data_6EBK
#
_model_server_result.job_id            Ogx-HOLOvjK4Sn0O2me1iw 
_model_server_result.datetime_utc      '2024-11-04 22:33:27' 
_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          6ebk 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":1001}' 
#
_entry.id    6EBK 
#
_exptl.entry_id    6EBK 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              743.405 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_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    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 
_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
? 3 I N N 
? 3 J N N 
? 3 K N N 
? 3 L N N 
#
_chem_comp.formula           'C21 H28 N7 O17 P3' 
_chem_comp.formula_weight    743.405 
_chem_comp.id                NAP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" 
#
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
PA O1A NAP doub 237 n n 
PA O2A NAP sing 238 n n 
PA O5B NAP sing 239 n n 
PA O3 NAP sing 240 n n 
O2A HOA2 NAP sing 241 n n 
O5B C5B NAP sing 242 n n 
C5B C4B NAP sing 243 n n 
C5B H51A NAP sing 244 n n 
C5B H52A NAP sing 245 n n 
C4B O4B NAP sing 246 n n 
C4B C3B NAP sing 247 n n 
C4B H4B NAP sing 248 n n 
O4B C1B NAP sing 249 n n 
C3B O3B NAP sing 250 n n 
C3B C2B NAP sing 251 n n 
C3B H3B NAP sing 252 n n 
O3B HO3A NAP sing 253 n n 
C2B O2B NAP sing 254 n n 
C2B C1B NAP sing 255 n n 
C2B H2B NAP sing 256 n n 
O2B P2B NAP sing 257 n n 
C1B N9A NAP sing 258 n n 
C1B H1B NAP sing 259 n n 
N9A C8A NAP sing 260 n y 
N9A C4A NAP sing 261 n y 
C8A N7A NAP doub 262 n y 
C8A H8A NAP sing 263 n n 
N7A C5A NAP sing 264 n y 
C5A C6A NAP sing 265 n y 
C5A C4A NAP doub 266 n y 
C6A N6A NAP sing 267 n n 
C6A N1A NAP doub 268 n y 
N6A H61A NAP sing 269 n n 
N6A H62A NAP sing 270 n n 
N1A C2A NAP sing 271 n y 
C2A N3A NAP doub 272 n y 
C2A H2A NAP sing 273 n n 
N3A C4A NAP sing 274 n y 
O3 PN NAP sing 275 n n 
PN O1N NAP doub 276 n n 
PN O2N NAP sing 277 n n 
PN O5D NAP sing 278 n n 
O5D C5D NAP sing 279 n n 
C5D C4D NAP sing 280 n n 
C5D H51N NAP sing 281 n n 
C5D H52N NAP sing 282 n n 
C4D O4D NAP sing 283 n n 
C4D C3D NAP sing 284 n n 
C4D H4D NAP sing 285 n n 
O4D C1D NAP sing 286 n n 
C3D O3D NAP sing 287 n n 
C3D C2D NAP sing 288 n n 
C3D H3D NAP sing 289 n n 
O3D HO3N NAP sing 290 n n 
C2D O2D NAP sing 291 n n 
C2D C1D NAP sing 292 n n 
C2D H2D NAP sing 293 n n 
O2D HO2N NAP sing 294 n n 
C1D N1N NAP sing 295 n n 
C1D H1D NAP sing 296 n n 
N1N C2N NAP sing 297 n y 
N1N C6N NAP doub 298 n y 
C2N C3N NAP doub 299 n y 
C2N H2N NAP sing 300 n n 
C3N C7N NAP sing 301 n n 
C3N C4N NAP sing 302 n y 
C7N O7N NAP doub 303 n n 
C7N N7N NAP sing 304 n n 
N7N H71N NAP sing 305 n n 
N7N H72N NAP sing 306 n n 
C4N C5N NAP doub 307 n y 
C4N H4N NAP sing 308 n n 
C5N C6N NAP sing 309 n y 
C5N H5N NAP sing 310 n n 
C6N H6N NAP sing 311 n n 
P2B O1X NAP doub 312 n n 
P2B O2X NAP sing 313 n n 
P2B O3X NAP sing 314 n n 
O2X HOP2 NAP sing 315 n n 
O3X HOP3 NAP sing 316 n n 
#
_atom_sites.entry_id                     6EBK 
_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 NAP A 1 1001 1001 NAP NAP . 
J 3 NAP C 1 1001 1001 NAP NAP . 
K 3 NAP E 1 1001 1001 NAP NAP . 
L 3 NAP G 1 1001 1001 NAP NAP . 
M 4 HOH A 1 1101 2027 HOH HOH . 
M 4 HOH A 2 1102 2024 HOH HOH . 
M 4 HOH A 3 1103 2013 HOH HOH . 
M 4 HOH A 4 1104 2007 HOH HOH . 
M 4 HOH A 5 1105 2016 HOH HOH . 
M 4 HOH A 6 1106 2015 HOH HOH . 
M 4 HOH A 7 1107 2022 HOH HOH . 
M 4 HOH A 8 1108 2008 HOH HOH . 
M 4 HOH A 9 1109 2001 HOH HOH . 
M 4 HOH A 10 1110 2012 HOH HOH . 
M 4 HOH A 11 1111 2017 HOH HOH . 
M 4 HOH A 12 1112 2010 HOH HOH . 
M 4 HOH A 13 1113 2005 HOH HOH . 
M 4 HOH A 14 1114 2011 HOH HOH . 
M 4 HOH A 15 1115 2021 HOH HOH . 
M 4 HOH A 16 1116 2028 HOH HOH . 
M 4 HOH A 17 1117 2026 HOH HOH . 
M 4 HOH A 18 1118 2020 HOH HOH . 
M 4 HOH A 19 1119 2019 HOH HOH . 
M 4 HOH A 20 1120 2002 HOH HOH . 
M 4 HOH A 21 1121 2003 HOH HOH . 
M 4 HOH A 22 1122 2006 HOH HOH . 
M 4 HOH A 23 1123 2009 HOH HOH . 
M 4 HOH A 24 1124 2023 HOH HOH . 
M 4 HOH A 25 1125 2018 HOH HOH . 
M 4 HOH A 26 1126 2025 HOH HOH . 
M 4 HOH A 27 1127 2004 HOH HOH . 
N 4 HOH B 1 501 2003 HOH HOH . 
N 4 HOH B 2 502 2002 HOH HOH . 
N 4 HOH B 3 503 2001 HOH HOH . 
N 4 HOH B 4 504 2004 HOH HOH . 
O 4 HOH C 1 1101 2022 HOH HOH . 
O 4 HOH C 2 1102 2027 HOH HOH . 
O 4 HOH C 3 1103 2024 HOH HOH . 
O 4 HOH C 4 1104 2007 HOH HOH . 
O 4 HOH C 5 1105 2016 HOH HOH . 
O 4 HOH C 6 1106 2015 HOH HOH . 
O 4 HOH C 7 1107 2014 HOH HOH . 
O 4 HOH C 8 1108 2008 HOH HOH . 
O 4 HOH C 9 1109 2001 HOH HOH . 
O 4 HOH C 10 1110 2012 HOH HOH . 
O 4 HOH C 11 1111 2013 HOH HOH . 
O 4 HOH C 12 1112 2017 HOH HOH . 
O 4 HOH C 13 1113 2005 HOH HOH . 
O 4 HOH C 14 1114 2010 HOH HOH . 
O 4 HOH C 15 1115 2011 HOH HOH . 
O 4 HOH C 16 1116 2021 HOH HOH . 
O 4 HOH C 17 1117 2028 HOH HOH . 
O 4 HOH C 18 1118 2026 HOH HOH . 
O 4 HOH C 19 1119 2019 HOH HOH . 
O 4 HOH C 20 1120 2002 HOH HOH . 
O 4 HOH C 21 1121 2003 HOH HOH . 
O 4 HOH C 22 1122 2006 HOH HOH . 
O 4 HOH C 23 1123 2020 HOH HOH . 
O 4 HOH C 24 1124 2009 HOH HOH . 
O 4 HOH C 25 1125 2023 HOH HOH . 
O 4 HOH C 26 1126 2018 HOH HOH . 
O 4 HOH C 27 1127 2025 HOH HOH . 
O 4 HOH C 28 1128 2004 HOH HOH . 
P 4 HOH D 1 501 2003 HOH HOH . 
P 4 HOH D 2 502 2001 HOH HOH . 
P 4 HOH D 3 503 2002 HOH HOH . 
P 4 HOH D 4 504 2004 HOH HOH . 
Q 4 HOH E 1 1101 2027 HOH HOH . 
Q 4 HOH E 2 1102 2024 HOH HOH . 
Q 4 HOH E 3 1103 2013 HOH HOH . 
Q 4 HOH E 4 1104 2007 HOH HOH . 
Q 4 HOH E 5 1105 2015 HOH HOH . 
Q 4 HOH E 6 1106 2016 HOH HOH . 
Q 4 HOH E 7 1107 2014 HOH HOH . 
Q 4 HOH E 8 1108 2022 HOH HOH . 
Q 4 HOH E 9 1109 2008 HOH HOH . 
Q 4 HOH E 10 1110 2001 HOH HOH . 
Q 4 HOH E 11 1111 2012 HOH HOH . 
Q 4 HOH E 12 1112 2010 HOH HOH . 
Q 4 HOH E 13 1113 2017 HOH HOH . 
Q 4 HOH E 14 1114 2005 HOH HOH . 
Q 4 HOH E 15 1115 2011 HOH HOH . 
Q 4 HOH E 16 1116 2021 HOH HOH . 
Q 4 HOH E 17 1117 2028 HOH HOH . 
Q 4 HOH E 18 1118 2026 HOH HOH . 
Q 4 HOH E 19 1119 2019 HOH HOH . 
Q 4 HOH E 20 1120 2020 HOH HOH . 
Q 4 HOH E 21 1121 2002 HOH HOH . 
Q 4 HOH E 22 1122 2003 HOH HOH . 
Q 4 HOH E 23 1123 2006 HOH HOH . 
Q 4 HOH E 24 1124 2009 HOH HOH . 
Q 4 HOH E 25 1125 2023 HOH HOH . 
Q 4 HOH E 26 1126 2018 HOH HOH . 
Q 4 HOH E 27 1127 2025 HOH HOH . 
Q 4 HOH E 28 1128 2004 HOH HOH . 
R 4 HOH F 1 501 2003 HOH HOH . 
R 4 HOH F 2 502 2001 HOH HOH . 
R 4 HOH F 3 503 2002 HOH HOH . 
R 4 HOH F 4 504 2004 HOH HOH . 
S 4 HOH G 1 1101 2022 HOH HOH . 
S 4 HOH G 2 1102 2027 HOH HOH . 
S 4 HOH G 3 1103 2024 HOH HOH . 
S 4 HOH G 4 1104 2013 HOH HOH . 
S 4 HOH G 5 1105 2015 HOH HOH . 
S 4 HOH G 6 1106 2007 HOH HOH . 
S 4 HOH G 7 1107 2016 HOH HOH . 
S 4 HOH G 8 1108 2008 HOH HOH . 
S 4 HOH G 9 1109 2019 HOH HOH . 
S 4 HOH G 10 1110 2001 HOH HOH . 
S 4 HOH G 11 1111 2012 HOH HOH . 
S 4 HOH G 12 1112 2017 HOH HOH . 
S 4 HOH G 13 1113 2010 HOH HOH . 
S 4 HOH G 14 1114 2005 HOH HOH . 
S 4 HOH G 15 1115 2020 HOH HOH . 
S 4 HOH G 16 1116 2011 HOH HOH . 
S 4 HOH G 17 1117 2021 HOH HOH . 
S 4 HOH G 18 1118 2028 HOH HOH . 
S 4 HOH G 19 1119 2026 HOH HOH . 
S 4 HOH G 20 1120 2002 HOH HOH . 
S 4 HOH G 21 1121 2003 HOH HOH . 
S 4 HOH G 22 1122 2006 HOH HOH . 
S 4 HOH G 23 1123 2009 HOH HOH . 
S 4 HOH G 24 1124 2023 HOH HOH . 
S 4 HOH G 25 1125 2014 HOH HOH . 
S 4 HOH G 26 1126 2018 HOH HOH . 
S 4 HOH G 27 1127 2025 HOH HOH . 
S 4 HOH G 28 1128 2004 HOH HOH . 
S 4 HOH G 29 1129 2014 HOH HOH . 
T 4 HOH H 1 501 2003 HOH HOH . 
T 4 HOH H 2 502 2001 HOH HOH . 
T 4 HOH H 3 503 2002 HOH HOH . 
T 4 HOH H 4 504 2004 HOH HOH . 
#
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 PA NAP . . . I 3 144.754 197.055 232.355 1 39.12 ? PA NAP 1001 A 1 
HETATM 2 O O1A NAP . . . I 3 144.572 197.676 231.048 1 38.81 -1 O1A NAP 1001 A 1 
HETATM 3 O O2A NAP . . . I 3 144.856 195.477 232.539 1 49.17 ? O2A NAP 1001 A 1 
HETATM 4 O O5B NAP . . . I 3 145.399 197.987 233.558 1 40.39 ? O5B NAP 1001 A 1 
HETATM 5 C C5B NAP . . . I 3 144.541 198.014 234.723 1 43.79 ? C5B NAP 1001 A 1 
HETATM 6 C C4B NAP . . . I 3 145.133 199.008 235.744 1 47.41 ? C4B NAP 1001 A 1 
HETATM 7 O O4B NAP . . . I 3 144.547 200.291 235.264 1 46.14 ? O4B NAP 1001 A 1 
HETATM 8 C C3B NAP . . . I 3 144.578 198.91 237.166 1 46.39 ? C3B NAP 1001 A 1 
HETATM 9 O O3B NAP . . . I 3 145.656 198.752 238.073 1 48.83 ? O3B NAP 1001 A 1 
HETATM 10 C C2B NAP . . . I 3 143.72 200.146 237.5 1 47.77 ? C2B NAP 1001 A 1 
HETATM 11 O O2B NAP . . . I 3 144.028 201.04 238.652 1 52.36 ? O2B NAP 1001 A 1 
HETATM 12 C C1B NAP . . . I 3 143.485 200.808 236.161 1 43.81 ? C1B NAP 1001 A 1 
HETATM 13 N N9A NAP . . . I 3 142.048 200.425 235.898 1 44.8 ? N9A NAP 1001 A 1 
HETATM 14 C C8A NAP . . . I 3 141.525 199.221 235.466 1 45.64 ? C8A NAP 1001 A 1 
HETATM 15 N N7A NAP . . . I 3 140.222 199.266 235.383 1 43.58 ? N7A NAP 1001 A 1 
HETATM 16 C C5A NAP . . . I 3 139.799 200.488 235.755 1 44.38 ? C5A NAP 1001 A 1 
HETATM 17 C C6A NAP . . . I 3 138.526 201.126 235.88 1 42.71 ? C6A NAP 1001 A 1 
HETATM 18 N N6A NAP . . . I 3 137.357 200.453 235.585 1 44.22 ? N6A NAP 1001 A 1 
HETATM 19 N N1A NAP . . . I 3 138.482 202.398 236.296 1 42.19 ? N1A NAP 1001 A 1 
HETATM 20 C C2A NAP . . . I 3 139.589 203.08 236.598 1 43.93 ? C2A NAP 1001 A 1 
HETATM 21 N N3A NAP . . . I 3 140.805 202.531 236.504 1 43.83 ? N3A NAP 1001 A 1 
HETATM 22 C C4A NAP . . . I 3 140.963 201.256 236.091 1 44.95 ? C4A NAP 1001 A 1 
HETATM 23 O O3 NAP . . . I 3 146.267 197.107 231.711 1 41.01 ? O3 NAP 1001 A 1 
HETATM 24 P PN NAP . . . I 3 147.338 196.021 232.558 1 35.59 ? PN NAP 1001 A 1 
HETATM 25 O O1N NAP . . . I 3 147.223 196.065 234.104 1 32.76 -1 O1N NAP 1001 A 1 
HETATM 26 O O2N NAP . . . I 3 148.768 196.414 232.171 1 37.39 ? O2N NAP 1001 A 1 
HETATM 27 O O5D NAP . . . I 3 147.075 194.499 232.172 1 37.73 ? O5D NAP 1001 A 1 
HETATM 28 C C5D NAP . . . I 3 147.968 193.865 233.044 1 44.16 ? C5D NAP 1001 A 1 
HETATM 29 C C4D NAP . . . I 3 147.94 192.376 232.98 1 41.17 ? C4D NAP 1001 A 1 
HETATM 30 O O4D NAP . . . I 3 148.29 191.841 231.677 1 42.74 ? O4D NAP 1001 A 1 
HETATM 31 C C3D NAP . . . I 3 148.916 191.863 234.032 1 41.54 ? C3D NAP 1001 A 1 
HETATM 32 O O3D NAP . . . I 3 148.207 191.334 235.096 1 48.73 ? O3D NAP 1001 A 1 
HETATM 33 C C2D NAP . . . I 3 149.813 190.879 233.297 1 41.92 ? C2D NAP 1001 A 1 
HETATM 34 O O2D NAP . . . I 3 149.675 189.562 233.835 1 42.97 ? O2D NAP 1001 A 1 
HETATM 35 C C1D NAP . . . I 3 149.447 190.953 231.803 1 41.86 ? C1D NAP 1001 A 1 
HETATM 36 N N1N NAP . . . I 3 150.669 191.504 231.12 1 42.39 ? N1N NAP 1001 A 1 
HETATM 37 C C2N NAP . . . I 3 151.414 190.695 230.338 1 41 ? C2N NAP 1001 A 1 
HETATM 38 C C3N NAP . . . I 3 152.602 191.199 229.705 1 40.56 ? C3N NAP 1001 A 1 
HETATM 39 C C7N NAP . . . I 3 153.436 190.344 228.842 1 36.16 ? C7N NAP 1001 A 1 
HETATM 40 O O7N NAP . . . I 3 153.129 189.199 228.632 1 40.54 ? O7N NAP 1001 A 1 
HETATM 41 N N7N NAP . . . I 3 154.538 190.832 228.285 1 36.55 ? N7N NAP 1001 A 1 
HETATM 42 C C4N NAP . . . I 3 152.975 192.561 229.926 1 41.2 ? C4N NAP 1001 A 1 
HETATM 43 C C5N NAP . . . I 3 152.169 193.371 230.738 1 42.24 ? C5N NAP 1001 A 1 
HETATM 44 C C6N NAP . . . I 3 151.024 192.815 231.323 1 42.13 ? C6N NAP 1001 A 1 
HETATM 45 P P2B NAP . . . I 3 145.25 202.088 238.56 1 46.7 ? P2B NAP 1001 A 1 
HETATM 46 O O1X NAP . . . I 3 145.083 203.04 237.455 1 53.58 ? O1X NAP 1001 A 1 
HETATM 47 O O2X NAP . . . I 3 145.296 202.868 239.923 1 54.39 -1 O2X NAP 1001 A 1 
HETATM 48 O O3X NAP . . . I 3 146.643 201.341 238.416 1 55.3 ? O3X NAP 1001 A 1 
#
_model_server_stats.io_time_ms              67 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           48 
#