data_2XD4
#
_model_server_result.job_id            gOOX0KHltLY4DrWOT7iFIg 
_model_server_result.datetime_utc      '2024-11-05 00:34:16' 
_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          2xd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":461}' 
#
_entry.id    2XD4 
#
_exptl.entry_id    2XD4 
_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         90 
_cell.entry_id            2XD4 
_cell.length_a            56.99 
_cell.length_b            84.41 
_cell.length_c            85.72 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2XD4 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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                      3 
_struct_asym.id                             E 
_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 NE2 HIS 167 A HIS 167 1_655 C MG MG . A MG 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
metalc ? metalc2 A OD2 ASP 172 A ASP 172 1_655 C MG MG . A MG 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? 
metalc ? metalc3 A OE1 GLU 283 A GLU 283 1_555 B MG MG . A MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc4 A OE2 GLU 283 A GLU 283 1_555 B MG MG . A MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
metalc ? metalc5 A OE2 GLU 283 A GLU 283 1_555 D MG MG . A MG 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc6 A OD1 ASN 285 A ASN 285 1_555 B MG MG . A MG 451 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? 
metalc ? metalc7 B MG MG . A MG 451 1_555 E O3B ADP . A ADP 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc8 B MG MG . A MG 451 1_555 F O HOH . A HOH 2070 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? 
metalc ? metalc9 C MG MG . A MG 452 1_555 F O HOH . A HOH 2038 1_655 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
metalc ? metalc10 D MG MG . A MG 453 1_555 E O2A ADP . A ADP 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? 
metalc ? metalc11 D MG MG . A MG 453 1_555 E O2B ADP . A ADP 461 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? 
#
_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                     2XD4 
_atom_sites.fract_transf_matrix[1][1]    0.017547 
_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]    0.011847 
_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]    0.011666 
_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 1 451 451 MG MG . 
C 2 MG A 1 452 452 MG MG . 
D 2 MG A 1 453 453 MG MG . 
E 3 ADP A 1 461 461 ADP ADP . 
F 4 HOH A 1 2001 2001 HOH HOH . 
F 4 HOH A 2 2002 2002 HOH HOH . 
F 4 HOH A 3 2003 2003 HOH HOH . 
F 4 HOH A 4 2004 2004 HOH HOH . 
F 4 HOH A 5 2005 2005 HOH HOH . 
F 4 HOH A 6 2006 2006 HOH HOH . 
F 4 HOH A 7 2007 2007 HOH HOH . 
F 4 HOH A 8 2008 2008 HOH HOH . 
F 4 HOH A 9 2009 2009 HOH HOH . 
F 4 HOH A 10 2010 2010 HOH HOH . 
F 4 HOH A 11 2011 2011 HOH HOH . 
F 4 HOH A 12 2012 2012 HOH HOH . 
F 4 HOH A 13 2013 2013 HOH HOH . 
F 4 HOH A 14 2014 2014 HOH HOH . 
F 4 HOH A 15 2015 2015 HOH HOH . 
F 4 HOH A 16 2016 2016 HOH HOH . 
F 4 HOH A 17 2017 2017 HOH HOH . 
F 4 HOH A 18 2018 2018 HOH HOH . 
F 4 HOH A 19 2019 2019 HOH HOH . 
F 4 HOH A 20 2020 2020 HOH HOH . 
F 4 HOH A 21 2021 2021 HOH HOH . 
F 4 HOH A 22 2022 2022 HOH HOH . 
F 4 HOH A 23 2023 2023 HOH HOH . 
F 4 HOH A 24 2024 2024 HOH HOH . 
F 4 HOH A 25 2025 2025 HOH HOH . 
F 4 HOH A 26 2026 2026 HOH HOH . 
F 4 HOH A 27 2027 2027 HOH HOH . 
F 4 HOH A 28 2028 2028 HOH HOH . 
F 4 HOH A 29 2029 2029 HOH HOH . 
F 4 HOH A 30 2030 2030 HOH HOH . 
F 4 HOH A 31 2031 2031 HOH HOH . 
F 4 HOH A 32 2032 2032 HOH HOH . 
F 4 HOH A 33 2033 2033 HOH HOH . 
F 4 HOH A 34 2034 2034 HOH HOH . 
F 4 HOH A 35 2035 2035 HOH HOH . 
F 4 HOH A 36 2036 2036 HOH HOH . 
F 4 HOH A 37 2037 2037 HOH HOH . 
F 4 HOH A 38 2038 2038 HOH HOH . 
F 4 HOH A 39 2039 2039 HOH HOH . 
F 4 HOH A 40 2040 2040 HOH HOH . 
F 4 HOH A 41 2041 2041 HOH HOH . 
F 4 HOH A 42 2042 2042 HOH HOH . 
F 4 HOH A 43 2043 2043 HOH HOH . 
F 4 HOH A 44 2044 2044 HOH HOH . 
F 4 HOH A 45 2045 2045 HOH HOH . 
F 4 HOH A 46 2046 2046 HOH HOH . 
F 4 HOH A 47 2047 2047 HOH HOH . 
F 4 HOH A 48 2048 2048 HOH HOH . 
F 4 HOH A 49 2049 2049 HOH HOH . 
F 4 HOH A 50 2050 2050 HOH HOH . 
F 4 HOH A 51 2051 2051 HOH HOH . 
F 4 HOH A 52 2052 2052 HOH HOH . 
F 4 HOH A 53 2053 2053 HOH HOH . 
F 4 HOH A 54 2054 2054 HOH HOH . 
F 4 HOH A 55 2055 2055 HOH HOH . 
F 4 HOH A 56 2056 2056 HOH HOH . 
F 4 HOH A 57 2057 2057 HOH HOH . 
F 4 HOH A 58 2058 2058 HOH HOH . 
F 4 HOH A 59 2059 2059 HOH HOH . 
F 4 HOH A 60 2060 2060 HOH HOH . 
F 4 HOH A 61 2061 2061 HOH HOH . 
F 4 HOH A 62 2062 2062 HOH HOH . 
F 4 HOH A 63 2063 2063 HOH HOH . 
F 4 HOH A 64 2064 2064 HOH HOH . 
F 4 HOH A 65 2065 2065 HOH HOH . 
F 4 HOH A 66 2066 2066 HOH HOH . 
F 4 HOH A 67 2067 2067 HOH HOH . 
F 4 HOH A 68 2068 2068 HOH HOH . 
F 4 HOH A 69 2069 2069 HOH HOH . 
F 4 HOH A 70 2070 2070 HOH HOH . 
F 4 HOH A 71 2071 2071 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 . . . E 3 12.309 45.441 35.44 1 48.73 ? PB ADP 461 A 1 
HETATM 2 O O1B ADP . . . E 3 11.066 45.047 36.06 1 50.68 ? O1B ADP 461 A 1 
HETATM 3 O O2B ADP . . . E 3 13.006 44.391 34.782 1 47.48 ? O2B ADP 461 A 1 
HETATM 4 O O3B ADP . . . E 3 13.18 46.116 36.435 1 47.3 ? O3B ADP 461 A 1 
HETATM 5 P PA ADP . . . E 3 12.351 46.538 32.675 1 38.85 ? PA ADP 461 A 1 
HETATM 6 O O1A ADP . . . E 3 12.228 47.939 32.337 1 37.84 ? O1A ADP 461 A 1 
HETATM 7 O O2A ADP . . . E 3 13.631 45.995 32.292 1 36.9 ? O2A ADP 461 A 1 
HETATM 8 O O3A ADP . . . E 3 12.019 46.477 34.238 1 42.63 ? O3A ADP 461 A 1 
HETATM 9 O O5' ADP . . . E 3 11.19 45.72 32.011 1 38.54 ? O5' ADP 461 A 1 
HETATM 10 C C5' ADP . . . E 3 11.021 44.303 32.092 1 38.03 ? C5' ADP 461 A 1 
HETATM 11 C C4' ADP . . . E 3 11.042 43.658 30.746 1 34.96 ? C4' ADP 461 A 1 
HETATM 12 O O4' ADP . . . E 3 9.99 44.215 29.873 1 36.79 ? O4' ADP 461 A 1 
HETATM 13 C C3' ADP . . . E 3 12.281 43.874 29.932 1 34.91 ? C3' ADP 461 A 1 
HETATM 14 O O3' ADP . . . E 3 13.363 43.032 30.233 1 34.3 ? O3' ADP 461 A 1 
HETATM 15 C C2' ADP . . . E 3 11.79 43.755 28.467 1 33.85 ? C2' ADP 461 A 1 
HETATM 16 O O2' ADP . . . E 3 11.776 42.423 28.05 1 34.05 ? O2' ADP 461 A 1 
HETATM 17 C C1' ADP . . . E 3 10.389 44.427 28.547 1 33.48 ? C1' ADP 461 A 1 
HETATM 18 N N9 ADP . . . E 3 10.256 45.892 28.251 1 32.4 ? N9 ADP 461 A 1 
HETATM 19 C C8 ADP . . . E 3 10.38 46.967 29.108 1 33.86 ? C8 ADP 461 A 1 
HETATM 20 N N7 ADP . . . E 3 10.21 48.15 28.564 1 35.02 ? N7 ADP 461 A 1 
HETATM 21 C C5 ADP . . . E 3 9.946 47.899 27.231 1 31.85 ? C5 ADP 461 A 1 
HETATM 22 C C6 ADP . . . E 3 9.673 48.693 26.1 1 31.4 ? C6 ADP 461 A 1 
HETATM 23 N N6 ADP . . . E 3 9.607 49.94 26.082 1 28.19 ? N6 ADP 461 A 1 
HETATM 24 N N1 ADP . . . E 3 9.444 48.096 24.857 1 33.33 ? N1 ADP 461 A 1 
HETATM 25 C C2 ADP . . . E 3 9.493 46.741 24.776 1 30.82 ? C2 ADP 461 A 1 
HETATM 26 N N3 ADP . . . E 3 9.744 45.917 25.791 1 30.59 ? N3 ADP 461 A 1 
HETATM 27 C C4 ADP . . . E 3 9.967 46.534 27.011 1 32.02 ? C4 ADP 461 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           228 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#