data_4R8C
#
_model_server_result.job_id            '_ToBFjTQrNJqkWgD9SOdPg' 
_model_server_result.datetime_utc      '2025-07-03 23:28:24' 
_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          4r8c 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":204}' 
#
_entry.id    4R8C 
#
_exptl.entry_id    4R8C 
_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    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            4R8C 
_cell.length_a            67.305 
_cell.length_b            67.305 
_cell.length_c            84.294 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4R8C 
_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,G,H,I,J,K,U 1 1,2,3,4 
B,L,M,N,O,P,Q,R,S,T,V 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_575 -x,-y+2,z -1 0 0 0 -1 0 0 0 1 0 134.61 0 
3 'crystal symmetry operation' 3_665 -y+1,x+1,z 0 -1 0 1 0 0 0 0 1 67.305 67.305 0 
4 'crystal symmetry operation' 4_465 y-1,-x+1,z 0 1 0 -1 0 0 0 0 1 -67.305 67.305 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 O 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 C RB RB . A RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.615 ? 
metalc ? metalc2 A O THR 46 A THR 63 1_555 D RB RB . A RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? 
metalc ? metalc3 A OG1 THR 46 A THR 63 1_555 D RB RB . A RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.981 ? 
metalc ? metalc4 A O VAL 47 A VAL 64 1_555 C RB RB . A RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? 
metalc ? metalc5 A O VAL 47 A VAL 64 1_555 E RB RB . A RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? 
metalc ? metalc6 A O GLY 48 A GLY 65 1_555 E RB RB . A RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.03 ? 
metalc ? metalc7 B OG1 THR 46 B THR 63 1_555 M RB RB . B RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.862 ? 
metalc ? metalc8 B O THR 46 B THR 63 1_555 M RB RB . B RB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.874 ? 
metalc ? metalc9 B O THR 46 B THR 63 1_555 N RB RB . B RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? 
metalc ? metalc10 B O VAL 47 B VAL 64 1_555 L RB RB . B RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.082 ? 
metalc ? metalc11 B O VAL 47 B VAL 64 1_555 N RB RB . B RB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? 
metalc ? metalc12 B O GLY 48 B GLY 65 1_555 L RB RB . B RB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? 
#
_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                     4R8C 
_atom_sites.fract_transf_matrix[1][1]    0.014858 
_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]    0.014858 
_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]    0.011863 
_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 2 RB RB . 
D 2 RB A 1 202 3 RB RB . 
E 2 RB A 1 203 6 RB RB . 
F 3 MPD A 1 204 2 MPD MPD . 
G 4 GLY A 1 205 3 GLY GLY . 
H 4 GLY A 1 206 4 GLY GLY . 
I 4 GLY A 1 207 6 GLY GLY . 
J 4 GLY A 1 208 7 GLY GLY . 
K 4 GLY A 1 209 10 GLY GLY . 
L 2 RB B 1 201 1 RB RB . 
M 2 RB B 1 202 4 RB RB . 
N 2 RB B 1 203 5 RB RB . 
O 3 MPD B 1 204 1 MPD MPD . 
P 4 GLY B 1 205 1 GLY GLY . 
Q 4 GLY B 1 206 2 GLY GLY . 
R 4 GLY B 1 207 5 GLY GLY . 
S 4 GLY B 1 208 8 GLY GLY . 
T 4 GLY B 1 209 9 GLY GLY . 
U 5 HOH A 1 301 1 HOH HOH . 
U 5 HOH A 2 302 2 HOH HOH . 
U 5 HOH A 3 303 6 HOH HOH . 
U 5 HOH A 4 304 7 HOH HOH . 
U 5 HOH A 5 305 8 HOH HOH . 
U 5 HOH A 6 306 10 HOH HOH . 
U 5 HOH A 7 307 11 HOH HOH . 
U 5 HOH A 8 308 12 HOH HOH . 
U 5 HOH A 9 309 15 HOH HOH . 
U 5 HOH A 10 310 16 HOH HOH . 
U 5 HOH A 11 311 17 HOH HOH . 
U 5 HOH A 12 312 20 HOH HOH . 
U 5 HOH A 13 313 21 HOH HOH . 
U 5 HOH A 14 314 23 HOH HOH . 
U 5 HOH A 15 315 26 HOH HOH . 
V 5 HOH B 1 301 3 HOH HOH . 
V 5 HOH B 2 302 4 HOH HOH . 
V 5 HOH B 3 303 5 HOH HOH . 
V 5 HOH B 4 304 9 HOH HOH . 
V 5 HOH B 5 305 13 HOH HOH . 
V 5 HOH B 6 306 14 HOH HOH . 
V 5 HOH B 7 307 18 HOH HOH . 
V 5 HOH B 8 308 19 HOH HOH . 
V 5 HOH B 9 309 22 HOH HOH . 
V 5 HOH B 10 310 24 HOH HOH . 
V 5 HOH B 11 311 25 HOH HOH . 
V 5 HOH B 12 312 27 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 14.109 61.212 44.436 1 80.41 ? C1 MPD 204 A 1 
HETATM 2 C C2 MPD . . . F 3 14.385 62.393 43.512 1 79.32 ? C2 MPD 204 A 1 
HETATM 3 O O2 MPD . . . F 3 15.755 62.348 43.073 1 88.05 ? O2 MPD 204 A 1 
HETATM 4 C CM MPD . . . F 3 13.459 62.265 42.308 1 84.4 ? CM MPD 204 A 1 
HETATM 5 C C3 MPD . . . F 3 14.152 63.733 44.229 1 87.89 ? C3 MPD 204 A 1 
HETATM 6 C C4 MPD . . . F 3 14.617 65.014 43.49 1 81.72 ? C4 MPD 204 A 1 
HETATM 7 O O4 MPD . . . F 3 15.45 64.784 42.33 1 81.53 ? O4 MPD 204 A 1 
HETATM 8 C C5 MPD . . . F 3 13.441 65.898 43.049 1 86.52 ? C5 MPD 204 A 1 
#
_model_server_stats.io_time_ms              86 
_model_server_stats.parse_time_ms           37 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           354 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           8 
#