data_8Y40
#
_model_server_result.job_id            fy2aCRfTcOyR-oqAbfYarw 
_model_server_result.datetime_utc      '2025-03-05 03:36:25' 
_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          8y40 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":5105}' 
#
_entry.id    8Y40 
#
_exptl.entry_id    8Y40 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              194.191 
_entity.id                          8 
_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    12-meric 
_pdbx_struct_assembly.oligomeric_count      12 
_pdbx_struct_assembly.details               author_and_software_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    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
? 8 Q N N 
? 8 V N N 
? 8 AA N N 
? 8 FA 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 3967 A GLU 3967 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc2 I OE2 GLU 3967 A GLU 3967 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.118 ? 
metalc ? metalc3 I SG CYS 4961 A CYS 4961 1_555 N ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? 
metalc ? metalc4 I ND1 HIS 4978 A HIS 4978 1_555 N ZN ZN . A ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.693 ? 
metalc ? metalc5 I O THR 5001 A THR 5001 1_555 O CA CA . A CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? 
metalc ? metalc6 J OE1 GLU 3967 B GLU 3967 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? 
metalc ? metalc7 J OE2 GLU 3967 B GLU 3967 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.113 ? 
metalc ? metalc8 J SG CYS 4961 B CYS 4961 1_555 S ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? 
metalc ? metalc9 J ND1 HIS 4978 B HIS 4978 1_555 S ZN ZN . B ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? 
metalc ? metalc10 J O THR 5001 B THR 5001 1_555 T CA CA . B CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? 
metalc ? metalc11 K OE1 GLU 3967 C GLU 3967 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? 
metalc ? metalc12 K OE2 GLU 3967 C GLU 3967 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? 
metalc ? metalc13 K SG CYS 4961 C CYS 4961 1_555 X ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.567 ? 
metalc ? metalc14 K ND1 HIS 4978 C HIS 4978 1_555 X ZN ZN . C ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc15 K O THR 5001 C THR 5001 1_555 Y CA CA . C CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? 
metalc ? metalc16 L OE1 GLU 3967 D GLU 3967 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc17 L OE2 GLU 3967 D GLU 3967 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.117 ? 
metalc ? metalc18 L SG CYS 4961 D CYS 4961 1_555 CA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.57 ? 
metalc ? metalc19 L ND1 HIS 4978 D HIS 4978 1_555 CA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.573 ? 
metalc ? metalc20 L O THR 5001 D THR 5001 1_555 DA CA CA . D CA 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
#
_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 119 n y 
N1 C10 CFF sing 120 n n 
N1 C6 CFF sing 121 n y 
C2 N3 CFF sing 122 n y 
C2 O11 CFF doub 123 n n 
C10 H101 CFF sing 124 n n 
C10 H102 CFF sing 125 n n 
C10 H103 CFF sing 126 n n 
C6 C5 CFF sing 127 n y 
C6 O13 CFF doub 128 n n 
N3 C12 CFF sing 129 n n 
N3 C4 CFF sing 130 n y 
C12 H121 CFF sing 131 n n 
C12 H122 CFF sing 132 n n 
C12 H123 CFF sing 133 n n 
C4 C5 CFF doub 134 n y 
C4 N9 CFF sing 135 n y 
C5 N7 CFF sing 136 n y 
N9 C8 CFF doub 137 n y 
N7 C8 CFF sing 138 n y 
N7 C14 CFF sing 139 n n 
C8 H81 CFF sing 140 n n 
C14 H141 CFF sing 141 n n 
C14 H142 CFF sing 142 n n 
C14 H143 CFF sing 143 n n 
#
_atom_sites.entry_id                     8Y40 
_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 F0U A 1 5101 1 F0U CHL . 
N 5 ZN A 1 5102 1 ZN ZN . 
O 6 CA A 1 5103 1 CA CA . 
P 7 ATP A 1 5104 1 ATP ATP . 
Q 8 CFF A 1 5105 1 CFF CFF . 
R 4 F0U B 1 5101 2 F0U CHL . 
S 5 ZN B 1 5102 2 ZN ZN . 
T 6 CA B 1 5103 2 CA CA . 
U 7 ATP B 1 5104 2 ATP ATP . 
V 8 CFF B 1 5105 2 CFF CFF . 
W 4 F0U C 1 5101 3 F0U CHL . 
X 5 ZN C 1 5102 3 ZN ZN . 
Y 6 CA C 1 5103 3 CA CA . 
Z 7 ATP C 1 5104 3 ATP ATP . 
AA 8 CFF C 1 5105 3 CFF CFF . 
BA 4 F0U D 1 5101 4 F0U CHL . 
CA 5 ZN D 1 5102 4 ZN ZN . 
DA 6 CA D 1 5103 4 CA CA . 
EA 7 ATP D 1 5104 4 ATP ATP . 
FA 8 CFF D 1 5105 4 CFF CFF . 
#
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 . . . Q 8 233.716 290.818 309.82 1 20 ? N1 CFF 5105 A 1 
HETATM 2 C C2 CFF . . . Q 8 234.156 291.509 310.979 1 20 ? C2 CFF 5105 A 1 
HETATM 3 C C10 CFF . . . Q 8 232.39 291.134 309.277 1 20 ? C10 CFF 5105 A 1 
HETATM 4 C C6 CFF . . . Q 8 234.541 289.845 309.212 1 20 ? C6 CFF 5105 A 1 
HETATM 5 N N3 CFF . . . Q 8 235.417 291.273 311.58 1 20 ? N3 CFF 5105 A 1 
HETATM 6 O O11 CFF . . . Q 8 233.4 292.361 311.487 1 20 ? O11 CFF 5105 A 1 
HETATM 7 C C12 CFF . . . Q 8 235.821 292.015 312.774 1 20 ? C12 CFF 5105 A 1 
HETATM 8 C C4 CFF . . . Q 8 236.224 290.367 311.042 1 20 ? C4 CFF 5105 A 1 
HETATM 9 C C5 CFF . . . Q 8 235.848 289.62 309.858 1 20 ? C5 CFF 5105 A 1 
HETATM 10 N N9 CFF . . . Q 8 237.45 289.951 311.395 1 20 ? N9 CFF 5105 A 1 
HETATM 11 O O13 CFF . . . Q 8 234.206 289.207 308.194 1 20 ? O13 CFF 5105 A 1 
HETATM 12 N N7 CFF . . . Q 8 236.848 288.802 309.564 1 20 ? N7 CFF 5105 A 1 
HETATM 13 C C8 CFF . . . Q 8 237.815 288.999 310.487 1 20 ? C8 CFF 5105 A 1 
HETATM 14 C C14 CFF . . . Q 8 236.898 287.85 308.432 1 20 ? C14 CFF 5105 A 1 
HETATM 15 H H101 CFF . . . Q 8 232.245 290.653 308.346 1 20 ? H101 CFF 5105 A 1 
HETATM 16 H H102 CFF . . . Q 8 232.304 292.18 309.143 1 20 ? H102 CFF 5105 A 1 
HETATM 17 H H103 CFF . . . Q 8 231.645 290.808 309.957 1 20 ? H103 CFF 5105 A 1 
HETATM 18 H H121 CFF . . . Q 8 236.739 291.637 313.141 1 20 ? H121 CFF 5105 A 1 
HETATM 19 H H122 CFF . . . Q 8 235.075 291.913 313.518 1 20 ? H122 CFF 5105 A 1 
HETATM 20 H H123 CFF . . . Q 8 235.935 293.038 312.525 1 20 ? H123 CFF 5105 A 1 
HETATM 21 H H81 CFF . . . Q 8 238.758 288.468 310.501 1 20 ? H81 CFF 5105 A 1 
HETATM 22 H H141 CFF . . . Q 8 236.802 288.385 307.525 1 20 ? H141 CFF 5105 A 1 
HETATM 23 H H142 CFF . . . Q 8 236.102 287.158 308.521 1 20 ? H142 CFF 5105 A 1 
HETATM 24 H H143 CFF . . . Q 8 237.825 287.337 308.445 1 20 ? H143 CFF 5105 A 1 
#
_model_server_stats.io_time_ms              45 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    188 
_model_server_stats.query_time_ms           227 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           24 
#