data_6E4U
#
_model_server_result.job_id            JRmuPBSD3G9_KsvdNO8eEw 
_model_server_result.datetime_utc      '2025-03-04 18:19:04' 
_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          6e4u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":403}' 
#
_entry.id    6E4U 
#
_exptl.entry_id    6E4U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          8 
_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            6E4U 
_cell.length_a            124.5 
_cell.length_b            124.5 
_cell.length_c            402.78 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6E4U 
_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 -62.25 -107.820163 -67.13 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      8 
_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 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
covale ? covale2 A C TPO 174 A TPO 172 1_555 A N SER 175 A SER 173 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? 
covale ? covale3 B C ARG 41 B ARG 107 1_555 B N SEP 42 B SEP 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? 
covale ? covale4 B C SEP 42 B SEP 108 1_555 B N GLN 43 B GLN 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? 
#
_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                     6E4U 
_atom_sites.fract_transf_matrix[1][1]    0.008032 
_atom_sites.fract_transf_matrix[1][2]    0.004637 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009275 
_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]    0.002483 
_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 1549 STU STU . 
E 5 HU7 A 1 602 4000 HU7 PFE . 
F 6 CL A 1 603 4 CL CL . 
G 6 CL A 1 604 5 CL CL . 
H 6 CL A 1 605 1 CL CL . 
I 6 CL A 1 606 3 CL CL . 
J 7 AMP C 1 401 1 AMP AMP . 
K 7 AMP C 1 402 2 AMP AMP . 
L 8 ADP C 1 403 0 ADP ADP . 
M 9 SO4 C 1 404 2 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 8 20.349 -40.117 14.937 1 168.31 ? PB ADP 403 C 1 
HETATM 2 O O1B ADP . . . L 8 21.348 -40.951 14.138 1 168.78 ? O1B ADP 403 C 1 
HETATM 3 O O2B ADP . . . L 8 19.07 -40.847 15.173 1 165.48 ? O2B ADP 403 C 1 
HETATM 4 O O3B ADP . . . L 8 21.033 -39.672 16.24 1 170.6 ? O3B ADP 403 C 1 
HETATM 5 P PA ADP . . . L 8 20.913 -37.978 13.007 1 172.61 ? PA ADP 403 C 1 
HETATM 6 O O1A ADP . . . L 8 21.317 -38.966 11.92 1 172.56 ? O1A ADP 403 C 1 
HETATM 7 O O2A ADP . . . L 8 22.135 -37.423 13.629 1 175.46 ? O2A ADP 403 C 1 
HETATM 8 O O3A ADP . . . L 8 20.072 -38.792 14.091 1 169.6 ? O3A ADP 403 C 1 
HETATM 9 O O5' ADP . . . L 8 20.032 -36.844 12.317 1 173.34 ? O5' ADP 403 C 1 
HETATM 10 C C5' ADP . . . L 8 19.939 -35.419 12.54 1 175.78 ? C5' ADP 403 C 1 
HETATM 11 C C4' ADP . . . L 8 19.384 -34.717 11.323 1 177.4 ? C4' ADP 403 C 1 
HETATM 12 O O4' ADP . . . L 8 20.232 -34.951 10.177 1 179.88 ? O4' ADP 403 C 1 
HETATM 13 C C3' ADP . . . L 8 17.955 -35.085 10.905 1 174.99 ? C3' ADP 403 C 1 
HETATM 14 O O3' ADP . . . L 8 17.133 -33.926 10.85 1 175.92 ? O3' ADP 403 C 1 
HETATM 15 C C2' ADP . . . L 8 18.133 -35.76 9.536 1 175.72 ? C2' ADP 403 C 1 
HETATM 16 O O2' ADP . . . L 8 17.041 -35.509 8.657 1 175.79 ? O2' ADP 403 C 1 
HETATM 17 C C1' ADP . . . L 8 19.423 -35.115 9.033 1 179.84 ? C1' ADP 403 C 1 
HETATM 18 N N9 ADP . . . L 8 20.169 -35.896 8.043 1 181.17 ? N9 ADP 403 C 1 
HETATM 19 C C8 ADP . . . L 8 20.635 -37.178 8.184 1 179.51 ? C8 ADP 403 C 1 
HETATM 20 N N7 ADP . . . L 8 21.376 -37.593 7.186 1 181.24 ? N7 ADP 403 C 1 
HETATM 21 C C5 ADP . . . L 8 21.385 -36.515 6.313 1 184.47 ? C5 ADP 403 C 1 
HETATM 22 C C6 ADP . . . L 8 21.991 -36.317 5.055 1 187.67 ? C6 ADP 403 C 1 
HETATM 23 N N6 ADP . . . L 8 22.763 -37.224 4.452 1 187.96 ? N6 ADP 403 C 1 
HETATM 24 N N1 ADP . . . L 8 21.786 -35.129 4.439 1 190.88 ? N1 ADP 403 C 1 
HETATM 25 C C2 ADP . . . L 8 21.03 -34.207 5.049 1 190.7 ? C2 ADP 403 C 1 
HETATM 26 N N3 ADP . . . L 8 20.417 -34.279 6.237 1 187.67 ? N3 ADP 403 C 1 
HETATM 27 C C4 ADP . . . L 8 20.636 -35.465 6.824 1 184.56 ? C4 ADP 403 C 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           331 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#