 1 22.59 ? C5' ADP 600 B 1 
HETATM 11 C C4' ADP . . . I 2 -15.989 -18.459 49.374 1 23.46 ? C4' ADP 600 B 1 
HETATM 12 O O4' ADP . . . I 2 -15.036 -19.104 50.236 1 26.06 ? O4' ADP 600 B 1 
HETATM 13 C C3' ADP . . . I 2 -17.27 -18.363 50.194 1 26.41 ? C3' ADP 600 B 1 
HETATM 14 O O3' ADP . . . I 2 -18.047 -19.526 49.97 1 27.5 ? O3' ADP 600 B 1 
HETATM 15 C C2' ADP . . . I 2 -16.768 -18.379 51.633 1 25.5 ? C2' ADP 600 B 1 
HETATM 16 O O2' ADP . . . I 2 -17.718 -18.883 52.555 1 26.17 ? O2' ADP 600 B 1 
HETATM 17 C C1' ADP . . . I 2 -15.561 -19.279 51.541 1 23.15 ? C1' ADP 600 B 1 
HETATM 18 N N9 ADP . . . I 2 -14.579 -18.925 52.528 1 24.12 ? N9 ADP 600 B 1 
HETATM 19 C C8 ADP . . . I 2 -13.802 -17.808 52.509 1 24.43 ? C8 ADP 600 B 1 
HETATM 20 N N7 ADP . . . I 2 -13.001 -17.768 53.578 1 24.79 ? N7 ADP 600 B 1 
HETATM 21 C C5 ADP . . . I 2 -13.291 -18.894 54.315 1 26.19 ? C5 ADP 600 B 1 
HETATM 22 C C6 ADP . . . I 2 -12.796 -19.52 55.567 1 26.94 ? C6 ADP 600 B 1 
HETATM 23 N N6 ADP . . . I 2 -11.846 -18.916 56.286 1 27.27 ? N6 ADP 600 B 1 
HETATM 24 N N1 ADP . . . I 2 -13.382 -20.655 55.993 1 28.71 ? N1 ADP 600 B 1 
HETATM 25 C C2 ADP . . . I 2 -14.351 -21.296 55.298 1 27.31 ? C2 ADP 600 B 1 
HETATM 26 N N3 ADP . . . I 2 -14.826 -20.807 54.148 1 25.92 ? N3 ADP 600 B 1 
HETATM 27 C C4 ADP . . . I 2 -14.336 -19.643 53.621 1 24.93 ? C4 ADP 600 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           218 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#