data_3DXJ
#
_model_server_result.job_id            i5rFIlQqkXsg6slLr2bOaA 
_model_server_result.datetime_utc      '2024-11-28 07:05:11' 
_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          3dxj 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":1120}' 
#
_entry.id    3DXJ 
#
_exptl.entry_id    3DXJ 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          8 
_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         120 
_cell.entry_id            3DXJ 
_cell.length_a            235.09 
_cell.length_b            235.09 
_cell.length_c            250.88 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3DXJ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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 hexameric 6 author_and_software_defined_assembly 1 
PISA hexameric 6 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,B,C,D,E,F,M,N,O,P,Q,R,S,T,U,AA,BA,CA,DA,EA 1 1 
G,H,I,J,K,L,V,W,X,Y,Z,FA,GA,HA 2 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
? 8 O N N 
? 8 P N N 
? 8 V 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 B OD2 ASP 168 B ASP 168 1_555 N MG MG . B MG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? 
metalc ? metalc2 N MG MG . B MG 701 1_555 D O LYS 840 D LYS 840 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? 
metalc ? metalc3 D SG CYS 58 D CYS 58 1_555 Q ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? 
metalc ? metalc4 D SG CYS 60 D CYS 60 1_555 Q ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? 
metalc ? metalc5 D SG CYS 73 D CYS 73 1_555 Q ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc6 D SG CYS 76 D CYS 76 1_555 Q ZN ZN . D ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.507 ? 
metalc ? metalc7 D SG CYS 1112 D CYS 1112 1_555 R ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.451 ? 
metalc ? metalc8 D SG CYS 1194 D CYS 1194 1_555 R ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? 
metalc ? metalc9 D SG CYS 1201 D CYS 1201 1_555 R ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? 
metalc ? metalc10 D SG CYS 1204 D CYS 1204 1_555 R ZN ZN . D ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.471 ? 
metalc ? metalc11 J SG CYS 58 N CYS 58 1_555 W ZN ZN . N ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? 
metalc ? metalc12 J SG CYS 60 N CYS 60 1_555 W ZN ZN . N ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? 
metalc ? metalc13 J SG CYS 73 N CYS 73 1_555 W ZN ZN . N ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.495 ? 
metalc ? metalc14 J SG CYS 76 N CYS 76 1_555 W ZN ZN . N ZN 1525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.406 ? 
metalc ? metalc15 J OD1 ASP 741 N ASP 741 1_555 Y MG MG . N MG 1527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc16 J OD2 ASP 743 N ASP 743 1_555 Y MG MG . N MG 1527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? 
metalc ? metalc17 J SG CYS 1112 N CYS 1112 1_555 X ZN ZN . N ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? 
metalc ? metalc18 J SG CYS 1194 N CYS 1194 1_555 X ZN ZN . N ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? 
metalc ? metalc19 J SG CYS 1201 N CYS 1201 1_555 X ZN ZN . N ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc20 J SG CYS 1204 N CYS 1204 1_555 X ZN ZN . N ZN 1526 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? 
#
_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 237 n n 
C1 H11 MPD sing 238 n n 
C1 H12 MPD sing 239 n n 
C1 H13 MPD sing 240 n n 
C2 O2 MPD sing 241 n n 
C2 CM MPD sing 242 n n 
C2 C3 MPD sing 243 n n 
O2 HO2 MPD sing 244 n n 
CM HM1 MPD sing 245 n n 
CM HM2 MPD sing 246 n n 
CM HM3 MPD sing 247 n n 
C3 C4 MPD sing 248 n n 
C3 H31 MPD sing 249 n n 
C3 H32 MPD sing 250 n n 
C4 O4 MPD sing 251 n n 
C4 C5 MPD sing 252 n n 
C4 H4 MPD sing 253 n n 
O4 HO4 MPD sing 254 n n 
C5 H51 MPD sing 255 n n 
C5 H52 MPD sing 256 n n 
C5 H53 MPD sing 257 n n 
#
_atom_sites.entry_id                     3DXJ 
_atom_sites.fract_transf_matrix[1][1]    0.004254 
_atom_sites.fract_transf_matrix[1][2]    0.002456 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.004912 
_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]    0.003986 
_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
M 6 PO4 A 1 316 316 PO4 PO4 . 
N 7 MG B 1 701 701 MG MG . 
O 8 MPD C 1 1120 1120 MPD MPD . 
P 8 MPD C 1 1121 1121 MPD MPD . 
Q 9 ZN D 1 1525 1525 ZN ZN . 
R 9 ZN D 1 1526 1526 ZN ZN . 
S 7 MG D 1 1527 1527 MG MG . 
T 6 PO4 D 1 1528 1528 PO4 PO4 . 
U 10 NE6 D 1 1529 1529 NE6 NE6 . 
V 8 MPD M 1 1120 1120 MPD MPD . 
W 9 ZN N 1 1525 1525 ZN ZN . 
X 9 ZN N 1 1526 1526 ZN ZN . 
Y 7 MG N 1 1527 1527 MG MG . 
Z 10 NE6 N 1 1528 1528 NE6 NE6 . 
AA 11 HOH A 1 317 317 HOH HOH . 
BA 11 HOH B 1 702 702 HOH HOH . 
CA 11 HOH C 1 1122 1122 HOH HOH . 
CA 11 HOH C 2 1123 1123 HOH HOH . 
CA 11 HOH C 3 1124 1124 HOH HOH . 
CA 11 HOH C 4 1125 1125 HOH HOH . 
CA 11 HOH C 5 1126 1126 HOH HOH . 
CA 11 HOH C 6 1127 1127 HOH HOH . 
CA 11 HOH C 7 1128 1128 HOH HOH . 
DA 11 HOH D 1 1530 1530 HOH HOH . 
DA 11 HOH D 2 1531 1531 HOH HOH . 
DA 11 HOH D 3 1532 1532 HOH HOH . 
DA 11 HOH D 4 1533 1533 HOH HOH . 
DA 11 HOH D 5 1534 1534 HOH HOH . 
DA 11 HOH D 6 1535 1535 HOH HOH . 
DA 11 HOH D 7 1536 1536 HOH HOH . 
DA 11 HOH D 8 1537 1537 HOH HOH . 
DA 11 HOH D 9 1538 1538 HOH HOH . 
DA 11 HOH D 10 1539 1539 HOH HOH . 
EA 11 HOH F 1 424 424 HOH HOH . 
FA 11 HOH M 1 1121 1121 HOH HOH . 
FA 11 HOH M 2 1122 1122 HOH HOH . 
FA 11 HOH M 3 1123 1123 HOH HOH . 
FA 11 HOH M 4 1124 1124 HOH HOH . 
FA 11 HOH M 5 1125 1125 HOH HOH . 
GA 11 HOH N 1 1529 1529 HOH HOH . 
GA 11 HOH N 2 1530 1530 HOH HOH . 
GA 11 HOH N 3 1531 1531 HOH HOH . 
GA 11 HOH N 4 1532 1532 HOH HOH . 
HA 11 HOH O 1 100 100 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 . . . O 8 -23.186 -0.968 5.454 1 56.55 ? C1 MPD 1120 C 1 
HETATM 2 C C2 MPD . . . O 8 -23.152 -2.459 5.521 1 57.77 ? C2 MPD 1120 C 1 
HETATM 3 O O2 MPD . . . O 8 -22.22 -2.749 6.387 1 56.37 ? O2 MPD 1120 C 1 
HETATM 4 C CM MPD . . . O 8 -24.417 -3.041 6.092 1 56.77 ? CM MPD 1120 C 1 
HETATM 5 C C3 MPD . . . O 8 -22.631 -3.073 4.27 1 57.47 ? C3 MPD 1120 C 1 
HETATM 6 C C4 MPD . . . O 8 -22.433 -2.265 3.022 1 55.49 ? C4 MPD 1120 C 1 
HETATM 7 O O4 MPD . . . O 8 -21.096 -2.001 2.825 1 51.74 ? O4 MPD 1120 C 1 
HETATM 8 C C5 MPD . . . O 8 -23.04 -3.116 1.929 1 55.24 ? C5 MPD 1120 C 1 
#
_model_server_stats.io_time_ms              126 
_model_server_stats.parse_time_ms           157 
_model_server_stats.create_model_time_ms    181 
_model_server_stats.query_time_ms           276 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           8 
#