data_8VJK
#
_model_server_result.job_id            yWE09qAcew2dxpUxxk2eBw 
_model_server_result.datetime_utc      '2024-11-22 03:36:08' 
_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":"Y","auth_seq_id":8003}' 
#
_entry.id    8VJK 
#
_exptl.entry_id    8VJK 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              507.181 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "ADENOSINE-5'-TRIPHOSPHATE" 
_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            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
? 5 K N N 
? 5 M N N 
? 5 R N N 
? 5 T N N 
? 5 Y N N 
? 5 AA N N 
? 5 GA N N 
? 5 IA 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           'C10 H16 N5 O13 P3' 
_chem_comp.formula_weight    507.181 
_chem_comp.id                ATP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "ADENOSINE-5'-TRIPHOSPHATE" 
_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
PG O1G ATP doub 70 n n 
PG O2G ATP sing 71 n n 
PG O3G ATP sing 72 n n 
PG O3B ATP sing 73 n n 
O2G HOG2 ATP sing 74 n n 
O3G HOG3 ATP sing 75 n n 
PB O1B ATP doub 76 n n 
PB O2B ATP sing 77 n n 
PB O3B ATP sing 78 n n 
PB O3A ATP sing 79 n n 
O2B HOB2 ATP sing 80 n n 
PA O1A ATP doub 81 n n 
PA O2A ATP sing 82 n n 
PA O3A ATP sing 83 n n 
PA O5' ATP sing 84 n n 
O2A HOA2 ATP sing 85 n n 
O5' C5' ATP sing 86 n n 
C5' C4' ATP sing 87 n n 
C5' "H5'1" ATP sing 88 n n 
C5' "H5'2" ATP sing 89 n n 
C4' O4' ATP sing 90 n n 
C4' C3' ATP sing 91 n n 
C4' H4' ATP sing 92 n n 
O4' C1' ATP sing 93 n n 
C3' O3' ATP sing 94 n n 
C3' C2' ATP sing 95 n n 
C3' H3' ATP sing 96 n n 
O3' HO3' ATP sing 97 n n 
C2' O2' ATP sing 98 n n 
C2' C1' ATP sing 99 n n 
C2' H2' ATP sing 100 n n 
O2' HO2' ATP sing 101 n n 
C1' N9 ATP sing 102 n n 
C1' H1' ATP sing 103 n n 
N9 C8 ATP sing 104 n y 
N9 C4 ATP sing 105 n y 
C8 N7 ATP doub 106 n y 
C8 H8 ATP sing 107 n n 
N7 C5 ATP sing 108 n y 
C5 C6 ATP sing 109 n y 
C5 C4 ATP doub 110 n y 
C6 N6 ATP sing 111 n n 
C6 N1 ATP doub 112 n y 
N6 HN61 ATP sing 113 n n 
N6 HN62 ATP sing 114 n n 
N1 C2 ATP sing 115 n y 
C2 N3 ATP doub 116 n y 
C2 H2 ATP sing 117 n n 
N3 C4 ATP sing 118 n y 
#
_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 P PG ATP . . . Y 5 228.117 234.231 169.837 1 87.6 ? PG ATP 8003 C 1 
HETATM 2 O O1G ATP . . . Y 5 227.076 233.154 169.662 1 87.6 ? O1G ATP 8003 C 1 
HETATM 3 O O2G ATP . . . Y 5 229.481 233.806 169.356 1 87.6 ? O2G ATP 8003 C 1 
HETATM 4 O O3G ATP . . . Y 5 227.683 235.556 169.264 1 87.6 ? O3G ATP 8003 C 1 
HETATM 5 P PB ATP . . . Y 5 227.338 235.114 172.54 1 87.6 ? PB ATP 8003 C 1 
HETATM 6 O O1B ATP . . . Y 5 228.199 235.876 173.491 1 87.6 ? O1B ATP 8003 C 1 
HETATM 7 O O2B ATP . . . Y 5 226.193 235.798 171.869 1 87.6 ? O2B ATP 8003 C 1 
HETATM 8 O O3B ATP . . . Y 5 228.276 234.455 171.425 1 87.6 ? O3B ATP 8003 C 1 
HETATM 9 P PA ATP . . . Y 5 225.893 232.573 172.795 1 87.6 ? PA ATP 8003 C 1 
HETATM 10 O O1A ATP . . . Y 5 226.79 231.489 172.295 1 87.6 ? O1A ATP 8003 C 1 
HETATM 11 O O2A ATP . . . Y 5 224.826 233.082 171.884 1 87.6 ? O2A ATP 8003 C 1 
HETATM 12 O O3A ATP . . . Y 5 226.795 233.805 173.281 1 87.6 ? O3A ATP 8003 C 1 
HETATM 13 O O5' ATP . . . Y 5 225.235 232.127 174.186 1 87.6 ? O5' ATP 8003 C 1 
HETATM 14 C C5' ATP . . . Y 5 225.761 230.96 174.863 1 87.6 ? C5' ATP 8003 C 1 
HETATM 15 C C4' ATP . . . Y 5 224.665 229.934 174.999 1 87.6 ? C4' ATP 8003 C 1 
HETATM 16 O O4' ATP . . . Y 5 225.214 228.735 175.604 1 87.6 ? O4' ATP 8003 C 1 
HETATM 17 C C3' ATP . . . Y 5 223.475 230.336 175.882 1 87.6 ? C3' ATP 8003 C 1 
HETATM 18 O O3' ATP . . . Y 5 222.257 229.844 175.339 1 87.6 ? O3' ATP 8003 C 1 
HETATM 19 C C2' ATP . . . Y 5 223.817 229.679 177.221 1 87.6 ? C2' ATP 8003 C 1 
HETATM 20 O O2' ATP . . . Y 5 222.688 229.434 178.03 1 87.6 ? O2' ATP 8003 C 1 
HETATM 21 C C1' ATP . . . Y 5 224.457 228.383 176.737 1 87.6 ? C1' ATP 8003 C 1 
HETATM 22 N N9 ATP . . . Y 5 225.338 227.743 177.707 1 87.6 ? N9 ATP 8003 C 1 
HETATM 23 C C8 ATP . . . Y 5 225.161 226.513 178.28 1 87.6 ? C8 ATP 8003 C 1 
HETATM 24 N N7 ATP . . . Y 5 226.118 226.207 179.123 1 87.6 ? N7 ATP 8003 C 1 
HETATM 25 C C5 ATP . . . Y 5 226.971 227.302 179.099 1 87.6 ? C5 ATP 8003 C 1 
HETATM 26 C C6 ATP . . . Y 5 228.17 227.586 179.777 1 87.6 ? C6 ATP 8003 C 1 
HETATM 27 N N6 ATP . . . Y 5 228.738 226.758 180.647 1 87.6 ? N6 ATP 8003 C 1 
HETATM 28 N N1 ATP . . . Y 5 228.763 228.775 179.52 1 87.6 ? N1 ATP 8003 C 1 
HETATM 29 C C2 ATP . . . Y 5 228.183 229.604 178.643 1 87.6 ? C2 ATP 8003 C 1 
HETATM 30 N N3 ATP . . . Y 5 227.06 229.442 177.95 1 87.6 ? N3 ATP 8003 C 1 
HETATM 31 C C4 ATP . . . Y 5 226.497 228.256 178.227 1 87.6 ? C4 ATP 8003 C 1 
#
_model_server_stats.io_time_ms              52 
_model_server_stats.parse_time_ms           23 
_model_server_stats.create_model_time_ms    605 
_model_server_stats.query_time_ms           268 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           31 
#