data_4V0U
#
_model_server_result.job_id            xIHbk5QVDBTwDqGd8C2GoA 
_model_server_result.datetime_utc      '2025-09-11 21:23:13' 
_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          4v0u 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"DA","auth_seq_id":1376}' 
#
_entry.id    4V0U 
#
_exptl.entry_id    4V0U 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              395.513 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'LATRUNCULIN B' 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          91.03 
_cell.angle_gamma         90 
_cell.entry_id            4V0U 
_cell.length_a            103.91 
_cell.length_b            149.93 
_cell.length_c            318.72 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4V0U 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA dimeric 2 author_and_software_defined_assembly 4 
PISA dimeric 2 author_and_software_defined_assembly 5 
PISA monomeric 1 author_and_software_defined_assembly 6 
PISA monomeric 1 author_and_software_defined_assembly 7 
PISA monomeric 1 author_and_software_defined_assembly 8 
PISA monomeric 1 author_and_software_defined_assembly 9 
PISA monomeric 1 author_and_software_defined_assembly 10 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
J,K,BA,CA 1 1 
F,G,X,Y 2 1 
N,O,HA,IA 3 1 
H,I,Z,AA 4 1 
D,E,V,W 5 1 
A,P,Q 6 1 
B,R,S 7 1 
C,T,U 8 1 
L,DA,EA 9 1 
M,FA,GA 10 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 P N N 
? 4 R N N 
? 4 T N N 
? 4 DA 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
metalc ? metalc1 D OD2 ASP 64 D ASP 64 1_555 V MN MN . D MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? 
metalc ? metalc2 D NE2 HIS 66 D HIS 66 1_555 V MN MN . D MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? 
metalc ? metalc3 D OD2 ASP 92 D ASP 92 1_555 V MN MN . D MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? 
metalc ? metalc4 D OD2 ASP 92 D ASP 92 1_555 W MN MN . D MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc5 D NE2 HIS 173 D HIS 173 1_555 W MN MN . D MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc6 D ND1 HIS 248 D HIS 248 1_555 W MN MN . D MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc7 V MN MN . D MN 1301 1_555 W MN MN . D MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
metalc ? metalc8 F OD2 ASP 64 F ASP 64 1_555 X MN MN . F MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? 
metalc ? metalc9 F NE2 HIS 66 F HIS 66 1_555 X MN MN . F MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc10 F OD2 ASP 92 F ASP 92 1_555 X MN MN . F MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc11 F OD2 ASP 92 F ASP 92 1_555 Y MN MN . F MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? 
metalc ? metalc12 F NE2 HIS 173 F HIS 173 1_555 Y MN MN . F MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.274 ? 
metalc ? metalc13 F ND1 HIS 248 F HIS 248 1_555 Y MN MN . F MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc14 X MN MN . F MN 1301 1_555 Y MN MN . F MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
metalc ? metalc15 H OD2 ASP 64 H ASP 64 1_555 Z MN MN . H MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.953 ? 
metalc ? metalc16 H NE2 HIS 66 H HIS 66 1_555 Z MN MN . H MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? 
metalc ? metalc17 H OD2 ASP 92 H ASP 92 1_555 Z MN MN . H MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc18 H OD2 ASP 92 H ASP 92 1_555 AA MN MN . H MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc19 H NE2 HIS 173 H HIS 173 1_555 AA MN MN . H MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? 
metalc ? metalc20 H ND1 HIS 248 H HIS 248 1_555 AA MN MN . H MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? 
metalc ? metalc21 Z MN MN . H MN 1301 1_555 AA MN MN . H MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
metalc ? metalc22 J OD2 ASP 64 J ASP 64 1_555 BA MN MN . J MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.955 ? 
metalc ? metalc23 J NE2 HIS 66 J HIS 66 1_555 BA MN MN . J MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.16 ? 
metalc ? metalc24 J OD2 ASP 92 J ASP 92 1_555 BA MN MN . J MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
metalc ? metalc25 J OD2 ASP 92 J ASP 92 1_555 CA MN MN . J MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc26 J NE2 HIS 173 J HIS 173 1_555 CA MN MN . J MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? 
metalc ? metalc27 J ND1 HIS 248 J HIS 248 1_555 CA MN MN . J MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.326 ? 
metalc ? metalc28 BA MN MN . J MN 1301 1_555 CA MN MN . J MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
metalc ? metalc29 N OD2 ASP 64 N ASP 64 1_555 HA MN MN . N MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? 
metalc ? metalc30 N NE2 HIS 66 N HIS 66 1_555 HA MN MN . N MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? 
metalc ? metalc31 N OD2 ASP 92 N ASP 92 1_555 HA MN MN . N MN 1301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? 
metalc ? metalc32 N OD2 ASP 92 N ASP 92 1_555 IA MN MN . N MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? 
metalc ? metalc33 N NE2 HIS 173 N HIS 173 1_555 IA MN MN . N MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? 
metalc ? metalc34 N ND1 HIS 248 N HIS 248 1_555 IA MN MN . N MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? 
metalc ? metalc35 HA MN MN . N MN 1301 1_555 IA MN MN . N MN 1302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? 
#
_chem_comp.formula           'C20 H29 N O5 S' 
_chem_comp.formula_weight    395.513 
_chem_comp.id                LAB 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'LATRUNCULIN B' 
_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
O5 C18 LAB doub 220 n n 
C18 N1 LAB sing 221 n n 
C18 S1 LAB sing 222 n n 
N1 C16 LAB sing 223 n n 
N1 HN1 LAB sing 224 n n 
C16 C15 LAB sing 225 n n 
C16 C17 LAB sing 226 n n 
C16 H16 LAB sing 227 n n 
C17 S1 LAB sing 228 n n 
C17 H171 LAB sing 229 n n 
C17 H172 LAB sing 230 n n 
C15 O3 LAB sing 231 n n 
C15 C14 LAB sing 232 n n 
C15 O4 LAB sing 233 n n 
O4 HO4 LAB sing 234 n n 
C14 C13 LAB sing 235 n n 
C14 H141 LAB sing 236 n n 
C14 H142 LAB sing 237 n n 
C13 C12 LAB sing 238 n n 
C13 O2 LAB sing 239 n n 
C13 H13 LAB sing 240 n n 
O2 C1 LAB sing 241 n n 
C12 C11 LAB sing 242 n n 
C12 H121 LAB sing 243 n n 
C12 H122 LAB sing 244 n n 
C11 C10 LAB sing 245 n n 
C11 O3 LAB sing 246 n n 
C11 H11 LAB sing 247 n n 
C10 C9 LAB sing 248 n n 
C10 H101 LAB sing 249 n n 
C10 H102 LAB sing 250 n n 
C9 C8 LAB sing 251 n n 
C9 H91 LAB sing 252 n n 
C9 H92 LAB sing 253 n n 
C8 C7 LAB sing 254 n n 
C8 C20 LAB sing 255 n n 
C8 H8 LAB sing 256 n n 
C20 H201 LAB sing 257 n n 
C20 H202 LAB sing 258 n n 
C20 H203 LAB sing 259 n n 
C7 C6 LAB doub 260 z n 
C7 H7 LAB sing 261 n n 
C6 C5 LAB sing 262 n n 
C6 H6 LAB sing 263 n n 
C5 C4 LAB sing 264 n n 
C5 H51 LAB sing 265 n n 
C5 H52 LAB sing 266 n n 
C4 C3 LAB sing 267 n n 
C4 H41 LAB sing 268 n n 
C4 H42 LAB sing 269 n n 
C3 C2 LAB doub 270 z n 
C3 C19 LAB sing 271 n n 
C19 H191 LAB sing 272 n n 
C19 H192 LAB sing 273 n n 
C19 H193 LAB sing 274 n n 
C2 C1 LAB sing 275 n n 
C2 H2 LAB sing 276 n n 
C1 O1 LAB doub 277 n n 
#
_atom_sites.entry_id                     4V0U 
_atom_sites.fract_transf_matrix[1][1]    0.009624 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000173 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00667 
_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]    0.003138 
_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
P 4 LAB A 1 1376 1376 LAB LAB . 
Q 5 ATP A 1 1377 1377 ATP ATP . 
R 4 LAB B 1 1376 1376 LAB LAB . 
S 5 ATP B 1 1377 1377 ATP ATP . 
T 4 LAB C 1 1376 1376 LAB LAB . 
U 5 ATP C 1 1377 1377 ATP ATP . 
V 6 MN D 1 1301 1301 MN MN . 
W 6 MN D 1 1302 1302 MN MN . 
X 6 MN F 1 1301 1301 MN MN . 
Y 6 MN F 1 1302 1302 MN MN . 
Z 6 MN H 1 1301 1301 MN MN . 
AA 6 MN H 1 1302 1302 MN MN . 
BA 6 MN J 1 1301 1301 MN MN . 
CA 6 MN J 1 1302 1302 MN MN . 
DA 4 LAB L 1 1376 1376 LAB LAB . 
EA 5 ATP L 1 1377 1377 ATP ATP . 
FA 4 LAB M 1 1376 1376 LAB LAB . 
GA 5 ATP M 1 1377 1377 ATP ATP . 
HA 6 MN N 1 1301 1301 MN MN . 
IA 6 MN N 1 1302 1302 MN MN . 
#
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 O O5 LAB . . . DA 4 40.984 -43.283 9.127 1 325.21 ? O5 LAB 1376 L 1 
HETATM 2 C C18 LAB . . . DA 4 40.516 -42.044 9.372 1 329.58 ? C18 LAB 1376 L 1 
HETATM 3 N N1 LAB . . . DA 4 39.507 -41.759 8.28 1 327.94 ? N1 LAB 1376 L 1 
HETATM 4 C C16 LAB . . . DA 4 39.6 -40.248 7.895 1 330.23 ? C16 LAB 1376 L 1 
HETATM 5 C C17 LAB . . . DA 4 40.597 -39.611 8.951 1 334.06 ? C17 LAB 1376 L 1 
HETATM 6 S S1 LAB . . . DA 4 41.6 -40.766 9.55 1 332.04 ? S1 LAB 1376 L 1 
HETATM 7 C C15 LAB . . . DA 4 39.945 -39.997 6.443 1 325.54 ? C15 LAB 1376 L 1 
HETATM 8 O O4 LAB . . . DA 4 41.313 -40.151 6.314 1 322.86 ? O4 LAB 1376 L 1 
HETATM 9 C C14 LAB . . . DA 4 39.252 -40.949 5.489 1 321.4 ? C14 LAB 1376 L 1 
HETATM 10 C C13 LAB . . . DA 4 39.126 -40.496 4.172 1 318.79 ? C13 LAB 1376 L 1 
HETATM 11 O O2 LAB . . . DA 4 40.407 -40.612 3.466 1 314.55 ? O2 LAB 1376 L 1 
HETATM 12 C C12 LAB . . . DA 4 38.729 -39.088 4.048 1 322.37 ? C12 LAB 1376 L 1 
HETATM 13 C C11 LAB . . . DA 4 39.674 -38.296 4.843 1 325.02 ? C11 LAB 1376 L 1 
HETATM 14 O O3 LAB . . . DA 4 39.606 -38.641 6.201 1 328.59 ? O3 LAB 1376 L 1 
HETATM 15 C C10 LAB . . . DA 4 39.502 -36.79 4.729 1 328.64 ? C10 LAB 1376 L 1 
HETATM 16 C C9 LAB . . . DA 4 40.671 -35.964 5.28 1 330.55 ? C9 LAB 1376 L 1 
HETATM 17 C C8 LAB . . . DA 4 42.052 -36.176 4.7 1 326.1 ? C8 LAB 1376 L 1 
HETATM 18 C C20 LAB . . . DA 4 43.015 -35.171 5.287 1 329.23 ? C20 LAB 1376 L 1 
HETATM 19 C C7 LAB . . . DA 4 41.968 -36.026 3.188 1 321.82 ? C7 LAB 1376 L 1 
HETATM 20 C C6 LAB . . . DA 4 42.504 -36.931 2.269 1 316.32 ? C6 LAB 1376 L 1 
HETATM 21 C C5 LAB . . . DA 4 42.788 -38.388 2.544 1 313.58 ? C5 LAB 1376 L 1 
HETATM 22 C C4 LAB . . . DA 4 42.159 -39.3 1.518 1 309.66 ? C4 LAB 1376 L 1 
HETATM 23 C C3 LAB . . . DA 4 42.642 -40.735 1.315 1 305.68 ? C3 LAB 1376 L 1 
HETATM 24 C C19 LAB . . . DA 4 44.151 -40.79 1.046 1 303.34 ? C19 LAB 1376 L 1 
HETATM 25 C C2 LAB . . . DA 4 42.227 -41.84 2.297 1 306.51 ? C2 LAB 1376 L 1 
HETATM 26 C C1 LAB . . . DA 4 40.919 -41.817 3.044 1 310.14 ? C1 LAB 1376 L 1 
HETATM 27 O O1 LAB . . . DA 4 40.339 -42.866 3.311 1 309.47 ? O1 LAB 1376 L 1 
#
_model_server_stats.io_time_ms              60 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           319 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           27 
#