data_6EBV
#
_model_server_result.job_id            0jMsVPg0Hm9YqyoRokOsaA 
_model_server_result.datetime_utc      '2024-11-22 18:01:38' 
_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          6ebv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":301}' 
#
_entry.id    6EBV 
#
_exptl.entry_id    6EBV 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          99.81 
_cell.angle_gamma         90 
_cell.entry_id            6EBV 
_cell.length_a            72.8 
_cell.length_b            56.72 
_cell.length_c            133.62 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6EBV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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 dimeric 2 software_defined_assembly 1 
PISA dimeric 2 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,C,E,F,I,J,M,O 1 1 
B,D,G,H,K,L,N,P 2 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 E N N 
? 2 G N N 
? 2 I N N 
? 2 K N N 
#
_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 59 n n 
PB O2B ADP sing 60 n n 
PB O3B ADP sing 61 n n 
PB O3A ADP sing 62 n n 
O2B HOB2 ADP sing 63 n n 
O3B HOB3 ADP sing 64 n n 
PA O1A ADP doub 65 n n 
PA O2A ADP sing 66 n n 
PA O3A ADP sing 67 n n 
PA O5' ADP sing 68 n n 
O2A HOA2 ADP sing 69 n n 
O5' C5' ADP sing 70 n n 
C5' C4' ADP sing 71 n n 
C5' "H5'1" ADP sing 72 n n 
C5' "H5'2" ADP sing 73 n n 
C4' O4' ADP sing 74 n n 
C4' C3' ADP sing 75 n n 
C4' H4' ADP sing 76 n n 
O4' C1' ADP sing 77 n n 
C3' O3' ADP sing 78 n n 
C3' C2' ADP sing 79 n n 
C3' H3' ADP sing 80 n n 
O3' HO3' ADP sing 81 n n 
C2' O2' ADP sing 82 n n 
C2' C1' ADP sing 83 n n 
C2' H2' ADP sing 84 n n 
O2' HO2' ADP sing 85 n n 
C1' N9 ADP sing 86 n n 
C1' H1' ADP sing 87 n n 
N9 C8 ADP sing 88 n y 
N9 C4 ADP sing 89 n y 
C8 N7 ADP doub 90 n y 
C8 H8 ADP sing 91 n n 
N7 C5 ADP sing 92 n y 
C5 C6 ADP sing 93 n y 
C5 C4 ADP doub 94 n y 
C6 N6 ADP sing 95 n n 
C6 N1 ADP doub 96 n y 
N6 HN61 ADP sing 97 n n 
N6 HN62 ADP sing 98 n n 
N1 C2 ADP sing 99 n y 
C2 N3 ADP doub 100 n y 
C2 H2 ADP sing 101 n n 
N3 C4 ADP sing 102 n y 
#
_atom_sites.entry_id                     6EBV 
_atom_sites.fract_transf_matrix[1][1]    0.013736 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002375 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.01763 
_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]    0.007595 
_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 ADP A 1 301 304 ADP ADP . 
F 3 27Q A 1 302 2 27Q NEW . 
G 2 ADP B 1 301 302 ADP ADP . 
H 3 27Q B 1 302 3 27Q NEW . 
I 2 ADP C 1 301 301 ADP ADP . 
J 3 27Q C 1 302 1 27Q NEW . 
K 2 ADP D 1 301 303 ADP ADP . 
L 3 27Q D 1 302 4 27Q NEW . 
M 4 HOH A 1 401 24 HOH HOH . 
M 4 HOH A 2 402 25 HOH HOH . 
M 4 HOH A 3 403 32 HOH HOH . 
M 4 HOH A 4 404 44 HOH HOH . 
M 4 HOH A 5 405 30 HOH HOH . 
M 4 HOH A 6 406 16 HOH HOH . 
M 4 HOH A 7 407 15 HOH HOH . 
N 4 HOH B 1 401 4 HOH HOH . 
N 4 HOH B 2 402 10 HOH HOH . 
N 4 HOH B 3 403 51 HOH HOH . 
N 4 HOH B 4 404 6 HOH HOH . 
N 4 HOH B 5 405 41 HOH HOH . 
N 4 HOH B 6 406 36 HOH HOH . 
N 4 HOH B 7 407 22 HOH HOH . 
N 4 HOH B 8 408 5 HOH HOH . 
N 4 HOH B 9 409 47 HOH HOH . 
N 4 HOH B 10 410 3 HOH HOH . 
N 4 HOH B 11 411 38 HOH HOH . 
N 4 HOH B 12 412 17 HOH HOH . 
N 4 HOH B 13 413 14 HOH HOH . 
N 4 HOH B 14 414 18 HOH HOH . 
O 4 HOH C 1 401 8 HOH HOH . 
O 4 HOH C 2 402 7 HOH HOH . 
O 4 HOH C 3 403 1 HOH HOH . 
O 4 HOH C 4 404 2 HOH HOH . 
O 4 HOH C 5 405 9 HOH HOH . 
O 4 HOH C 6 406 49 HOH HOH . 
O 4 HOH C 7 407 26 HOH HOH . 
O 4 HOH C 8 408 27 HOH HOH . 
P 4 HOH D 1 401 34 HOH HOH . 
P 4 HOH D 2 402 19 HOH HOH . 
P 4 HOH D 3 403 35 HOH HOH . 
P 4 HOH D 4 404 13 HOH HOH . 
P 4 HOH D 5 405 43 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 . . . I 2 2.111 -20.327 64.732 1 38.74 ? PB ADP 301 C 1 
HETATM 2 O O1B ADP . . . I 2 1.761 -19.483 63.537 1 38.32 ? O1B ADP 301 C 1 
HETATM 3 O O2B ADP . . . I 2 1.333 -19.912 66.014 1 39.86 ? O2B ADP 301 C 1 
HETATM 4 O O3B ADP . . . I 2 1.991 -21.836 64.509 1 36.42 ? O3B ADP 301 C 1 
HETATM 5 P PA ADP . . . I 2 4.708 -20.623 66.104 1 39.64 ? PA ADP 301 C 1 
HETATM 6 O O1A ADP . . . I 2 4.268 -21.911 66.682 1 40.12 ? O1A ADP 301 C 1 
HETATM 7 O O2A ADP . . . I 2 4.945 -19.578 67.233 1 36.73 ? O2A ADP 301 C 1 
HETATM 8 O O3A ADP . . . I 2 3.647 -20.058 65.055 1 42.01 ? O3A ADP 301 C 1 
HETATM 9 O O5' ADP . . . I 2 5.962 -20.743 65.105 1 32.89 ? O5' ADP 301 C 1 
HETATM 10 C C5' ADP . . . I 2 6.062 -21.674 64.009 1 25.55 ? C5' ADP 301 C 1 
HETATM 11 C C4' ADP . . . I 2 7.532 -21.904 63.8 1 23.1 ? C4' ADP 301 C 1 
HETATM 12 O O4' ADP . . . I 2 8.105 -22.467 64.997 1 26.18 ? O4' ADP 301 C 1 
HETATM 13 C C3' ADP . . . I 2 7.906 -22.892 62.713 1 22.23 ? C3' ADP 301 C 1 
HETATM 14 O O3' ADP . . . I 2 7.853 -22.259 61.445 1 20.74 ? O3' ADP 301 C 1 
HETATM 15 C C2' ADP . . . I 2 9.322 -23.299 63.131 1 26.72 ? C2' ADP 301 C 1 
HETATM 16 O O2' ADP . . . I 2 10.257 -22.281 62.791 1 30.64 ? O2' ADP 301 C 1 
HETATM 17 C C1' ADP . . . I 2 9.218 -23.279 64.663 1 26.81 ? C1' ADP 301 C 1 
HETATM 18 N N9 ADP . . . I 2 9.145 -24.56 65.389 1 26.05 ? N9 ADP 301 C 1 
HETATM 19 C C8 ADP . . . I 2 9.561 -24.752 66.682 1 23.66 ? C8 ADP 301 C 1 
HETATM 20 N N7 ADP . . . I 2 9.434 -25.985 67.111 1 20.15 ? N7 ADP 301 C 1 
HETATM 21 C C5 ADP . . . I 2 8.887 -26.654 66.027 1 22.24 ? C5 ADP 301 C 1 
HETATM 22 C C6 ADP . . . I 2 8.475 -27.992 65.846 1 23.55 ? C6 ADP 301 C 1 
HETATM 23 N N6 ADP . . . I 2 8.586 -28.939 66.781 1 22.43 ? N6 ADP 301 C 1 
HETATM 24 N N1 ADP . . . I 2 7.899 -28.318 64.669 1 27.68 ? N1 ADP 301 C 1 
HETATM 25 C C2 ADP . . . I 2 7.74 -27.365 63.742 1 30.37 ? C2 ADP 301 C 1 
HETATM 26 N N3 ADP . . . I 2 8.096 -26.078 63.795 1 29.12 ? N3 ADP 301 C 1 
HETATM 27 C C4 ADP . . . I 2 8.682 -25.785 64.965 1 25.47 ? C4 ADP 301 C 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           27 
#