data_8XKH
#
_model_server_result.job_id            oq_S3cPC-5RLM6UIzRdyWg 
_model_server_result.datetime_utc      '2025-03-05 03:35:46' 
_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          8xkh 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":5104}' 
#
_entry.id    8XKH 
#
_exptl.entry_id    8XKH 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              194.191 
_entity.id                          7 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            CAFFEINE 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dodecameric 
_pdbx_struct_assembly.oligomeric_count      12 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    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    ? 
_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
? 7 P N N 
? 7 U N N 
? 7 Z N N 
? 7 EA 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 I OE1 GLU 3893 D GLU 3893 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? 
metalc ? metalc2 I OE1 GLU 3967 D GLU 3967 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.14 ? 
metalc ? metalc3 I OE2 GLU 3967 D GLU 3967 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? 
metalc ? metalc4 I OE1 GLN 3970 D GLN 3970 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc5 I SG CYS 4958 D CYS 4958 1_555 M ZN ZN . D ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? 
metalc ? metalc6 I SG CYS 4961 D CYS 4961 1_555 M ZN ZN . D ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc7 I NE2 HIS 4978 D HIS 4978 1_555 M ZN ZN . D ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? 
metalc ? metalc8 I O THR 5001 D THR 5001 1_555 N CA CA . D CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? 
metalc ? metalc9 J OE1 GLU 3893 A GLU 3893 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? 
metalc ? metalc10 J OE1 GLU 3967 A GLU 3967 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.14 ? 
metalc ? metalc11 J OE2 GLU 3967 A GLU 3967 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? 
metalc ? metalc12 J OE1 GLN 3970 A GLN 3970 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc13 J SG CYS 4958 A CYS 4958 1_555 R ZN ZN . A ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc14 J SG CYS 4961 A CYS 4961 1_555 R ZN ZN . A ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc15 J NE2 HIS 4978 A HIS 4978 1_555 R ZN ZN . A ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? 
metalc ? metalc16 J O THR 5001 A THR 5001 1_555 S CA CA . A CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? 
metalc ? metalc17 K OE1 GLU 3893 B GLU 3893 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.95 ? 
metalc ? metalc18 K OE1 GLU 3967 B GLU 3967 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.141 ? 
metalc ? metalc19 K OE2 GLU 3967 B GLU 3967 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc20 K OE1 GLN 3970 B GLN 3970 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc21 K SG CYS 4958 B CYS 4958 1_555 W ZN ZN . B ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc22 K SG CYS 4961 B CYS 4961 1_555 W ZN ZN . B ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc23 K NE2 HIS 4978 B HIS 4978 1_555 W ZN ZN . B ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? 
metalc ? metalc24 K O THR 5001 B THR 5001 1_555 X CA CA . B CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? 
metalc ? metalc25 L OE1 GLU 3893 C GLU 3893 1_555 CA CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.949 ? 
metalc ? metalc26 L OE1 GLU 3967 C GLU 3967 1_555 CA CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.14 ? 
metalc ? metalc27 L OE2 GLU 3967 C GLU 3967 1_555 CA CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc28 L OE1 GLN 3970 C GLN 3970 1_555 CA CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? 
metalc ? metalc29 L SG CYS 4958 C CYS 4958 1_555 BA ZN ZN . C ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? 
metalc ? metalc30 L SG CYS 4961 C CYS 4961 1_555 BA ZN ZN . C ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
metalc ? metalc31 L NE2 HIS 4978 C HIS 4978 1_555 BA ZN ZN . C ZN 5101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? 
metalc ? metalc32 L O THR 5001 C THR 5001 1_555 CA CA CA . C CA 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.992 ? 
#
_chem_comp.formula           'C8 H10 N4 O2' 
_chem_comp.formula_weight    194.191 
_chem_comp.id                CFF 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              CAFFEINE 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     3,7-DIHYDRO-1,3,7-TRIMETHYL-1H-PURINE-2,6-DIONE 
#
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
N1 C2 CFF sing 176 n y 
N1 C10 CFF sing 177 n n 
N1 C6 CFF sing 178 n y 
C2 N3 CFF sing 179 n y 
C2 O11 CFF doub 180 n n 
C10 H101 CFF sing 181 n n 
C10 H102 CFF sing 182 n n 
C10 H103 CFF sing 183 n n 
C6 C5 CFF sing 184 n y 
C6 O13 CFF doub 185 n n 
N3 C12 CFF sing 186 n n 
N3 C4 CFF sing 187 n y 
C12 H121 CFF sing 188 n n 
C12 H122 CFF sing 189 n n 
C12 H123 CFF sing 190 n n 
C4 C5 CFF doub 191 n y 
C4 N9 CFF sing 192 n y 
C5 N7 CFF sing 193 n y 
N9 C8 CFF doub 194 n y 
N7 C8 CFF sing 195 n y 
N7 C14 CFF sing 196 n n 
C8 H81 CFF sing 197 n n 
C14 H141 CFF sing 198 n n 
C14 H142 CFF sing 199 n n 
C14 H143 CFF sing 200 n n 
#
_atom_sites.entry_id                     8XKH 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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
M 4 ZN D 1 5101 1 ZN ZN . 
N 5 CA D 1 5102 1 CA CA . 
O 6 ATP D 1 5103 4 ATP ATP . 
P 7 CFF D 1 5104 4 CFF CFF . 
Q 8 A1LV1 D 1 5105 1 A1LV1 TET . 
R 4 ZN A 1 5101 2 ZN ZN . 
S 5 CA A 1 5102 3 CA CA . 
T 6 ATP A 1 5103 1 ATP ATP . 
U 7 CFF A 1 5104 1 CFF CFF . 
V 8 A1LV1 A 1 5105 2 A1LV1 TET . 
W 4 ZN B 1 5101 3 ZN ZN . 
X 5 CA B 1 5102 2 CA CA . 
Y 6 ATP B 1 5103 2 ATP ATP . 
Z 7 CFF B 1 5104 2 CFF CFF . 
AA 8 A1LV1 B 1 5105 3 A1LV1 TET . 
BA 4 ZN C 1 5101 4 ZN ZN . 
CA 5 CA C 1 5102 4 CA CA . 
DA 6 ATP C 1 5103 3 ATP ATP . 
EA 7 CFF C 1 5104 3 CFF CFF . 
FA 8 A1LV1 C 1 5105 4 A1LV1 TET . 
#
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 N N1 CFF . . . Z 7 314.533 282.263 310.009 1 50.1 ? N1 CFF 5104 B 1 
HETATM 2 C C2 CFF . . . Z 7 314.051 281.837 311.278 1 50.1 ? C2 CFF 5104 B 1 
HETATM 3 C C10 CFF . . . Z 7 315.973 282.284 309.749 1 50.1 ? C10 CFF 5104 B 1 
HETATM 4 C C6 CFF . . . Z 7 313.641 282.667 308.993 1 50.1 ? C6 CFF 5104 B 1 
HETATM 5 N N3 CFF . . . Z 7 312.668 281.797 311.592 1 50.1 ? N3 CFF 5104 B 1 
HETATM 6 O O11 CFF . . . Z 7 314.874 281.489 312.15 1 50.1 ? O11 CFF 5104 B 1 
HETATM 7 C C12 CFF . . . Z 7 312.208 281.354 312.909 1 50.1 ? C12 CFF 5104 B 1 
HETATM 8 C C4 CFF . . . Z 7 311.792 282.168 310.663 1 50.1 ? C4 CFF 5104 B 1 
HETATM 9 C C5 CFF . . . Z 7 312.208 282.615 309.343 1 50.1 ? C5 CFF 5104 B 1 
HETATM 10 N N9 CFF . . . Z 7 310.452 282.223 310.698 1 50.1 ? N9 CFF 5104 B 1 
HETATM 11 O O13 CFF . . . Z 7 314.044 283.045 307.873 1 50.1 ? O13 CFF 5104 B 1 
HETATM 12 N N7 CFF . . . Z 7 311.115 282.914 308.653 1 50.1 ? N7 CFF 5104 B 1 
HETATM 13 C C8 CFF . . . Z 7 310.065 282.677 309.471 1 50.1 ? C8 CFF 5104 B 1 
HETATM 14 C C14 CFF . . . Z 7 311.06 283.41 307.256 1 50.1 ? C14 CFF 5104 B 1 
#
_model_server_stats.io_time_ms              47 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    267 
_model_server_stats.query_time_ms           399 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           14 
#