data_5T5T
#
_model_server_result.job_id            01dm0RSjE0zf7nc0OBvAfg 
_model_server_result.datetime_utc      '2024-12-23 12:27:16' 
_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          5t5t 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":403}' 
#
_entry.id    5T5T 
#
_exptl.entry_id    5T5T 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          9 
_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         120 
_cell.entry_id            5T5T 
_cell.length_a            125.04 
_cell.length_b            125.04 
_cell.length_c            403.36 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5T5T 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        178 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 61 2 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA hexameric 6 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M 2 1,2 
#
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' 10_444 -y-1,-x-1,-z-1/6 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -62.52 -108.287816 -67.226667 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      9 
_struct_asym.id                             L 
_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
covale ? covale1 A C ARG 173 A ARG 171 1_555 A N TPO 174 A TPO 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.354 ? 
covale ? covale2 A C TPO 174 A TPO 172 1_555 A N SER 175 A SER 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? 
#
_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 43 n n 
PB O2B ADP sing 44 n n 
PB O3B ADP sing 45 n n 
PB O3A ADP sing 46 n n 
O2B HOB2 ADP sing 47 n n 
O3B HOB3 ADP sing 48 n n 
PA O1A ADP doub 49 n n 
PA O2A ADP sing 50 n n 
PA O3A ADP sing 51 n n 
PA O5' ADP sing 52 n n 
O2A HOA2 ADP sing 53 n n 
O5' C5' ADP sing 54 n n 
C5' C4' ADP sing 55 n n 
C5' "H5'1" ADP sing 56 n n 
C5' "H5'2" ADP sing 57 n n 
C4' O4' ADP sing 58 n n 
C4' C3' ADP sing 59 n n 
C4' H4' ADP sing 60 n n 
O4' C1' ADP sing 61 n n 
C3' O3' ADP sing 62 n n 
C3' C2' ADP sing 63 n n 
C3' H3' ADP sing 64 n n 
O3' HO3' ADP sing 65 n n 
C2' O2' ADP sing 66 n n 
C2' C1' ADP sing 67 n n 
C2' H2' ADP sing 68 n n 
O2' HO2' ADP sing 69 n n 
C1' N9 ADP sing 70 n n 
C1' H1' ADP sing 71 n n 
N9 C8 ADP sing 72 n y 
N9 C4 ADP sing 73 n y 
C8 N7 ADP doub 74 n y 
C8 H8 ADP sing 75 n n 
N7 C5 ADP sing 76 n y 
C5 C6 ADP sing 77 n y 
C5 C4 ADP doub 78 n y 
C6 N6 ADP sing 79 n n 
C6 N1 ADP doub 80 n y 
N6 HN61 ADP sing 81 n n 
N6 HN62 ADP sing 82 n n 
N1 C2 ADP sing 83 n y 
C2 N3 ADP doub 84 n y 
C2 H2 ADP sing 85 n n 
N3 C4 ADP sing 86 n y 
#
_atom_sites.entry_id                     5T5T 
_atom_sites.fract_transf_matrix[1][1]    0.007997 
_atom_sites.fract_transf_matrix[1][2]    0.004617 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009235 
_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]    0.002479 
_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
D 4 STU A 1 601 4000 STU STU . 
E 5 CL A 1 602 1 CL CL . 
F 5 CL A 1 603 4 CL CL . 
G 5 CL A 1 604 5 CL CL . 
H 6 SO4 A 1 605 2 SO4 SO4 . 
I 7 75O B 1 4000 4000 75O PFE . 
J 8 AMP C 1 401 1 AMP AMP . 
K 8 AMP C 1 402 2 AMP AMP . 
L 9 ADP C 1 403 3 ADP ADP . 
M 6 SO4 C 1 404 1 SO4 SO4 . 
#
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 . . . L 9 21.067 -40.075 14.534 1 195.79 ? PB ADP 403 C 1 
HETATM 2 O O1B ADP . . . L 9 21.596 -40.952 13.399 1 195.66 ? O1B ADP 403 C 1 
HETATM 3 O O2B ADP . . . L 9 19.743 -40.573 15.081 1 193.84 ? O2B ADP 403 C 1 
HETATM 4 O O3B ADP . . . L 9 22.168 -39.99 15.606 1 197.43 ? O3B ADP 403 C 1 
HETATM 5 P PA ADP . . . L 9 21.814 -37.643 13.05 1 198.07 ? PA ADP 403 C 1 
HETATM 6 O O1A ADP . . . L 9 22.631 -38.504 12.091 1 198.25 ? O1A ADP 403 C 1 
HETATM 7 O O2A ADP . . . L 9 22.735 -36.885 13.93 1 200.22 ? O2A ADP 403 C 1 
HETATM 8 O O3A ADP . . . L 9 20.896 -38.608 13.929 1 196.43 ? O3A ADP 403 C 1 
HETATM 9 O O5' ADP . . . L 9 20.889 -36.684 12.182 1 198.21 ? O5' ADP 403 C 1 
HETATM 10 C C5' ADP . . . L 9 20.452 -35.325 12.41 1 199.22 ? C5' ADP 403 C 1 
HETATM 11 C C4' ADP . . . L 9 19.826 -34.737 11.167 1 200.17 ? C4' ADP 403 C 1 
HETATM 12 O O4' ADP . . . L 9 20.744 -34.825 10.055 1 201.99 ? O4' ADP 403 C 1 
HETATM 13 C C3' ADP . . . L 9 18.501 -35.355 10.706 1 197.77 ? C3' ADP 403 C 1 
HETATM 14 O O3' ADP . . . L 9 17.499 -34.362 10.525 1 198.74 ? O3' ADP 403 C 1 
HETATM 15 C C2' ADP . . . L 9 18.871 -36.089 9.41 1 198.39 ? C2' ADP 403 C 1 
HETATM 16 O O2' ADP . . . L 9 17.806 -36.099 8.465 1 199.18 ? O2' ADP 403 C 1 
HETATM 17 C C1' ADP . . . L 9 20.057 -35.269 8.904 1 201.62 ? C1' ADP 403 C 1 
HETATM 18 N N9 ADP . . . L 9 20.994 -36.01 8.056 1 201.45 ? N9 ADP 403 C 1 
HETATM 19 C C8 ADP . . . L 9 21.891 -36.968 8.464 1 199.4 ? C8 ADP 403 C 1 
HETATM 20 N N7 ADP . . . L 9 22.656 -37.425 7.497 1 200.45 ? N7 ADP 403 C 1 
HETATM 21 C C5 ADP . . . L 9 22.23 -36.727 6.383 1 203.32 ? C5 ADP 403 C 1 
HETATM 22 C C6 ADP . . . L 9 22.649 -36.746 5.034 1 206.27 ? C6 ADP 403 C 1 
HETATM 23 N N6 ADP . . . L 9 23.63 -37.525 4.573 1 206.54 ? N6 ADP 403 C 1 
HETATM 24 N N1 ADP . . . L 9 22.013 -35.922 4.168 1 209.27 ? N1 ADP 403 C 1 
HETATM 25 C C2 ADP . . . L 9 21.028 -35.139 4.624 1 208.92 ? C2 ADP 403 C 1 
HETATM 26 N N3 ADP . . . L 9 20.55 -35.034 5.87 1 206.2 ? N3 ADP 403 C 1 
HETATM 27 C C4 ADP . . . L 9 21.201 -35.857 6.709 1 203.74 ? C4 ADP 403 C 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    49 
_model_server_stats.query_time_ms           346 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           27 
#