data_8Y2M
#
_model_server_result.job_id            52rEzpnP86VDF7B-93XpHQ 
_model_server_result.datetime_utc      '2024-12-26 16:40:33' 
_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          8y2m 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":502}' 
#
_entry.id    8Y2M 
#
_exptl.entry_id    8Y2M 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              721.83 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2~{R})-2-[2-[(5~{R},6~{R},7~{S},9~{S},11~{R},16~{R},18~{S},19~{S})-19-azanyl-6-[(3~{R})-3-carboxy-5-oxidanyl-5-oxidanylidene-pentanoyl]oxy-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid' 
_entity.pdbx_number_of_molecules    2 
_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            8Y2M 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Y2M 
_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    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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 
_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 F N N 
? 4 K 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 B SG CYS 53 B CYS 53 1_555 B SG CYS 75 B CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf2 B SG CYS 102 B CYS 102 1_555 B SG CYS 142 B CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf3 D SG CYS 53 D CYS 53 1_555 D SG CYS 75 D CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 D SG CYS 102 D CYS 102 1_555 D SG CYS 142 D CYS 142 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
#
_chem_comp.formula           'C34 H59 N O15' 
_chem_comp.formula_weight    721.83 
_chem_comp.id                A1D5V 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2~{R})-2-[2-[(5~{R},6~{R},7~{S},9~{S},11~{R},16~{R},18~{S},19~{S})-19-azanyl-6-[(3~{R})-3-carboxy-5-oxidanyl-5-oxidanylidene-pentanoyl]oxy-5,9-dimethyl-11,16,18-tris(oxidanyl)icosan-7-yl]oxy-2-oxidanylidene-ethyl]butanedioic acid' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'Fumonisin b1;Macrofusine' 
#
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
NAP CBQ A1D5V sing 216 n n 
CBQ CBM A1D5V sing 217 n n 
CBQ CBT A1D5V sing 218 n n 
CBM CBJ A1D5V sing 219 n n 
CBM OAG A1D5V sing 220 n n 
CBJ CBG A1D5V sing 221 n n 
CBG CBF A1D5V sing 222 n n 
CBG OAD A1D5V sing 223 n n 
CBF CBD A1D5V sing 224 n n 
CBD CBC A1D5V sing 225 n n 
CBC CAZ A1D5V sing 226 n n 
CAZ CAX A1D5V sing 227 n n 
CAX CAV A1D5V sing 228 n n 
CAX OAC A1D5V sing 229 n n 
CAV CAS A1D5V sing 230 n n 
CAS CAY A1D5V sing 231 n n 
CAS CAT A1D5V sing 232 n n 
CBA CAU A1D5V sing 233 n n 
CAT CAQ A1D5V sing 234 n n 
CAQ OAA A1D5V sing 235 n n 
CAQ CAR A1D5V sing 236 n n 
OAA CBH A1D5V sing 237 n n 
CBE CBN A1D5V sing 238 n n 
CBE CBB A1D5V sing 239 n n 
CAW CAU A1D5V sing 240 n n 
CAW CBB A1D5V sing 241 n n 
CAU CAR A1D5V sing 242 n n 
CBK CBH A1D5V sing 243 n n 
CBK CBO A1D5V sing 244 n n 
CBH OAE A1D5V doub 245 n n 
CAR OAB A1D5V sing 246 n n 
CBR CBO A1D5V sing 247 n n 
CBR CBW A1D5V sing 248 n n 
OAB CBI A1D5V sing 249 n n 
CBO CBU A1D5V sing 250 n n 
OAL CBW A1D5V doub 251 n n 
CBW OAN A1D5V sing 252 n n 
CBU OAJ A1D5V doub 253 n n 
CBU OAH A1D5V sing 254 n n 
OAK CBV A1D5V doub 255 n n 
CBI OAF A1D5V doub 256 n n 
CBI CBL A1D5V sing 257 n n 
CBV OAI A1D5V sing 258 n n 
CBV CBP A1D5V sing 259 n n 
CBL CBP A1D5V sing 260 n n 
CBS CBP A1D5V sing 261 n n 
CBS CBX A1D5V sing 262 n n 
CBX OAO A1D5V doub 263 n n 
CBX OAM A1D5V sing 264 n n 
CAQ H1 A1D5V sing 265 n n 
CAR H2 A1D5V sing 266 n n 
CAS H3 A1D5V sing 267 n n 
CAT H4 A1D5V sing 268 n n 
CAT H5 A1D5V sing 269 n n 
CAU H6 A1D5V sing 270 n n 
CAV H7 A1D5V sing 271 n n 
CAV H8 A1D5V sing 272 n n 
CAW H9 A1D5V sing 273 n n 
CAW H10 A1D5V sing 274 n n 
CAX H11 A1D5V sing 275 n n 
CAY H12 A1D5V sing 276 n n 
CAY H13 A1D5V sing 277 n n 
CAY H14 A1D5V sing 278 n n 
CAZ H15 A1D5V sing 279 n n 
CAZ H16 A1D5V sing 280 n n 
CBA H17 A1D5V sing 281 n n 
CBA H18 A1D5V sing 282 n n 
CBA H19 A1D5V sing 283 n n 
CBB H20 A1D5V sing 284 n n 
CBB H21 A1D5V sing 285 n n 
CBC H22 A1D5V sing 286 n n 
CBC H23 A1D5V sing 287 n n 
CBD H24 A1D5V sing 288 n n 
CBD H25 A1D5V sing 289 n n 
CBE H26 A1D5V sing 290 n n 
CBE H27 A1D5V sing 291 n n 
CBF H28 A1D5V sing 292 n n 
CBF H29 A1D5V sing 293 n n 
CBG H30 A1D5V sing 294 n n 
CBJ H31 A1D5V sing 295 n n 
CBJ H32 A1D5V sing 296 n n 
CBK H33 A1D5V sing 297 n n 
CBK H34 A1D5V sing 298 n n 
CBL H35 A1D5V sing 299 n n 
CBL H36 A1D5V sing 300 n n 
CBM H37 A1D5V sing 301 n n 
CBN H38 A1D5V sing 302 n n 
CBN H39 A1D5V sing 303 n n 
CBN H40 A1D5V sing 304 n n 
CBO H41 A1D5V sing 305 n n 
CBP H42 A1D5V sing 306 n n 
CBQ H43 A1D5V sing 307 n n 
CBR H44 A1D5V sing 308 n n 
CBR H45 A1D5V sing 309 n n 
CBS H46 A1D5V sing 310 n n 
CBS H47 A1D5V sing 311 n n 
CBT H48 A1D5V sing 312 n n 
CBT H49 A1D5V sing 313 n n 
CBT H50 A1D5V sing 314 n n 
NAP H51 A1D5V sing 315 n n 
NAP H52 A1D5V sing 316 n n 
OAC H54 A1D5V sing 317 n n 
OAD H55 A1D5V sing 318 n n 
OAG H56 A1D5V sing 319 n n 
OAH H57 A1D5V sing 320 n n 
OAI H58 A1D5V sing 321 n n 
OAM H59 A1D5V sing 322 n n 
OAN H60 A1D5V sing 323 n n 
#
_atom_sites.entry_id                     8Y2M 
_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
E 3 6PL A 1 501 3 6PL 6PL . 
F 4 A1D5V A 1 502 1 A1D5V DRG . 
G 5 7PO A 1 503 1 7PO 7PO . 
H 3 6PL B 1 201 1 6PL 6PL . 
I 3 6PL B 1 202 2 6PL 6PL . 
J 3 6PL C 1 501 6 6PL 6PL . 
K 4 A1D5V C 1 502 2 A1D5V DRG . 
L 5 7PO C 1 503 2 7PO 7PO . 
M 3 6PL D 1 201 4 6PL 6PL . 
N 3 6PL D 1 202 5 6PL 6PL . 
#
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 C CAQ A1D5V . . . F 4 121.239 99.462 156.598 1 79.84 ? CAQ A1D5V 502 A 1 
HETATM 2 C CAR A1D5V . . . F 4 120.712 98.635 157.814 1 79.84 ? CAR A1D5V 502 A 1 
HETATM 3 C CAS A1D5V . . . F 4 123.486 100.43 155.61 1 79.84 ? CAS A1D5V 502 A 1 
HETATM 4 C CAT A1D5V . . . F 4 122.76 99.26 156.327 1 79.84 ? CAT A1D5V 502 A 1 
HETATM 5 C CAU A1D5V . . . F 4 120.028 97.295 157.435 1 79.84 ? CAU A1D5V 502 A 1 
HETATM 6 C CAV A1D5V . . . F 4 123.411 100.551 154.071 1 79.84 ? CAV A1D5V 502 A 1 
HETATM 7 C CAW A1D5V . . . F 4 118.534 97.477 157.177 1 79.84 ? CAW A1D5V 502 A 1 
HETATM 8 C CAX A1D5V . . . F 4 123.64 102.064 153.693 1 79.84 ? CAX A1D5V 502 A 1 
HETATM 9 C CAY A1D5V . . . F 4 124.906 100.603 156.11 1 79.84 ? CAY A1D5V 502 A 1 
HETATM 10 C CAZ A1D5V . . . F 4 122.788 102.696 152.674 1 79.84 ? CAZ A1D5V 502 A 1 
HETATM 11 C CBA A1D5V . . . F 4 120.676 96.603 156.242 1 79.84 ? CBA A1D5V 502 A 1 
HETATM 12 C CBB A1D5V . . . F 4 117.81 96.369 157.943 1 79.84 ? CBB A1D5V 502 A 1 
HETATM 13 C CBC A1D5V . . . F 4 123.179 104.176 152.362 1 79.84 ? CBC A1D5V 502 A 1 
HETATM 14 C CBD A1D5V . . . F 4 123.491 104.135 150.729 1 79.84 ? CBD A1D5V 502 A 1 
HETATM 15 C CBE A1D5V . . . F 4 117.006 95.495 156.986 1 79.84 ? CBE A1D5V 502 A 1 
HETATM 16 C CBF A1D5V . . . F 4 123.384 105.345 149.663 1 79.84 ? CBF A1D5V 502 A 1 
HETATM 17 C CBG A1D5V . . . F 4 122.018 106.118 149.523 1 79.84 ? CBG A1D5V 502 A 1 
HETATM 18 C CBH A1D5V . . . F 4 121.257 101.623 157.752 1 79.84 ? CBH A1D5V 502 A 1 
HETATM 19 C CBI A1D5V . . . F 4 121.31 98.041 160.052 1 79.84 ? CBI A1D5V 502 A 1 
HETATM 20 C CBJ A1D5V . . . F 4 121.799 106.813 148.135 1 79.84 ? CBJ A1D5V 502 A 1 
HETATM 21 C CBK A1D5V . . . F 4 121.239 103.103 157.615 1 79.84 ? CBK A1D5V 502 A 1 
HETATM 22 C CBL A1D5V . . . F 4 121.38 99.066 161.096 1 79.84 ? CBL A1D5V 502 A 1 
HETATM 23 C CBM A1D5V . . . F 4 121.664 108.404 148.023 1 79.84 ? CBM A1D5V 502 A 1 
HETATM 24 C CBN A1D5V . . . F 4 117.032 94.054 157.497 1 79.84 ? CBN A1D5V 502 A 1 
HETATM 25 C CBO A1D5V . . . F 4 121.343 103.77 158.982 1 79.84 ? CBO A1D5V 502 A 1 
HETATM 26 C CBP A1D5V . . . F 4 122.704 99.194 161.752 1 79.84 ? CBP A1D5V 502 A 1 
HETATM 27 C CBQ A1D5V . . . F 4 120.275 109.14 147.608 1 79.84 ? CBQ A1D5V 502 A 1 
HETATM 28 C CBR A1D5V . . . F 4 121.524 105.273 158.78 1 79.84 ? CBR A1D5V 502 A 1 
HETATM 29 C CBS A1D5V . . . F 4 123.329 97.804 161.724 1 79.84 ? CBS A1D5V 502 A 1 
HETATM 30 C CBT A1D5V . . . F 4 119.096 108.907 148.557 1 79.84 ? CBT A1D5V 502 A 1 
HETATM 31 C CBU A1D5V . . . F 4 120.062 103.522 159.782 1 79.84 ? CBU A1D5V 502 A 1 
HETATM 32 C CBV A1D5V . . . F 4 123.633 100.166 161.033 1 79.84 ? CBV A1D5V 502 A 1 
HETATM 33 C CBW A1D5V . . . F 4 122.644 105.756 159.598 1 79.84 ? CBW A1D5V 502 A 1 
HETATM 34 C CBX A1D5V . . . F 4 123.752 97.396 163.139 1 79.84 ? CBX A1D5V 502 A 1 
HETATM 35 N NAP A1D5V . . . F 4 119.949 108.678 146.252 1 79.84 ? NAP A1D5V 502 A 1 
HETATM 36 O OAA A1D5V . . . F 4 120.879 100.854 156.769 1 79.84 ? OAA A1D5V 502 A 1 
HETATM 37 O OAB A1D5V . . . F 4 121.753 98.387 158.782 1 79.84 ? OAB A1D5V 502 A 1 
HETATM 38 O OAC A1D5V . . . F 4 123.117 102.894 154.634 1 79.84 ? OAC A1D5V 502 A 1 
HETATM 39 O OAD A1D5V . . . F 4 121.879 107.038 150.556 1 79.84 ? OAD A1D5V 502 A 1 
HETATM 40 O OAE A1D5V . . . F 4 121.68 101.136 158.727 1 79.84 ? OAE A1D5V 502 A 1 
HETATM 41 O OAF A1D5V . . . F 4 120.71 97.018 160.328 1 79.84 ? OAF A1D5V 502 A 1 
HETATM 42 O OAG A1D5V . . . F 4 122.275 108.943 149.168 1 79.84 ? OAG A1D5V 502 A 1 
HETATM 43 O OAH A1D5V . . . F 4 119.783 102.329 159.94 1 79.84 ? OAH A1D5V 502 A 1 
HETATM 44 O OAI A1D5V . . . F 4 123.82 101.302 161.461 1 79.84 ? OAI A1D5V 502 A 1 
HETATM 45 O OAJ A1D5V . . . F 4 119.207 104.442 159.798 1 79.84 ? OAJ A1D5V 502 A 1 
HETATM 46 O OAK A1D5V . . . F 4 123.534 99.859 159.865 1 79.84 ? OAK A1D5V 502 A 1 
HETATM 47 O OAL A1D5V . . . F 4 123.347 106.59 159.033 1 79.84 ? OAL A1D5V 502 A 1 
HETATM 48 O OAM A1D5V . . . F 4 123.037 96.564 163.741 1 79.84 ? OAM A1D5V 502 A 1 
HETATM 49 O OAN A1D5V . . . F 4 122.84 105.236 160.716 1 79.84 ? OAN A1D5V 502 A 1 
HETATM 50 O OAO A1D5V . . . F 4 124.753 97.95 163.598 1 79.84 ? OAO A1D5V 502 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    49 
_model_server_stats.query_time_ms           348 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           50 
#