data_3RUQ
#
_model_server_result.job_id            YMjJol4PigCw5uVd_jhb0A 
_model_server_result.datetime_utc      '2024-11-13 07:20:48' 
_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          3ruq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":545}' 
#
_entry.id    3RUQ 
#
_exptl.entry_id    3RUQ 
_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    4 
_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            3RUQ 
_cell.length_a            162.164 
_cell.length_b            185.002 
_cell.length_c            184.769 
_cell.Z_PDB               32 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RUQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 2 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexadecameric 
_pdbx_struct_assembly.oligomeric_count      16 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3,4 
#
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' 2_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -162.164 0 0 
3 'crystal symmetry operation' 3_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -162.164 0 0 
4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 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
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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 OD1 ASP 91 A ASP 91 1_555 E MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? 
metalc ? metalc2 A OD2 ASP 91 A ASP 91 1_555 E MG MG . A MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? 
metalc ? metalc3 E MG MG . A MG 544 1_555 F O2A ADP . A ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? 
metalc ? metalc4 E MG MG . A MG 544 1_555 F O3B ADP . A ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc5 E MG MG . A MG 544 1_555 M O HOH . A HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? 
metalc ? metalc6 E MG MG . A MG 544 1_555 M O HOH . A HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? 
metalc ? metalc7 B OD1 ASP 91 B ASP 91 1_555 G MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? 
metalc ? metalc8 B OD2 ASP 91 B ASP 91 1_555 G MG MG . B MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? 
metalc ? metalc9 G MG MG . B MG 544 1_555 H O3B ADP . B ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? 
metalc ? metalc10 G MG MG . B MG 544 1_555 H O2A ADP . B ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc11 G MG MG . B MG 544 1_555 N O HOH . B HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.51 ? 
metalc ? metalc12 G MG MG . B MG 544 1_555 N O HOH . B HOH 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.668 ? 
metalc ? metalc13 G MG MG . B MG 544 1_555 N O HOH . B HOH 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc14 C OD1 ASP 91 C ASP 91 1_555 I MG MG . C MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? 
metalc ? metalc15 I MG MG . C MG 544 1_555 J O2A ADP . C ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc16 I MG MG . C MG 544 1_555 J O3B ADP . C ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? 
metalc ? metalc17 I MG MG . C MG 544 1_555 O O HOH . C HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? 
metalc ? metalc18 I MG MG . C MG 544 1_555 O O HOH . C HOH 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc19 I MG MG . C MG 544 1_555 O O HOH . C HOH 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.553 ? 
metalc ? metalc20 D OD1 ASP 91 D ASP 91 1_555 K MG MG . D MG 544 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
metalc ? metalc21 K MG MG . D MG 544 1_555 L O2A ADP . D ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? 
metalc ? metalc22 K MG MG . D MG 544 1_555 L O1B ADP . D ADP 545 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.369 ? 
metalc ? metalc23 K MG MG . D MG 544 1_555 P O HOH . D HOH 546 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc24 K MG MG . D MG 544 1_555 P O HOH . D HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? 
metalc ? metalc25 K MG MG . D MG 544 1_555 P O HOH . D HOH 554 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
#
_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                     3RUQ 
_atom_sites.fract_transf_matrix[1][1]    0.006167 
_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]    0.005405 
_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]    0.005412 
_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 2 MG A 1 544 544 MG MG . 
F 3 ADP A 1 545 545 ADP ADP . 
G 2 MG B 1 544 544 MG MG . 
H 3 ADP B 1 545 545 ADP ADP . 
I 2 MG C 1 544 544 MG MG . 
J 3 ADP C 1 545 545 ADP ADP . 
K 2 MG D 1 544 544 MG MG . 
L 3 ADP D 1 545 545 ADP ADP . 
M 4 HOH A 1 546 1 HOH HOH . 
M 4 HOH A 2 547 12 HOH HOH . 
M 4 HOH A 3 548 13 HOH HOH . 
M 4 HOH A 4 549 14 HOH HOH . 
M 4 HOH A 5 550 17 HOH HOH . 
M 4 HOH A 6 551 19 HOH HOH . 
M 4 HOH A 7 552 22 HOH HOH . 
M 4 HOH A 8 553 26 HOH HOH . 
M 4 HOH A 9 554 30 HOH HOH . 
M 4 HOH A 10 555 31 HOH HOH . 
M 4 HOH A 11 556 37 HOH HOH . 
M 4 HOH A 12 557 38 HOH HOH . 
M 4 HOH A 13 558 39 HOH HOH . 
M 4 HOH A 14 559 43 HOH HOH . 
M 4 HOH A 15 560 44 HOH HOH . 
M 4 HOH A 16 561 50 HOH HOH . 
M 4 HOH A 17 562 59 HOH HOH . 
N 4 HOH B 1 546 2 HOH HOH . 
N 4 HOH B 2 547 8 HOH HOH . 
N 4 HOH B 3 548 11 HOH HOH . 
N 4 HOH B 4 549 20 HOH HOH . 
N 4 HOH B 5 550 28 HOH HOH . 
N 4 HOH B 6 551 29 HOH HOH . 
N 4 HOH B 7 552 32 HOH HOH . 
N 4 HOH B 8 553 34 HOH HOH . 
N 4 HOH B 9 554 45 HOH HOH . 
N 4 HOH B 10 555 46 HOH HOH . 
N 4 HOH B 11 556 60 HOH HOH . 
N 4 HOH B 12 557 61 HOH HOH . 
O 4 HOH C 1 546 3 HOH HOH . 
O 4 HOH C 2 547 7 HOH HOH . 
O 4 HOH C 3 548 10 HOH HOH . 
O 4 HOH C 4 549 16 HOH HOH . 
O 4 HOH C 5 550 18 HOH HOH . 
O 4 HOH C 6 551 21 HOH HOH . 
O 4 HOH C 7 552 23 HOH HOH . 
O 4 HOH C 8 553 24 HOH HOH . 
O 4 HOH C 9 554 25 HOH HOH . 
O 4 HOH C 10 555 35 HOH HOH . 
O 4 HOH C 11 556 40 HOH HOH . 
O 4 HOH C 12 557 41 HOH HOH . 
O 4 HOH C 13 558 51 HOH HOH . 
O 4 HOH C 14 559 52 HOH HOH . 
O 4 HOH C 15 560 53 HOH HOH . 
O 4 HOH C 16 561 62 HOH HOH . 
P 4 HOH D 1 546 5 HOH HOH . 
P 4 HOH D 2 547 6 HOH HOH . 
P 4 HOH D 3 548 9 HOH HOH . 
P 4 HOH D 4 549 27 HOH HOH . 
P 4 HOH D 5 550 33 HOH HOH . 
P 4 HOH D 6 551 36 HOH HOH . 
P 4 HOH D 7 552 42 HOH HOH . 
P 4 HOH D 8 553 48 HOH HOH . 
P 4 HOH D 9 554 54 HOH HOH . 
P 4 HOH D 10 555 55 HOH HOH . 
P 4 HOH D 11 556 56 HOH HOH . 
P 4 HOH D 12 557 57 HOH HOH . 
P 4 HOH D 13 558 58 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 . . . H 3 -66.867 20.362 51.31 1 44.59 ? PB ADP 545 B 1 
HETATM 2 O O1B ADP . . . H 3 -66.864 20.677 49.82 1 38.38 ? O1B ADP 545 B 1 
HETATM 3 O O2B ADP . . . H 3 -68.158 19.72 51.759 1 39.93 ? O2B ADP 545 B 1 
HETATM 4 O O3B ADP . . . H 3 -66.398 21.476 52.223 1 53.25 ? O3B ADP 545 B 1 
HETATM 5 P PA ADP . . . H 3 -64.202 19.268 51.683 1 43.56 ? PA ADP 545 B 1 
HETATM 6 O O1A ADP . . . H 3 -63.547 18.23 50.786 1 47.32 ? O1A ADP 545 B 1 
HETATM 7 O O2A ADP . . . H 3 -63.79 20.698 51.489 1 38.41 ? O2A ADP 545 B 1 
HETATM 8 O O3A ADP . . . H 3 -65.812 19.16 51.53 1 51.13 ? O3A ADP 545 B 1 
HETATM 9 O O5' ADP . . . H 3 -64.081 18.786 53.224 1 43.47 ? O5' ADP 545 B 1 
HETATM 10 C C5' ADP . . . H 3 -64.698 19.516 54.292 1 51.92 ? C5' ADP 545 B 1 
HETATM 11 C C4' ADP . . . H 3 -64.61 18.718 55.594 1 52.87 ? C4' ADP 545 B 1 
HETATM 12 O O4' ADP . . . H 3 -63.247 18.478 55.956 1 56.34 ? O4' ADP 545 B 1 
HETATM 13 C C3' ADP . . . H 3 -65.229 19.477 56.757 1 64.22 ? C3' ADP 545 B 1 
HETATM 14 O O3' ADP . . . H 3 -66.081 18.588 57.495 1 68.89 ? O3' ADP 545 B 1 
HETATM 15 C C2' ADP . . . H 3 -64.056 19.879 57.628 1 61.01 ? C2' ADP 545 B 1 
HETATM 16 O O2' ADP . . . H 3 -64.411 19.919 59.009 1 65.13 ? O2' ADP 545 B 1 
HETATM 17 C C1' ADP . . . H 3 -63.074 18.762 57.344 1 53.08 ? C1' ADP 545 B 1 
HETATM 18 N N9 ADP . . . H 3 -61.687 19.169 57.668 1 46.71 ? N9 ADP 545 B 1 
HETATM 19 C C8 ADP . . . H 3 -61.022 20.23 57.181 1 61.49 ? C8 ADP 545 B 1 
HETATM 20 N N7 ADP . . . H 3 -59.765 20.309 57.707 1 62.89 ? N7 ADP 545 B 1 
HETATM 21 C C5 ADP . . . H 3 -59.617 19.28 58.555 1 56.86 ? C5 ADP 545 B 1 
HETATM 22 C C6 ADP . . . H 3 -58.544 18.766 59.434 1 65.68 ? C6 ADP 545 B 1 
HETATM 23 N N6 ADP . . . H 3 -57.348 19.392 59.513 1 70.53 ? N6 ADP 545 B 1 
HETATM 24 N N1 ADP . . . H 3 -58.794 17.653 60.153 1 65.63 ? N1 ADP 545 B 1 
HETATM 25 C C2 ADP . . . H 3 -59.976 17.025 60.074 1 54.18 ? C2 ADP 545 B 1 
HETATM 26 N N3 ADP . . . H 3 -60.991 17.437 59.298 1 45.86 ? N3 ADP 545 B 1 
HETATM 27 C C4 ADP . . . H 3 -60.883 18.539 58.529 1 49.61 ? C4 ADP 545 B 1 
#
_model_server_stats.io_time_ms              32 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           27 
#