data_6JJ9
#
_model_server_result.job_id            kOi5E_ucpvnpMgxUAKylVQ 
_model_server_result.datetime_utc      '2024-10-20 07:37:15' 
_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          6jj9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":601}' 
#
_entry.id    6JJ9 
#
_exptl.entry_id    6JJ9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              427.201 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-DIPHOSPHATE" 
_entity.pdbx_number_of_molecules    3 
_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            6JJ9 
_cell.length_a            131.12 
_cell.length_b            131.12 
_cell.length_c            186.192 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6JJ9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        154 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32 2 1' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G 1 1 
B,H,I,J,K 2 1 
C,L,M,N,O 3 1 
#
_pdbx_struct_oper_list.id                    1 
_pdbx_struct_oper_list.type                  'identity operation' 
_pdbx_struct_oper_list.name                  1_555 
_pdbx_struct_oper_list.symmetry_operation    x,y,z 
_pdbx_struct_oper_list.matrix[1][1]          1 
_pdbx_struct_oper_list.matrix[1][2]          0 
_pdbx_struct_oper_list.matrix[1][3]          0 
_pdbx_struct_oper_list.matrix[2][1]          0 
_pdbx_struct_oper_list.matrix[2][2]          1 
_pdbx_struct_oper_list.matrix[2][3]          0 
_pdbx_struct_oper_list.matrix[3][1]          0 
_pdbx_struct_oper_list.matrix[3][2]          0 
_pdbx_struct_oper_list.matrix[3][3]          1 
_pdbx_struct_oper_list.vector[1]             0 
_pdbx_struct_oper_list.vector[2]             0 
_pdbx_struct_oper_list.vector[3]             0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 D N N 
? 2 H N N 
? 2 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 D O2A ADP . C ADP 601 1_555 F MG MG . C MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc2 H O1A ADP . A ADP 601 1_555 J MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? 
metalc ? metalc3 C OE1 GLU 98 E GLU 136 1_555 N MG MG . E MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? 
metalc ? metalc4 L O2A ADP . E ADP 601 1_555 N MG MG . E MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.833 ? 
#
_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                     6JJ9 
_atom_sites.fract_transf_matrix[1][1]    0.007627 
_atom_sites.fract_transf_matrix[1][2]    0.004403 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008806 
_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]    0.005371 
_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 2 ADP C 1 601 602 ADP ADP . 
E 3 PO4 C 1 602 919 PO4 PO4 . 
F 4 MG C 1 603 1 MG MG . 
G 5 BGC C 1 604 1 BGC BGC . 
H 2 ADP A 1 601 602 ADP ADP . 
I 3 PO4 A 1 602 919 PO4 PO4 . 
J 4 MG A 1 603 2 MG MG . 
K 5 BGC A 1 604 1 BGC BGC . 
L 2 ADP E 1 601 602 ADP ADP . 
M 3 PO4 E 1 602 919 PO4 PO4 . 
N 4 MG E 1 603 3 MG MG . 
O 5 BGC E 1 604 1 BGC BGC . 
#
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 2 98.334 181.458 50.367 1 20.03 ? PB ADP 601 A 1 
HETATM 2 O O1B ADP . . . H 2 99.347 181.086 49.416 1 30.31 ? O1B ADP 601 A 1 
HETATM 3 O O2B ADP . . . H 2 98.83 181.62 51.698 1 15.88 ? O2B ADP 601 A 1 
HETATM 4 O O3B ADP . . . H 2 97.193 180.614 50.319 1 13.86 ? O3B ADP 601 A 1 
HETATM 5 P PA ADP . . . H 2 98.125 184.2 50.364 1 18.92 ? PA ADP 601 A 1 
HETATM 6 O O1A ADP . . . H 2 97.952 185.143 49.295 1 29.15 ? O1A ADP 601 A 1 
HETATM 7 O O2A ADP . . . H 2 99.388 184.129 51.03 1 38.3 ? O2A ADP 601 A 1 
HETATM 8 O O3A ADP . . . H 2 97.772 182.804 49.885 1 16.31 ? O3A ADP 601 A 1 
HETATM 9 O O5' ADP . . . H 2 96.975 184.476 51.337 1 24.37 ? O5' ADP 601 A 1 
HETATM 10 C C5' ADP . . . H 2 95.635 184.119 51.132 1 15.12 ? C5' ADP 601 A 1 
HETATM 11 C C4' ADP . . . H 2 95.091 183.831 52.505 1 15.09 ? C4' ADP 601 A 1 
HETATM 12 O O4' ADP . . . H 2 95.079 184.982 53.284 1 17.67 ? O4' ADP 601 A 1 
HETATM 13 C C3' ADP . . . H 2 93.695 183.386 52.442 1 17.7 ? C3' ADP 601 A 1 
HETATM 14 O O3' ADP . . . H 2 93.635 182.06 52.812 1 23.04 ? O3' ADP 601 A 1 
HETATM 15 C C2' ADP . . . H 2 93.109 183.962 53.662 1 16.81 ? C2' ADP 601 A 1 
HETATM 16 O O2' ADP . . . H 2 93.083 182.863 54.51 1 14.97 ? O2' ADP 601 A 1 
HETATM 17 C C1' ADP . . . H 2 93.997 185.025 54.152 1 15.75 ? C1' ADP 601 A 1 
HETATM 18 N N9 ADP . . . H 2 93.191 186.176 53.811 1 17.55 ? N9 ADP 601 A 1 
HETATM 19 C C8 ADP . . . H 2 93.031 186.611 52.603 1 17.86 ? C8 ADP 601 A 1 
HETATM 20 N N7 ADP . . . H 2 92.227 187.641 52.61 1 24.17 ? N7 ADP 601 A 1 
HETATM 21 C C5 ADP . . . H 2 91.847 187.854 53.852 1 18.68 ? C5 ADP 601 A 1 
HETATM 22 C C6 ADP . . . H 2 90.967 188.776 54.535 1 17.55 ? C6 ADP 601 A 1 
HETATM 23 N N6 ADP . . . H 2 90.327 189.722 53.867 1 17.96 ? N6 ADP 601 A 1 
HETATM 24 N N1 ADP . . . H 2 90.82 188.637 55.827 1 20.91 ? N1 ADP 601 A 1 
HETATM 25 C C2 ADP . . . H 2 91.443 187.705 56.491 1 17.36 ? C2 ADP 601 A 1 
HETATM 26 N N3 ADP . . . H 2 92.226 186.839 55.947 1 16.83 ? N3 ADP 601 A 1 
HETATM 27 C C4 ADP . . . H 2 92.475 186.867 54.644 1 16.62 ? C4 ADP 601 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           24 
_model_server_stats.create_model_time_ms    33 
_model_server_stats.query_time_ms           318 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           27 
#