data_2RD5
#
_model_server_result.job_id            g9Ha0XSvYSbSlnGbSLGIcg 
_model_server_result.datetime_utc      '2024-12-21 16:20:01' 
_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":"O","auth_seq_id":1000}' 
#
_entry.id    2RD5 
#
_exptl.entry_id    2RD5 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_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
? 7 M N N 
? 7 O 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 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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
PG O1G ATP doub 114 n n 
PG O2G ATP sing 115 n n 
PG O3G ATP sing 116 n n 
PG O3B ATP sing 117 n n 
O2G HOG2 ATP sing 118 n n 
O3G HOG3 ATP sing 119 n n 
PB O1B ATP doub 120 n n 
PB O2B ATP sing 121 n n 
PB O3B ATP sing 122 n n 
PB O3A ATP sing 123 n n 
O2B HOB2 ATP sing 124 n n 
PA O1A ATP doub 125 n n 
PA O2A ATP sing 126 n n 
PA O3A ATP sing 127 n n 
PA O5' ATP sing 128 n n 
O2A HOA2 ATP sing 129 n n 
O5' C5' ATP sing 130 n n 
C5' C4' ATP sing 131 n n 
C5' "H5'1" ATP sing 132 n n 
C5' "H5'2" ATP sing 133 n n 
C4' O4' ATP sing 134 n n 
C4' C3' ATP sing 135 n n 
C4' H4' ATP sing 136 n n 
O4' C1' ATP sing 137 n n 
C3' O3' ATP sing 138 n n 
C3' C2' ATP sing 139 n n 
C3' H3' ATP sing 140 n n 
O3' HO3' ATP sing 141 n n 
C2' O2' ATP sing 142 n n 
C2' C1' ATP sing 143 n n 
C2' H2' ATP sing 144 n n 
O2' HO2' ATP sing 145 n n 
C1' N9 ATP sing 146 n n 
C1' H1' ATP sing 147 n n 
N9 C8 ATP sing 148 n y 
N9 C4 ATP sing 149 n y 
C8 N7 ATP doub 150 n y 
C8 H8 ATP sing 151 n n 
N7 C5 ATP sing 152 n y 
C5 C6 ATP sing 153 n y 
C5 C4 ATP doub 154 n y 
C6 N6 ATP sing 155 n n 
C6 N1 ATP doub 156 n y 
N6 HN61 ATP sing 157 n n 
N6 HN62 ATP sing 158 n n 
N1 C2 ATP sing 159 n y 
C2 N3 ATP doub 160 n y 
C2 H2 ATP sing 161 n n 
N3 C4 ATP sing 162 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 PG ATP . . . O 7 62.326 33.802 40.498 1 60.56 ? PG ATP 1000 D 1 
HETATM 2 O O1G ATP . . . O 7 62.797 34.675 39.36 1 56.13 ? O1G ATP 1000 D 1 
HETATM 3 O O2G ATP . . . O 7 62.687 32.341 40.379 1 64.84 ? O2G ATP 1000 D 1 
HETATM 4 O O3G ATP . . . O 7 62.63 34.371 41.862 1 63.76 ? O3G ATP 1000 D 1 
HETATM 5 P PB ATP . . . O 7 59.692 33.58 41.547 1 60.77 ? PB ATP 1000 D 1 
HETATM 6 O O1B ATP . . . O 7 58.593 32.666 41.078 1 66.47 ? O1B ATP 1000 D 1 
HETATM 7 O O2B ATP . . . O 7 60.447 33.195 42.796 1 61.18 ? O2B ATP 1000 D 1 
HETATM 8 O O3B ATP . . . O 7 60.722 33.799 40.329 1 55.2 ? O3B ATP 1000 D 1 
HETATM 9 P PA ATP . . . O 7 59.688 36.183 42.678 1 60.88 ? PA ATP 1000 D 1 
HETATM 10 O O1A ATP . . . O 7 59.21 35.807 44.047 1 78.49 ? O1A ATP 1000 D 1 
HETATM 11 O O2A ATP . . . O 7 61.162 36.28 42.473 1 65.57 ? O2A ATP 1000 D 1 
HETATM 12 O O3A ATP . . . O 7 59.098 35.082 41.651 1 66.9 ? O3A ATP 1000 D 1 
HETATM 13 O O5' ATP . . . O 7 58.88 37.535 42.361 1 74.42 ? O5' ATP 1000 D 1 
HETATM 14 C C5' ATP . . . O 7 58.871 38.623 43.291 1 63.96 ? C5' ATP 1000 D 1 
HETATM 15 C C4' ATP . . . O 7 57.593 38.853 44.111 1 64.01 ? C4' ATP 1000 D 1 
HETATM 16 O O4' ATP . . . O 7 56.344 38.539 43.482 1 63.15 ? O4' ATP 1000 D 1 
HETATM 17 C C3' ATP . . . O 7 57.543 38.14 45.453 1 61.94 ? C3' ATP 1000 D 1 
HETATM 18 O O3' ATP . . . O 7 58.402 38.753 46.416 1 57.87 ? O3' ATP 1000 D 1 
HETATM 19 C C2' ATP . . . O 7 56.076 38.251 45.829 1 61.3 ? C2' ATP 1000 D 1 
HETATM 20 O O2' ATP . . . O 7 55.779 39.511 46.436 1 61.58 ? O2' ATP 1000 D 1 
HETATM 21 C C1' ATP . . . O 7 55.368 38.215 44.487 1 58.83 ? C1' ATP 1000 D 1 
HETATM 22 N N9 ATP . . . O 7 54.821 36.856 44.237 1 58.62 ? N9 ATP 1000 D 1 
HETATM 23 C C8 ATP . . . O 7 55.484 35.859 43.624 1 58.15 ? C8 ATP 1000 D 1 
HETATM 24 N N7 ATP . . . O 7 54.725 34.747 43.53 1 59.08 ? N7 ATP 1000 D 1 
HETATM 25 C C5 ATP . . . O 7 53.54 35.022 44.096 1 58 ? C5 ATP 1000 D 1 
HETATM 26 C C6 ATP . . . O 7 52.282 34.279 44.335 1 61.18 ? C6 ATP 1000 D 1 
HETATM 27 N N6 ATP . . . O 7 52.154 32.992 43.928 1 60.47 ? N6 ATP 1000 D 1 
HETATM 28 N N1 ATP . . . O 7 51.275 34.924 44.973 1 60.87 ? N1 ATP 1000 D 1 
HETATM 29 C C2 ATP . . . O 7 51.404 36.206 45.373 1 58.76 ? C2 ATP 1000 D 1 
HETATM 30 N N3 ATP . . . O 7 52.52 36.938 45.191 1 57.14 ? N3 ATP 1000 D 1 
HETATM 31 C C4 ATP . . . O 7 53.606 36.412 44.57 1 58.56 ? C4 ATP 1000 D 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           17 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           31 
#