data_4KXF
#
_model_server_result.job_id            kcj6uLgyTzhuJBWFr5slag 
_model_server_result.datetime_utc      '2024-12-21 11:34:18' 
_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          4kxf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":1101}' 
#
_entry.id    4KXF 
#
_exptl.entry_id    4KXF 
_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    8 
_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            4KXF 
_cell.length_a            334.052 
_cell.length_b            334.052 
_cell.length_c            177.567 
_cell.Z_PDB               64 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4KXF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 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
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
? monomeric 1 author_defined_assembly 4 
? monomeric 1 author_defined_assembly 5 
? monomeric 1 author_defined_assembly 6 
? monomeric 1 author_defined_assembly 7 
? monomeric 1 author_defined_assembly 8 
PISA tetrameric 4 software_defined_assembly 9 
PISA tetrameric 4 software_defined_assembly 10 
PISA tetrameric 4 software_defined_assembly 11 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,I 1 1 
B,J,K 2 1 
C,L 3 1 
D,M 4 1 
E,N 5 1 
F,O 6 1 
G,P,Q 7 1 
H,R 8 1 
A,I 9 1,2 
H,R 9 3,4 
B,D,E,F,J,K,M,N,O 10 1 
C,G,L,P,Q 11 1,5 
#
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' 8_555 -y,-x,-z+1/2 0 -1 0 -1 0 0 0 0 -1 0 0 88.7835 
3 'crystal symmetry operation' 4_444 y-1/2,-x-1/2,z-1/4 0 1 0 -1 0 0 0 0 1 -167.026 -167.026 -44.39175 
4 'crystal symmetry operation' 6_555 x+1/2,-y+1/2,-z+3/4 1 0 0 0 -1 0 0 0 -1 167.026 167.026 133.17525 
5 'crystal symmetry operation' 8_556 -y,-x,-z+3/2 0 -1 0 -1 0 0 0 0 -1 0 0 266.3505 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 I N N 
? 2 J N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 R 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
covale ? covale1 A C GLU 532 K GLU 532 1_555 A N SEP 533 K SEP 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C SEP 533 K SEP 533 1_555 A N ILE 534 K ILE 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale3 B C GLU 532 B GLU 532 1_555 B N SEP 533 B SEP 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B C SEP 533 B SEP 533 1_555 B N ILE 534 B ILE 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? 
covale ? covale5 C C GLU 532 D GLU 532 1_555 C N SEP 533 D SEP 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale6 C C SEP 533 D SEP 533 1_555 C N ILE 534 D ILE 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
covale ? covale7 D C GLU 532 F GLU 532 1_555 D N SEP 533 F SEP 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale8 D C SEP 533 F SEP 533 1_555 D N ILE 534 F ILE 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale9 E C GLU 532 H GLU 532 1_555 E N SEP 533 H SEP 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale10 E C SEP 533 H SEP 533 1_555 E N ILE 534 H ILE 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale11 F C GLU 532 L GLU 532 1_555 F N SEP 533 L SEP 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? 
covale ? covale12 F C SEP 533 L SEP 533 1_555 F N ILE 534 L ILE 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale13 G C SEP 533 N SEP 533 1_555 G N ILE 534 N ILE 534 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
#
_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                     4KXF 
_atom_sites.fract_transf_matrix[1][1]    0.002994 
_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]    0.002994 
_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]    0.005632 
_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
I 2 ADP K 1 1101 1101 ADP ADP . 
J 2 ADP B 1 1101 1101 ADP ADP . 
K 3 SO4 B 1 1102 1102 SO4 SO4 . 
L 2 ADP D 1 1101 1101 ADP ADP . 
M 2 ADP F 1 1101 1101 ADP ADP . 
N 2 ADP H 1 1101 1101 ADP ADP . 
O 2 ADP L 1 1101 1074 ADP ADP . 
P 2 ADP N 1 1101 1101 ADP ADP . 
Q 3 SO4 N 1 1102 1102 SO4 SO4 . 
R 2 ADP P 1 1101 1101 ADP ADP . 
#
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 . . . N 2 -15.053 120.039 81.51 1 5.34 ? PB ADP 1101 H 1 
HETATM 2 O O1B ADP . . . N 2 -15.97 120.789 80.574 1 6.25 ? O1B ADP 1101 H 1 
HETATM 3 O O2B ADP . . . N 2 -15.097 120.517 82.941 1 4.78 ? O2B ADP 1101 H 1 
HETATM 4 O O3B ADP . . . N 2 -13.65 119.866 80.981 1 4.92 ? O3B ADP 1101 H 1 
HETATM 5 P PA ADP . . . N 2 -16.735 118.031 82.6 1 5.93 ? PA ADP 1101 H 1 
HETATM 6 O O1A ADP . . . N 2 -18.085 118.572 82.188 1 5.03 ? O1A ADP 1101 H 1 
HETATM 7 O O2A ADP . . . N 2 -16.2 118.306 83.984 1 5.16 ? O2A ADP 1101 H 1 
HETATM 8 O O3A ADP . . . N 2 -15.646 118.536 81.521 1 5.32 ? O3A ADP 1101 H 1 
HETATM 9 O O5' ADP . . . N 2 -16.778 116.435 82.4 1 7.07 ? O5' ADP 1101 H 1 
HETATM 10 C C5' ADP . . . N 2 -16.85 115.846 81.104 1 6.39 ? C5' ADP 1101 H 1 
HETATM 11 C C4' ADP . . . N 2 -17.494 114.471 81.247 1 4.8 ? C4' ADP 1101 H 1 
HETATM 12 O O4' ADP . . . N 2 -16.489 113.471 81.409 1 5.18 ? O4' ADP 1101 H 1 
HETATM 13 C C3' ADP . . . N 2 -18.398 114.402 82.467 1 5.28 ? C3' ADP 1101 H 1 
HETATM 14 O O3' ADP . . . N 2 -19.775 114.455 82.082 1 5.32 ? O3' ADP 1101 H 1 
HETATM 15 C C2' ADP . . . N 2 -18.079 113.079 83.132 1 8.81 ? C2' ADP 1101 H 1 
HETATM 16 O O2' ADP . . . N 2 -19.138 112.153 82.877 1 4.6 ? O2' ADP 1101 H 1 
HETATM 17 C C1' ADP . . . N 2 -16.797 112.586 82.485 1 5.17 ? C1' ADP 1101 H 1 
HETATM 18 N N9 ADP . . . N 2 -15.702 112.675 83.479 1 5.41 ? N9 ADP 1101 H 1 
HETATM 19 C C8 ADP . . . N 2 -15.221 113.827 83.976 1 6.69 ? C8 ADP 1101 H 1 
HETATM 20 N N7 ADP . . . N 2 -14.224 113.607 84.87 1 6.42 ? N7 ADP 1101 H 1 
HETATM 21 C C5 ADP . . . N 2 -14.055 112.277 84.955 1 5.68 ? C5 ADP 1101 H 1 
HETATM 22 C C6 ADP . . . N 2 -13.166 111.37 85.715 1 5.58 ? C6 ADP 1101 H 1 
HETATM 23 N N6 ADP . . . N 2 -12.245 111.863 86.576 1 5.7 ? N6 ADP 1101 H 1 
HETATM 24 N N1 ADP . . . N 2 -13.306 110.041 85.518 1 5.09 ? N1 ADP 1101 H 1 
HETATM 25 C C2 ADP . . . N 2 -14.22 109.55 84.663 1 5.84 ? C2 ADP 1101 H 1 
HETATM 26 N N3 ADP . . . N 2 -15.058 110.314 83.94 1 5.1 ? N3 ADP 1101 H 1 
HETATM 27 C C4 ADP . . . N 2 -15.03 111.664 84.04 1 5.8 ? C4 ADP 1101 H 1 
#
_model_server_stats.io_time_ms              475 
_model_server_stats.parse_time_ms           43 
_model_server_stats.create_model_time_ms    153 
_model_server_stats.query_time_ms           675 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           27 
#