data_4PDM
#
_model_server_result.job_id            4BeT7ux-Yd0e8qGeiMpQyw 
_model_server_result.datetime_utc      '2024-11-12 20:40:32' 
_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          4pdm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":204}' 
#
_entry.id    4PDM 
#
_exptl.entry_id    4PDM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (4S)-2-METHYL-2,4-PENTANEDIOL 
_entity.pdbx_number_of_molecules    3 
_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            4PDM 
_cell.length_a            68.011 
_cell.length_b            68.011 
_cell.length_c            89.346 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PDM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 4' 
#
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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,L 1 1,2,3,4 
B,G,H,I,J,K,M 2 1,2,3,4 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 
3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 
4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 J N N 
? 3 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
metalc ? metalc1 A O THR 46 A THR 63 1_555 D RB RB . A RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? 
metalc ? metalc2 A O THR 46 A THR 63 1_555 D RB RB . A RB 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.04 ? 
metalc ? metalc3 A O THR 46 A THR 63 1_555 E RB RB . A RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? 
metalc ? metalc4 A OG1 THR 46 A THR 63 1_555 E RB RB . A RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? 
metalc ? metalc5 A O THR 46 A THR 63 1_555 E RB RB . A RB 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.937 ? 
metalc ? metalc6 A OG1 THR 46 A THR 63 1_555 E RB RB . A RB 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.909 ? 
metalc ? metalc7 A O VAL 47 A VAL 64 1_555 D RB RB . A RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? 
metalc ? metalc8 A O VAL 47 A VAL 64 1_555 D RB RB . A RB 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.827 ? 
metalc ? metalc9 A O GLY 48 A GLY 65 1_555 C RB RB . A RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? 
metalc ? metalc10 A O GLY 48 A GLY 65 1_555 C RB RB . A RB 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.875 ? 
metalc ? metalc11 A O TYR 49 A TYR 66 1_555 C RB RB . A RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.072 ? 
metalc ? metalc12 A O TYR 49 A TYR 66 1_555 C RB RB . A RB 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.072 ? 
metalc ? metalc13 B O THR 46 B THR 63 1_555 G RB RB . B RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? 
metalc ? metalc14 B OG1 THR 46 B THR 63 1_555 G RB RB . B RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc15 B O THR 46 B THR 63 1_555 G RB RB . B RB 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.941 ? 
metalc ? metalc16 B OG1 THR 46 B THR 63 1_555 G RB RB . B RB 201 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.896 ? 
metalc ? metalc17 B O THR 46 B THR 63 1_555 H RB RB . B RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.053 ? 
metalc ? metalc18 B O THR 46 B THR 63 1_555 H RB RB . B RB 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.053 ? 
metalc ? metalc19 B O VAL 47 B VAL 64 1_555 H RB RB . B RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? 
metalc ? metalc20 B O VAL 47 B VAL 64 1_555 H RB RB . B RB 202 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.891 ? 
metalc ? metalc21 B O GLY 48 B GLY 65 1_555 I RB RB . B RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? 
metalc ? metalc22 B O GLY 48 B GLY 65 1_555 I RB RB . B RB 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? 
metalc ? metalc23 B O TYR 49 B TYR 66 1_555 I RB RB . B RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? 
metalc ? metalc24 B O TYR 49 B TYR 66 1_555 I RB RB . B RB 203 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.99 ? 
#
_chem_comp.formula           'C6 H14 O2' 
_chem_comp.formula_weight    118.174 
_chem_comp.id                MPD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (4S)-2-METHYL-2,4-PENTANEDIOL 
_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
C1 C2 MPD sing 224 n n 
C1 H11 MPD sing 225 n n 
C1 H12 MPD sing 226 n n 
C1 H13 MPD sing 227 n n 
C2 O2 MPD sing 228 n n 
C2 CM MPD sing 229 n n 
C2 C3 MPD sing 230 n n 
O2 HO2 MPD sing 231 n n 
CM HM1 MPD sing 232 n n 
CM HM2 MPD sing 233 n n 
CM HM3 MPD sing 234 n n 
C3 C4 MPD sing 235 n n 
C3 H31 MPD sing 236 n n 
C3 H32 MPD sing 237 n n 
C4 O4 MPD sing 238 n n 
C4 C5 MPD sing 239 n n 
C4 H4 MPD sing 240 n n 
O4 HO4 MPD sing 241 n n 
C5 H51 MPD sing 242 n n 
C5 H52 MPD sing 243 n n 
C5 H53 MPD sing 244 n n 
#
_atom_sites.entry_id                     4PDM 
_atom_sites.fract_transf_matrix[1][1]    0.014704 
_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]    0.014704 
_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]    0.011192 
_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
C 2 RB A 1 201 1 RB RB . 
D 2 RB A 1 202 2 RB RB . 
E 2 RB A 1 203 3 RB RB . 
F 3 MPD A 1 204 4 MPD MPD . 
G 2 RB B 1 201 4 RB RB . 
H 2 RB B 1 202 5 RB RB . 
I 2 RB B 1 203 6 RB RB . 
J 3 MPD B 1 204 1 MPD MPD . 
K 3 MPD B 1 205 3 MPD MPD . 
L 4 HOH A 1 301 45 HOH HOH . 
L 4 HOH A 2 302 59 HOH HOH . 
L 4 HOH A 3 303 5 HOH HOH . 
L 4 HOH A 4 304 6 HOH HOH . 
L 4 HOH A 5 305 17 HOH HOH . 
L 4 HOH A 6 306 80 HOH HOH . 
L 4 HOH A 7 307 1 HOH HOH . 
L 4 HOH A 8 308 18 HOH HOH . 
L 4 HOH A 9 309 15 HOH HOH . 
L 4 HOH A 10 310 47 HOH HOH . 
L 4 HOH A 11 311 3 HOH HOH . 
L 4 HOH A 12 312 25 HOH HOH . 
L 4 HOH A 13 313 7 HOH HOH . 
L 4 HOH A 14 314 53 HOH HOH . 
L 4 HOH A 15 315 19 HOH HOH . 
L 4 HOH A 16 316 4 HOH HOH . 
L 4 HOH A 17 317 54 HOH HOH . 
L 4 HOH A 18 318 43 HOH HOH . 
L 4 HOH A 19 319 77 HOH HOH . 
L 4 HOH A 20 320 49 HOH HOH . 
L 4 HOH A 21 321 27 HOH HOH . 
L 4 HOH A 22 322 31 HOH HOH . 
L 4 HOH A 23 323 34 HOH HOH . 
L 4 HOH A 24 324 67 HOH HOH . 
L 4 HOH A 25 325 76 HOH HOH . 
L 4 HOH A 26 326 2 HOH HOH . 
L 4 HOH A 27 327 10 HOH HOH . 
L 4 HOH A 28 328 11 HOH HOH . 
L 4 HOH A 29 329 12 HOH HOH . 
L 4 HOH A 30 330 14 HOH HOH . 
L 4 HOH A 31 331 16 HOH HOH . 
L 4 HOH A 32 332 21 HOH HOH . 
L 4 HOH A 33 333 28 HOH HOH . 
L 4 HOH A 34 334 29 HOH HOH . 
L 4 HOH A 35 335 30 HOH HOH . 
L 4 HOH A 36 336 32 HOH HOH . 
L 4 HOH A 37 337 33 HOH HOH . 
L 4 HOH A 38 338 39 HOH HOH . 
L 4 HOH A 39 339 48 HOH HOH . 
L 4 HOH A 40 340 50 HOH HOH . 
L 4 HOH A 41 341 52 HOH HOH . 
L 4 HOH A 42 342 56 HOH HOH . 
L 4 HOH A 43 343 57 HOH HOH . 
L 4 HOH A 44 344 58 HOH HOH . 
L 4 HOH A 45 345 60 HOH HOH . 
L 4 HOH A 46 346 61 HOH HOH . 
L 4 HOH A 47 347 65 HOH HOH . 
L 4 HOH A 48 348 66 HOH HOH . 
L 4 HOH A 49 349 68 HOH HOH . 
L 4 HOH A 50 350 69 HOH HOH . 
L 4 HOH A 51 351 70 HOH HOH . 
L 4 HOH A 52 352 71 HOH HOH . 
L 4 HOH A 53 353 75 HOH HOH . 
L 4 HOH A 54 354 78 HOH HOH . 
L 4 HOH A 55 355 79 HOH HOH . 
M 4 HOH B 1 301 22 HOH HOH . 
M 4 HOH B 2 302 46 HOH HOH . 
M 4 HOH B 3 303 51 HOH HOH . 
M 4 HOH B 4 304 35 HOH HOH . 
M 4 HOH B 5 305 13 HOH HOH . 
M 4 HOH B 6 306 41 HOH HOH . 
M 4 HOH B 7 307 44 HOH HOH . 
M 4 HOH B 8 308 38 HOH HOH . 
M 4 HOH B 9 309 55 HOH HOH . 
M 4 HOH B 10 310 72 HOH HOH . 
M 4 HOH B 11 311 20 HOH HOH . 
M 4 HOH B 12 312 8 HOH HOH . 
M 4 HOH B 13 313 23 HOH HOH . 
M 4 HOH B 14 314 24 HOH HOH . 
M 4 HOH B 15 315 26 HOH HOH . 
M 4 HOH B 16 316 36 HOH HOH . 
M 4 HOH B 17 317 37 HOH HOH . 
M 4 HOH B 18 318 40 HOH HOH . 
M 4 HOH B 19 319 42 HOH HOH . 
M 4 HOH B 20 320 62 HOH HOH . 
M 4 HOH B 21 321 63 HOH HOH . 
M 4 HOH B 22 322 64 HOH HOH . 
M 4 HOH B 23 323 73 HOH HOH . 
M 4 HOH B 24 324 74 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 C C1 MPD . . . F 3 -13.877 -16.245 22.807 1 31.01 ? C1 MPD 204 A 1 
HETATM 2 C C2 MPD . . . F 3 -14.477 -14.872 23.09 1 37.65 ? C2 MPD 204 A 1 
HETATM 3 O O2 MPD . . . F 3 -14.924 -14.791 24.462 1 51.8 ? O2 MPD 204 A 1 
HETATM 4 C CM MPD . . . F 3 -13.366 -13.849 22.906 1 36.41 ? CM MPD 204 A 1 
HETATM 5 C C3 MPD . . . F 3 -15.657 -14.556 22.165 1 40.01 ? C3 MPD 204 A 1 
HETATM 6 C C4 MPD . . . F 3 -17.015 -15.113 22.607 1 37.68 ? C4 MPD 204 A 1 
HETATM 7 O O4 MPD . . . F 3 -17.981 -14.821 21.622 1 50.36 ? O4 MPD 204 A 1 
HETATM 8 C C5 MPD . . . F 3 -17.024 -16.622 22.764 1 31.42 ? C5 MPD 204 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           211 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           8 
#