data_5T9V
#
_model_server_result.job_id            wrr01y27Cl70OcylCvHJOw 
_model_server_result.datetime_utc      '2024-11-23 01:58:52' 
_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          5t9v 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"R","auth_seq_id":5102}' 
#
_entry.id    5T9V 
#
_exptl.entry_id    5T9V 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              194.191 
_entity.id                          4 
_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                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         90 
_cell.entry_id            5T9V 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5T9V 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    'P 1' 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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 
_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
? 4 J N N 
? 4 N N N 
? 4 R N N 
? 4 V 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
disulf ? disulf1 E SG CYS 4337 B CYS 4958 1_555 E SG CYS 4340 B CYS 4961 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf2 F SG CYS 4337 G CYS 4958 1_555 F SG CYS 4340 G CYS 4961 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf3 G SG CYS 4337 I CYS 4958 1_555 G SG CYS 4340 I CYS 4961 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf4 H SG CYS 4337 E CYS 4958 1_555 H SG CYS 4340 E CYS 4961 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
metalc ? metalc1 E OE2 GLU 3532 B GLU 3893 1_555 L CA CA . B CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc2 E OE2 GLU 3606 B GLU 3967 1_555 L CA CA . B CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc3 E SG CYS 4337 B CYS 4958 1_555 K ZN ZN . B ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? 
metalc ? metalc4 E NE2 HIS 4357 B HIS 4978 1_555 K ZN ZN . B ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? 
metalc ? metalc5 E NE2 HIS 4362 B HIS 4983 1_555 K ZN ZN . B ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc6 E O THR 4380 B THR 5001 1_555 L CA CA . B CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc7 F OE2 GLU 3532 G GLU 3893 1_555 P CA CA . G CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc8 F OE2 GLU 3606 G GLU 3967 1_555 P CA CA . G CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc9 F SG CYS 4337 G CYS 4958 1_555 O ZN ZN . G ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.539 ? 
metalc ? metalc10 F NE2 HIS 4357 G HIS 4978 1_555 O ZN ZN . G ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? 
metalc ? metalc11 F NE2 HIS 4362 G HIS 4983 1_555 O ZN ZN . G ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc12 F O THR 4380 G THR 5001 1_555 P CA CA . G CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc13 G OE2 GLU 3532 I GLU 3893 1_555 T CA CA . I CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? 
metalc ? metalc14 G OE2 GLU 3606 I GLU 3967 1_555 T CA CA . I CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc15 G SG CYS 4337 I CYS 4958 1_555 S ZN ZN . I ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? 
metalc ? metalc16 G NE2 HIS 4357 I HIS 4978 1_555 S ZN ZN . I ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.637 ? 
metalc ? metalc17 G NE2 HIS 4362 I HIS 4983 1_555 S ZN ZN . I ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc18 G O THR 4380 I THR 5001 1_555 T CA CA . I CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc19 H OE2 GLU 3532 E GLU 3893 1_555 X CA CA . E CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? 
metalc ? metalc20 H OE2 GLU 3606 E GLU 3967 1_555 X CA CA . E CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc21 H SG CYS 4337 E CYS 4958 1_555 W ZN ZN . E ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.54 ? 
metalc ? metalc22 H NE2 HIS 4357 E HIS 4978 1_555 W ZN ZN . E ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.636 ? 
metalc ? metalc23 H NE2 HIS 4362 E HIS 4983 1_555 W ZN ZN . E ZN 5103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc24 H O THR 4380 E THR 5001 1_555 X CA CA . E CA 5104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
#
_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                     5T9V 
_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
I 3 ATP B 1 5101 5300 ATP ATP . 
J 4 CFF B 1 5102 5400 CFF CFF . 
K 5 ZN B 1 5103 6000 ZN ZN . 
L 6 CA B 1 5104 7000 CA CA . 
M 3 ATP G 1 5101 5300 ATP ATP . 
N 4 CFF G 1 5102 5400 CFF CFF . 
O 5 ZN G 1 5103 6000 ZN ZN . 
P 6 CA G 1 5104 7000 CA CA . 
Q 3 ATP I 1 5101 5300 ATP ATP . 
R 4 CFF I 1 5102 5400 CFF CFF . 
S 5 ZN I 1 5103 6000 ZN ZN . 
T 6 CA I 1 5104 7000 CA CA . 
U 3 ATP E 1 5101 5300 ATP ATP . 
V 4 CFF E 1 5102 5400 CFF CFF . 
W 5 ZN E 1 5103 6000 ZN ZN . 
X 6 CA E 1 5104 7000 CA CA . 
#
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 . . . R 4 216.483 226.044 226.283 1 126.8 ? N1 CFF 5102 I 1 
HETATM 2 C C2 CFF . . . R 4 216.595 224.721 226.068 1 126.8 ? C2 CFF 5102 I 1 
HETATM 3 C C10 CFF . . . R 4 216.476 226.527 227.645 1 126.8 ? C10 CFF 5102 I 1 
HETATM 4 C C6 CFF . . . R 4 216.399 226.883 225.27 1 126.8 ? C6 CFF 5102 I 1 
HETATM 5 N N3 CFF . . . R 4 216.585 224.247 224.812 1 126.8 ? N3 CFF 5102 I 1 
HETATM 6 O O11 CFF . . . R 4 216.653 223.975 226.982 1 126.8 ? O11 CFF 5102 I 1 
HETATM 7 C C12 CFF . . . R 4 216.682 222.825 224.569 1 126.8 ? C12 CFF 5102 I 1 
HETATM 8 C C4 CFF . . . R 4 216.5 225.087 223.777 1 126.8 ? C4 CFF 5102 I 1 
HETATM 9 C C5 CFF . . . R 4 216.405 226.399 223.982 1 126.8 ? C5 CFF 5102 I 1 
HETATM 10 N N9 CFF . . . R 4 216.485 224.86 222.462 1 126.8 ? N9 CFF 5102 I 1 
HETATM 11 O O13 CFF . . . R 4 216.315 228.043 225.479 1 126.8 ? O13 CFF 5102 I 1 
HETATM 12 N N7 CFF . . . R 4 216.333 226.99 222.782 1 126.8 ? N7 CFF 5102 I 1 
HETATM 13 C C8 CFF . . . R 4 216.393 226.038 221.852 1 126.8 ? C8 CFF 5102 I 1 
HETATM 14 C C14 CFF . . . R 4 216.222 228.314 222.198 1 126.8 ? C14 CFF 5102 I 1 
#
_model_server_stats.io_time_ms              46 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    153 
_model_server_stats.query_time_ms           274 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           14 
#