data_2B9I
#
_model_server_result.job_id            qLXmtgQ6ikRhBQ7cDCPVoQ 
_model_server_result.datetime_utc      '2024-10-18 16:30:08' 
_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          2b9i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":500}' 
#
_entry.id    2B9I 
#
_exptl.entry_id    2B9I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          4 
_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            2B9I 
_cell.length_a            58.081 
_cell.length_b            63.618 
_cell.length_c            99.95 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2B9I 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 OD1 ASN 142 A ASN 142 1_555 C MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc2 A OD2 ASP 155 A ASP 155 1_555 C MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? 
metalc ? metalc3 D O3B ADP . A ADP 500 1_555 C MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.959 ? 
metalc ? metalc4 D O2A ADP . A ADP 500 1_555 C MG MG . A MG 700 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc5 C MG MG . A MG 700 1_555 E O HOH . A HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc6 C MG MG . A MG 700 1_555 E O HOH . A HOH 787 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? 
#
_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                     2B9I 
_atom_sites.fract_transf_matrix[1][1]    0.017217 
_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]    0.015719 
_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]    0.010005 
_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 3 MG A 1 700 700 MG MG2 . 
D 4 ADP A 1 500 500 ADP ADP . 
E 5 HOH A 1 701 1 HOH HOH . 
E 5 HOH A 2 702 2 HOH HOH . 
E 5 HOH A 3 703 3 HOH HOH . 
E 5 HOH A 4 704 4 HOH HOH . 
E 5 HOH A 5 705 5 HOH HOH . 
E 5 HOH A 6 706 6 HOH HOH . 
E 5 HOH A 7 707 7 HOH HOH . 
E 5 HOH A 8 708 8 HOH HOH . 
E 5 HOH A 9 709 9 HOH HOH . 
E 5 HOH A 10 710 10 HOH HOH . 
E 5 HOH A 11 711 11 HOH HOH . 
E 5 HOH A 12 712 12 HOH HOH . 
E 5 HOH A 13 713 13 HOH HOH . 
E 5 HOH A 14 714 14 HOH HOH . 
E 5 HOH A 15 715 15 HOH HOH . 
E 5 HOH A 16 716 16 HOH HOH . 
E 5 HOH A 17 717 17 HOH HOH . 
E 5 HOH A 18 718 18 HOH HOH . 
E 5 HOH A 19 719 19 HOH HOH . 
E 5 HOH A 20 720 20 HOH HOH . 
E 5 HOH A 21 721 21 HOH HOH . 
E 5 HOH A 22 722 22 HOH HOH . 
E 5 HOH A 23 723 23 HOH HOH . 
E 5 HOH A 24 724 24 HOH HOH . 
E 5 HOH A 25 725 25 HOH HOH . 
E 5 HOH A 26 726 26 HOH HOH . 
E 5 HOH A 27 727 27 HOH HOH . 
E 5 HOH A 28 728 28 HOH HOH . 
E 5 HOH A 29 729 29 HOH HOH . 
E 5 HOH A 30 730 30 HOH HOH . 
E 5 HOH A 31 731 31 HOH HOH . 
E 5 HOH A 32 732 33 HOH HOH . 
E 5 HOH A 33 733 34 HOH HOH . 
E 5 HOH A 34 734 35 HOH HOH . 
E 5 HOH A 35 735 36 HOH HOH . 
E 5 HOH A 36 736 37 HOH HOH . 
E 5 HOH A 37 737 38 HOH HOH . 
E 5 HOH A 38 738 39 HOH HOH . 
E 5 HOH A 39 739 40 HOH HOH . 
E 5 HOH A 40 740 41 HOH HOH . 
E 5 HOH A 41 741 42 HOH HOH . 
E 5 HOH A 42 742 43 HOH HOH . 
E 5 HOH A 43 743 44 HOH HOH . 
E 5 HOH A 44 744 45 HOH HOH . 
E 5 HOH A 45 745 46 HOH HOH . 
E 5 HOH A 46 746 47 HOH HOH . 
E 5 HOH A 47 747 48 HOH HOH . 
E 5 HOH A 48 748 49 HOH HOH . 
E 5 HOH A 49 749 50 HOH HOH . 
E 5 HOH A 50 750 51 HOH HOH . 
E 5 HOH A 51 751 52 HOH HOH . 
E 5 HOH A 52 752 53 HOH HOH . 
E 5 HOH A 53 753 54 HOH HOH . 
E 5 HOH A 54 754 55 HOH HOH . 
E 5 HOH A 55 755 56 HOH HOH . 
E 5 HOH A 56 756 57 HOH HOH . 
E 5 HOH A 57 757 58 HOH HOH . 
E 5 HOH A 58 758 59 HOH HOH . 
E 5 HOH A 59 759 60 HOH HOH . 
E 5 HOH A 60 760 61 HOH HOH . 
E 5 HOH A 61 761 62 HOH HOH . 
E 5 HOH A 62 762 63 HOH HOH . 
E 5 HOH A 63 763 64 HOH HOH . 
E 5 HOH A 64 764 65 HOH HOH . 
E 5 HOH A 65 765 66 HOH HOH . 
E 5 HOH A 66 766 67 HOH HOH . 
E 5 HOH A 67 767 68 HOH HOH . 
E 5 HOH A 68 768 69 HOH HOH . 
E 5 HOH A 69 769 70 HOH HOH . 
E 5 HOH A 70 770 71 HOH HOH . 
E 5 HOH A 71 771 73 HOH HOH . 
E 5 HOH A 72 772 74 HOH HOH . 
E 5 HOH A 73 773 75 HOH HOH . 
E 5 HOH A 74 774 76 HOH HOH . 
E 5 HOH A 75 775 77 HOH HOH . 
E 5 HOH A 76 776 78 HOH HOH . 
E 5 HOH A 77 777 79 HOH HOH . 
E 5 HOH A 78 778 80 HOH HOH . 
E 5 HOH A 79 779 81 HOH HOH . 
E 5 HOH A 80 780 82 HOH HOH . 
E 5 HOH A 81 781 83 HOH HOH . 
E 5 HOH A 82 782 84 HOH HOH . 
E 5 HOH A 83 783 85 HOH HOH . 
E 5 HOH A 84 784 86 HOH HOH . 
E 5 HOH A 85 785 87 HOH HOH . 
E 5 HOH A 86 786 88 HOH HOH . 
E 5 HOH A 87 787 89 HOH HOH . 
E 5 HOH A 88 788 90 HOH HOH . 
E 5 HOH A 89 789 91 HOH HOH . 
E 5 HOH A 90 790 92 HOH HOH . 
E 5 HOH A 91 791 94 HOH HOH . 
F 5 HOH C 1 44 32 HOH HOH . 
F 5 HOH C 2 45 72 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 . . . D 4 36.853 4.674 41.557 1 28.25 ? PB ADP 500 A 1 
HETATM 2 O O1B ADP . . . D 4 38.032 5.529 41.618 1 29.13 ? O1B ADP 500 A 1 
HETATM 3 O O2B ADP . . . D 4 36.613 3.882 42.801 1 28.94 ? O2B ADP 500 A 1 
HETATM 4 O O3B ADP . . . D 4 35.593 5.481 41.08 1 27.14 ? O3B ADP 500 A 1 
HETATM 5 P PA ADP . . . D 4 36.514 3.206 39.148 1 24.05 ? PA ADP 500 A 1 
HETATM 6 O O1A ADP . . . D 4 36.778 1.747 38.926 1 22.78 ? O1A ADP 500 A 1 
HETATM 7 O O2A ADP . . . D 4 35.061 3.639 39.149 1 19.68 ? O2A ADP 500 A 1 
HETATM 8 O O3A ADP . . . D 4 37.205 3.566 40.475 1 26.05 ? O3A ADP 500 A 1 
HETATM 9 O O5' ADP . . . D 4 37.412 3.915 38.04 1 21.33 ? O5' ADP 500 A 1 
HETATM 10 C C5' ADP . . . D 4 37.438 5.358 37.883 1 19.1 ? C5' ADP 500 A 1 
HETATM 11 C C4' ADP . . . D 4 37.611 5.777 36.412 1 20.27 ? C4' ADP 500 A 1 
HETATM 12 O O4' ADP . . . D 4 38.709 5.021 35.841 1 20.65 ? O4' ADP 500 A 1 
HETATM 13 C C3' ADP . . . D 4 36.447 5.451 35.489 1 20.23 ? C3' ADP 500 A 1 
HETATM 14 O O3' ADP . . . D 4 35.505 6.555 35.526 1 21.44 ? O3' ADP 500 A 1 
HETATM 15 C C2' ADP . . . D 4 37.143 5.21 34.161 1 19.22 ? C2' ADP 500 A 1 
HETATM 16 O O2' ADP . . . D 4 37.334 6.41 33.442 1 22.82 ? O2' ADP 500 A 1 
HETATM 17 C C1' ADP . . . D 4 38.5 4.639 34.498 1 17.47 ? C1' ADP 500 A 1 
HETATM 18 N N9 ADP . . . D 4 38.527 3.132 34.399 1 18.68 ? N9 ADP 500 A 1 
HETATM 19 C C8 ADP . . . D 4 38.266 2.247 35.402 1 15.52 ? C8 ADP 500 A 1 
HETATM 20 N N7 ADP . . . D 4 38.364 0.993 35.038 1 13.71 ? N7 ADP 500 A 1 
HETATM 21 C C5 ADP . . . D 4 38.706 1.064 33.729 1 17.14 ? C5 ADP 500 A 1 
HETATM 22 C C6 ADP . . . D 4 38.965 0.009 32.748 1 18.26 ? C6 ADP 500 A 1 
HETATM 23 N N6 ADP . . . D 4 38.907 -1.263 32.974 1 15.47 ? N6 ADP 500 A 1 
HETATM 24 N N1 ADP . . . D 4 39.298 0.482 31.478 1 18.64 ? N1 ADP 500 A 1 
HETATM 25 C C2 ADP . . . D 4 39.374 1.82 31.184 1 17.91 ? C2 ADP 500 A 1 
HETATM 26 N N3 ADP . . . D 4 39.131 2.786 32.09 1 19.14 ? N3 ADP 500 A 1 
HETATM 27 C C4 ADP . . . D 4 38.813 2.372 33.313 1 16.46 ? C4 ADP 500 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           238 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#