data_2RD5
#
_model_server_result.job_id            xmwmcdydWIS_hnm53U2x2g 
_model_server_result.datetime_utc      '2024-12-21 16:06:51' 
_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          2rd5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2000}' 
#
_entry.id    2RD5 
#
_exptl.entry_id    2RD5 
_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    2 
_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            2RD5 
_cell.length_a            171.133 
_cell.length_b            171.133 
_cell.length_c            171.133 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2RD5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_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,H,I,J,K,L,M,N,O,P,Q,R,S 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
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_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 J 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 J O1B ADP . B ADP 2000 1_555 H MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? 
metalc ? metalc2 J O2A ADP . B ADP 2000 1_555 H MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc3 C O GLY 49 C GLY 48 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc4 M O3G ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
metalc ? metalc5 M O2A ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? 
metalc ? metalc6 M O2B ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc7 M O1A ATP . C ATP 1000 1_555 L MG MG . C MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? 
metalc ? metalc8 D O GLY 49 D GLY 48 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? 
metalc ? metalc9 O O3G ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? 
metalc ? metalc10 O O2B ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? 
metalc ? metalc11 O O2A ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc12 O O1A ATP . D ATP 1000 1_555 N MG MG . D MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.743 ? 
#
_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                     2RD5 
_atom_sites.fract_transf_matrix[1][1]    0.005843 
_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]    0.005843 
_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]    0.005843 
_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
E 3 ARG A 1 1000 1000 ARG ARG . 
F 4 ADP A 1 2000 2000 ADP ADP . 
G 5 NLG A 1 2001 2001 NLG NLG . 
H 6 MG B 1 2002 2002 MG MG . 
I 3 ARG B 1 1000 1000 ARG ARG . 
J 4 ADP B 1 2000 2000 ADP ADP . 
K 5 NLG B 1 2001 2001 NLG NLG . 
L 6 MG C 1 1001 1001 MG MG . 
M 7 ATP C 1 1000 1000 ATP ATP . 
N 6 MG D 1 1001 1001 MG MG . 
O 7 ATP D 1 1000 1000 ATP ATP . 
P 8 HOH A 1 2002 10 HOH HOH . 
P 8 HOH A 2 2003 11 HOH HOH . 
P 8 HOH A 3 2004 12 HOH HOH . 
P 8 HOH A 4 2005 19 HOH HOH . 
P 8 HOH A 5 2006 20 HOH HOH . 
P 8 HOH A 6 2007 40 HOH HOH . 
P 8 HOH A 7 2008 41 HOH HOH . 
P 8 HOH A 8 2009 42 HOH HOH . 
P 8 HOH A 9 2010 43 HOH HOH . 
P 8 HOH A 10 2011 44 HOH HOH . 
P 8 HOH A 11 2012 45 HOH HOH . 
P 8 HOH A 12 2013 46 HOH HOH . 
P 8 HOH A 13 2014 47 HOH HOH . 
P 8 HOH A 14 2015 48 HOH HOH . 
P 8 HOH A 15 2016 49 HOH HOH . 
P 8 HOH A 16 2017 53 HOH HOH . 
P 8 HOH A 17 2018 54 HOH HOH . 
P 8 HOH A 18 2019 55 HOH HOH . 
P 8 HOH A 19 2020 56 HOH HOH . 
P 8 HOH A 20 2021 57 HOH HOH . 
P 8 HOH A 21 2022 58 HOH HOH . 
P 8 HOH A 22 2023 62 HOH HOH . 
P 8 HOH A 23 2024 63 HOH HOH . 
P 8 HOH A 24 2025 64 HOH HOH . 
Q 8 HOH B 1 2003 13 HOH HOH . 
Q 8 HOH B 2 2004 14 HOH HOH . 
Q 8 HOH B 3 2005 15 HOH HOH . 
Q 8 HOH B 4 2006 16 HOH HOH . 
Q 8 HOH B 5 2007 17 HOH HOH . 
Q 8 HOH B 6 2008 18 HOH HOH . 
Q 8 HOH B 7 2009 21 HOH HOH . 
Q 8 HOH B 8 2010 22 HOH HOH . 
Q 8 HOH B 9 2011 23 HOH HOH . 
Q 8 HOH B 10 2012 24 HOH HOH . 
Q 8 HOH B 11 2013 25 HOH HOH . 
Q 8 HOH B 12 2014 26 HOH HOH . 
Q 8 HOH B 13 2015 27 HOH HOH . 
Q 8 HOH B 14 2016 28 HOH HOH . 
Q 8 HOH B 15 2017 29 HOH HOH . 
Q 8 HOH B 16 2018 32 HOH HOH . 
Q 8 HOH B 17 2019 33 HOH HOH . 
Q 8 HOH B 18 2020 35 HOH HOH . 
Q 8 HOH B 19 2021 36 HOH HOH . 
Q 8 HOH B 20 2022 37 HOH HOH . 
Q 8 HOH B 21 2023 38 HOH HOH . 
Q 8 HOH B 22 2024 39 HOH HOH . 
Q 8 HOH B 23 2025 59 HOH HOH . 
Q 8 HOH B 24 2026 60 HOH HOH . 
Q 8 HOH B 25 2027 61 HOH HOH . 
R 8 HOH C 1 1002 2 HOH HOH . 
R 8 HOH C 2 1003 30 HOH HOH . 
R 8 HOH C 3 1004 31 HOH HOH . 
R 8 HOH C 4 1005 34 HOH HOH . 
S 8 HOH D 1 1002 1 HOH HOH . 
S 8 HOH D 2 1003 3 HOH HOH . 
S 8 HOH D 3 1004 4 HOH HOH . 
S 8 HOH D 4 1005 5 HOH HOH . 
S 8 HOH D 5 1006 6 HOH HOH . 
S 8 HOH D 6 1007 7 HOH HOH . 
S 8 HOH D 7 1008 8 HOH HOH . 
S 8 HOH D 8 1009 9 HOH HOH . 
S 8 HOH D 9 1010 50 HOH HOH . 
S 8 HOH D 10 1011 51 HOH HOH . 
S 8 HOH D 11 1012 52 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 . . . J 4 80.801 99.995 43.498 1 49.57 ? PB ADP 2000 B 1 
HETATM 2 O O1B ADP . . . J 4 80.517 100.569 44.866 1 42.48 ? O1B ADP 2000 B 1 
HETATM 3 O O2B ADP . . . J 4 81.829 98.896 43.424 1 51.77 ? O2B ADP 2000 B 1 
HETATM 4 O O3B ADP . . . J 4 79.55 99.645 42.714 1 51.03 ? O3B ADP 2000 B 1 
HETATM 5 P PA ADP . . . J 4 81.76 102.711 43.324 1 45.47 ? PA ADP 2000 B 1 
HETATM 6 O O1A ADP . . . J 4 81.756 103.636 42.139 1 63.57 ? O1A ADP 2000 B 1 
HETATM 7 O O2A ADP . . . J 4 80.809 102.965 44.467 1 54.37 ? O2A ADP 2000 B 1 
HETATM 8 O O3A ADP . . . J 4 81.534 101.219 42.714 1 50.25 ? O3A ADP 2000 B 1 
HETATM 9 O O5' ADP . . . J 4 83.274 102.675 43.891 1 55.53 ? O5' ADP 2000 B 1 
HETATM 10 C C5' ADP . . . J 4 84.394 102.373 43.04 1 51.22 ? C5' ADP 2000 B 1 
HETATM 11 C C4' ADP . . . J 4 84.967 103.65 42.415 1 55.57 ? C4' ADP 2000 B 1 
HETATM 12 O O4' ADP . . . J 4 85.705 104.447 43.352 1 50.72 ? O4' ADP 2000 B 1 
HETATM 13 C C3' ADP . . . J 4 85.96 103.416 41.282 1 55.19 ? C3' ADP 2000 B 1 
HETATM 14 O O3' ADP . . . J 4 85.303 103.156 40.04 1 50.08 ? O3' ADP 2000 B 1 
HETATM 15 C C2' ADP . . . J 4 86.738 104.716 41.227 1 52.94 ? C2' ADP 2000 B 1 
HETATM 16 O O2' ADP . . . J 4 86.148 105.62 40.293 1 55.48 ? O2' ADP 2000 B 1 
HETATM 17 C C1' ADP . . . J 4 86.565 105.325 42.61 1 51.03 ? C1' ADP 2000 B 1 
HETATM 18 N N9 ADP . . . J 4 87.854 105.524 43.325 1 50.48 ? N9 ADP 2000 B 1 
HETATM 19 C C8 ADP . . . J 4 88.118 106.605 44.085 1 50.67 ? C8 ADP 2000 B 1 
HETATM 20 N N7 ADP . . . J 4 89.348 106.53 44.645 1 52.8 ? N7 ADP 2000 B 1 
HETATM 21 C C5 ADP . . . J 4 89.897 105.373 44.24 1 49.61 ? C5 ADP 2000 B 1 
HETATM 22 C C6 ADP . . . J 4 91.186 104.68 44.46 1 49.91 ? C6 ADP 2000 B 1 
HETATM 23 N N6 ADP . . . J 4 92.144 105.233 45.239 1 50.54 ? N6 ADP 2000 B 1 
HETATM 24 N N1 ADP . . . J 4 91.368 103.481 43.859 1 53.91 ? N1 ADP 2000 B 1 
HETATM 25 C C2 ADP . . . J 4 90.42 102.922 43.076 1 51.42 ? C2 ADP 2000 B 1 
HETATM 26 N N3 ADP . . . J 4 89.228 103.5 42.838 1 55.1 ? N3 ADP 2000 B 1 
HETATM 27 C C4 ADP . . . J 4 88.91 104.707 43.373 1 49.26 ? C4 ADP 2000 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           387 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#