data_8VJK
#
_model_server_result.job_id            7KeBdEAIynXZvv2feRbWZQ 
_model_server_result.datetime_utc      '2024-11-22 03:08:47' 
_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          8vjk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"X","auth_seq_id":8002}' 
#
_entry.id    8VJK 
#
_exptl.entry_id    8VJK 
_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            8VJK 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8VJK 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_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_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,GA,HA,IA,JA 
_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
? 4 J N N 
? 4 Q N N 
? 4 X N N 
? 4 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
disulf ? disulf1 A SG CYS 3171 A CYS 3171 1_555 A SG CYS 3241 A CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf2 A SG CYS 4874 A CYS 4874 1_555 A SG CYS 4880 A CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 F SG CYS 3171 B CYS 3171 1_555 F SG CYS 3241 B CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf4 F SG CYS 4874 B CYS 4874 1_555 F SG CYS 4880 B CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 G SG CYS 3171 C CYS 3171 1_555 G SG CYS 3241 C CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf6 G SG CYS 4874 C CYS 4874 1_555 G SG CYS 4880 C CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf7 H SG CYS 3171 D CYS 3171 1_555 H SG CYS 3241 D CYS 3241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf8 H SG CYS 4874 D CYS 4874 1_555 H SG CYS 4880 D CYS 4880 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
metalc ? metalc1 A OE2 GLU 3896 A GLU 3896 1_555 L CA CA . A CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc2 A OE2 GLU 3970 A GLU 3970 1_555 L CA CA . A CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc3 A SG CYS 4956 A CYS 4956 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc4 A SG CYS 4959 A CYS 4959 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc5 A NE2 HIS 4976 A HIS 4976 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? 
metalc ? metalc6 A ND1 HIS 4981 A HIS 4981 1_555 I ZN ZN . A ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc7 A O THR 4999 A THR 4999 1_555 L CA CA . A CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc8 F OE2 GLU 3896 B GLU 3896 1_555 S CA CA . B CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc9 F OE2 GLU 3970 B GLU 3970 1_555 S CA CA . B CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc10 F SG CYS 4956 B CYS 4956 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc11 F SG CYS 4959 B CYS 4959 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc12 F NE2 HIS 4976 B HIS 4976 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc13 F ND1 HIS 4981 B HIS 4981 1_555 P ZN ZN . B ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc14 F O THR 4999 B THR 4999 1_555 S CA CA . B CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? 
metalc ? metalc15 G OE2 GLU 3896 C GLU 3896 1_555 Z CA CA . C CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc16 G OE2 GLU 3970 C GLU 3970 1_555 Z CA CA . C CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? 
metalc ? metalc17 G SG CYS 4956 C CYS 4956 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc18 G SG CYS 4959 C CYS 4959 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc19 G NE2 HIS 4976 C HIS 4976 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc20 G ND1 HIS 4981 C HIS 4981 1_555 W ZN ZN . C ZN 8001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc21 G O THR 4999 C THR 4999 1_555 Z CA CA . C CA 8004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
metalc ? metalc22 H OE2 GLU 3896 D GLU 3896 1_555 HA CA CA . D CA 5105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.484 ? 
metalc ? metalc23 H OE2 GLU 3970 D GLU 3970 1_555 HA CA CA . D CA 5105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? 
metalc ? metalc24 H SG CYS 4956 D CYS 4956 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.322 ? 
metalc ? metalc25 H SG CYS 4959 D CYS 4959 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc26 H NE2 HIS 4976 D HIS 4976 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? 
metalc ? metalc27 H ND1 HIS 4981 D HIS 4981 1_555 EA ZN ZN . D ZN 5102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc28 H O THR 4999 D THR 4999 1_555 HA CA CA . D CA 5105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? 
#
_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                     8VJK 
_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 ZN A 1 8001 8001 ZN ZN . 
J 4 CFF A 1 8002 8002 CFF CFF . 
K 5 ATP A 1 8003 8003 ATP ATP . 
L 6 CA A 1 8004 8004 CA CA . 
M 5 ATP A 1 8005 8005 ATP ATP . 
N 7 PCW A 1 8006 8007 PCW PCW . 
O 7 PCW A 1 8007 8008 PCW PCW . 
P 3 ZN B 1 8001 8001 ZN ZN . 
Q 4 CFF B 1 8002 8002 CFF CFF . 
R 5 ATP B 1 8003 8003 ATP ATP . 
S 6 CA B 1 8004 8004 CA CA . 
T 5 ATP B 1 8005 8005 ATP ATP . 
U 7 PCW B 1 8006 8007 PCW PCW . 
V 7 PCW B 1 8007 8008 PCW PCW . 
W 3 ZN C 1 8001 8001 ZN ZN . 
X 4 CFF C 1 8002 8002 CFF CFF . 
Y 5 ATP C 1 8003 8003 ATP ATP . 
Z 6 CA C 1 8004 8004 CA CA . 
AA 5 ATP C 1 8005 8005 ATP ATP . 
BA 7 PCW C 1 8006 8007 PCW PCW . 
CA 7 PCW C 1 8007 8008 PCW PCW . 
DA 7 PCW D 1 5101 8008 PCW PCW . 
EA 3 ZN D 1 5102 8001 ZN ZN . 
FA 4 CFF D 1 5103 8002 CFF CFF . 
GA 5 ATP D 1 5104 8003 ATP ATP . 
HA 6 CA D 1 5105 8004 CA CA . 
IA 5 ATP D 1 5106 8005 ATP ATP . 
JA 7 PCW D 1 5107 8007 PCW PCW . 
#
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 . . . X 4 249.525 227.251 180.349 1 77.73 ? N1 CFF 8002 C 1 
HETATM 2 C C2 CFF . . . X 4 250.599 227.384 181.235 1 77.73 ? C2 CFF 8002 C 1 
HETATM 3 C C10 CFF . . . X 4 248.555 226.191 180.661 1 77.73 ? C10 CFF 8002 C 1 
HETATM 4 C C6 CFF . . . X 4 249.288 228.024 179.2 1 77.73 ? C6 CFF 8002 C 1 
HETATM 5 N N3 CFF . . . X 4 251.521 228.367 180.966 1 77.73 ? N3 CFF 8002 C 1 
HETATM 6 O O11 CFF . . . X 4 250.709 226.65 182.206 1 77.73 ? O11 CFF 8002 C 1 
HETATM 7 C C12 CFF . . . X 4 252.666 228.548 181.861 1 77.73 ? C12 CFF 8002 C 1 
HETATM 8 C C4 CFF . . . X 4 251.359 229.165 179.863 1 77.73 ? C4 CFF 8002 C 1 
HETATM 9 C C5 CFF . . . X 4 250.294 229.01 179.01 1 77.73 ? C5 CFF 8002 C 1 
HETATM 10 N N9 CFF . . . X 4 252.185 230.167 179.476 1 77.73 ? N9 CFF 8002 C 1 
HETATM 11 O O13 CFF . . . X 4 248.308 227.821 178.493 1 77.73 ? O13 CFF 8002 C 1 
HETATM 12 N N7 CFF . . . X 4 250.462 229.975 178.03 1 77.73 ? N7 CFF 8002 C 1 
HETATM 13 C C8 CFF . . . X 4 251.607 230.633 178.364 1 77.73 ? C8 CFF 8002 C 1 
HETATM 14 C C14 CFF . . . X 4 249.581 230.212 176.889 1 77.73 ? C14 CFF 8002 C 1 
#
_model_server_stats.io_time_ms              55 
_model_server_stats.parse_time_ms           16 
_model_server_stats.create_model_time_ms    204 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           14 
#