data_5WJM
#
_model_server_result.job_id            DcivSDHV96onHg4gLoQWVg 
_model_server_result.datetime_utc      '2024-11-05 00:55:13' 
_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          5wjm 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":2009}' 
#
_entry.id    5WJM 
#
_exptl.entry_id    5WJM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              118.174 
_entity.id                          4 
_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            5WJM 
_cell.length_a            122.476 
_cell.length_b            122.476 
_cell.length_c            43.603 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5WJM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_and_software_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 
_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    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 I N N 
? 4 J 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 OD1 ASP 2 A ASP 1716 1_555 B CA CA . A CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.481 ? 
metalc ? metalc2 A O ASN 3 A ASN 1717 1_555 B CA CA . A CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc3 A OE1 GLU 19 A GLU 1733 1_555 C CA CA . A CA 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? 
metalc ? metalc4 A OE2 GLU 19 A GLU 1733 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? 
metalc ? metalc5 A OD1 ASP 33 A ASP 1747 1_555 B CA CA . A CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.936 ? 
metalc ? metalc6 A OD2 ASP 33 A ASP 1747 1_555 B CA CA . A CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? 
metalc ? metalc7 A OD2 ASP 35 A ASP 1749 1_555 B CA CA . A CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? 
metalc ? metalc8 A O ASN 39 A ASN 1753 1_555 B CA CA . A CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc9 A OD1 ASP 73 A ASP 1787 1_555 C CA CA . A CA 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? 
metalc ? metalc10 A OE2 GLU 75 A GLU 1789 1_555 C CA CA . A CA 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc11 A OE1 GLU 75 A GLU 1789 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? 
metalc ? metalc12 A OE2 GLU 75 A GLU 1789 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.165 ? 
metalc ? metalc13 A OD2 ASP 88 A ASP 1802 1_555 B CA CA . A CA 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? 
metalc ? metalc14 A OD1 ASP 106 A ASP 1820 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.15 ? 
metalc ? metalc15 A O ILE 107 A ILE 1821 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? 
metalc ? metalc16 A OD1 ASN 108 A ASN 1822 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc17 A OD2 ASP 109 A ASP 1823 1_555 C CA CA . A CA 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc18 A OD1 ASP 109 A ASP 1823 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.248 ? 
metalc ? metalc19 A O ASN 110 A ASN 1824 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.463 ? 
metalc ? metalc20 A OE2 GLU 125 A GLU 1839 1_555 F CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.554 ? 
metalc ? metalc21 A OE1 GLU 125 A GLU 1839 1_555 G CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc22 A OD1 ASP 140 A ASP 1854 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.384 ? 
metalc ? metalc23 A OD2 ASP 140 A ASP 1854 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.564 ? 
metalc ? metalc24 A OD1 ASP 142 A ASP 1856 1_555 D CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc25 A OD2 ASP 142 A ASP 1856 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc26 A O ASN 146 A ASN 1860 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? 
metalc ? metalc27 A OD1 ASP 178 A ASP 1892 1_555 G CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? 
metalc ? metalc28 A OE1 GLU 180 A GLU 1894 1_555 F CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? 
metalc ? metalc29 A OE2 GLU 180 A GLU 1894 1_555 G CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? 
metalc ? metalc30 A OD2 ASP 193 A ASP 1907 1_555 E CA CA . A CA 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? 
metalc ? metalc31 A OD1 ASP 204 A ASP 1918 1_555 H K K . A K 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.717 ? 
metalc ? metalc32 A OD2 ASP 204 A ASP 1918 1_555 H K K . A K 2007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? 
metalc ? metalc33 A OD1 ASP 214 A ASP 1928 1_555 F CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? 
metalc ? metalc34 A O GLU 215 A GLU 1929 1_555 F CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? 
metalc ? metalc35 A OD1 ASP 217 A ASP 1931 1_555 F CA CA . A CA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? 
metalc ? metalc36 A OD2 ASP 217 A ASP 1931 1_555 G CA CA . A CA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? 
#
_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                     5WJM 
_atom_sites.fract_transf_matrix[1][1]    0.008165 
_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]    0.008165 
_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]    0.022934 
_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
B 2 CA A 1 2001 1 CA CA . 
C 2 CA A 1 2002 2 CA CA . 
D 2 CA A 1 2003 3 CA CA . 
E 2 CA A 1 2004 4 CA CA . 
F 2 CA A 1 2005 5 CA CA . 
G 2 CA A 1 2006 6 CA CA . 
H 3 K A 1 2007 1 K K . 
I 4 MPD A 1 2008 1 MPD MPD . 
J 4 MPD A 1 2009 2 MPD MPD . 
K 5 HOH A 1 2101 19 HOH HOH . 
K 5 HOH A 2 2102 24 HOH HOH . 
K 5 HOH A 3 2103 38 HOH HOH . 
K 5 HOH A 4 2104 1 HOH HOH . 
K 5 HOH A 5 2105 31 HOH HOH . 
K 5 HOH A 6 2106 28 HOH HOH . 
K 5 HOH A 7 2107 8 HOH HOH . 
K 5 HOH A 8 2108 3 HOH HOH . 
K 5 HOH A 9 2109 40 HOH HOH . 
K 5 HOH A 10 2110 7 HOH HOH . 
K 5 HOH A 11 2111 4 HOH HOH . 
K 5 HOH A 12 2112 23 HOH HOH . 
K 5 HOH A 13 2113 25 HOH HOH . 
K 5 HOH A 14 2114 13 HOH HOH . 
K 5 HOH A 15 2115 32 HOH HOH . 
K 5 HOH A 16 2116 15 HOH HOH . 
K 5 HOH A 17 2117 2 HOH HOH . 
K 5 HOH A 18 2118 29 HOH HOH . 
K 5 HOH A 19 2119 17 HOH HOH . 
K 5 HOH A 20 2120 34 HOH HOH . 
K 5 HOH A 21 2121 33 HOH HOH . 
K 5 HOH A 22 2122 27 HOH HOH . 
K 5 HOH A 23 2123 16 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 . . . J 4 -6.533 -24.534 12.197 1 33.55 ? C1 MPD 2009 A 1 
HETATM 2 C C2 MPD . . . J 4 -5.204 -24.039 11.63 1 34.08 ? C2 MPD 2009 A 1 
HETATM 3 O O2 MPD . . . J 4 -4.797 -24.996 10.653 1 33.54 ? O2 MPD 2009 A 1 
HETATM 4 C CM MPD . . . J 4 -5.369 -22.68 10.947 1 34.1 ? CM MPD 2009 A 1 
HETATM 5 C C3 MPD . . . J 4 -4.145 -23.915 12.742 1 34.64 ? C3 MPD 2009 A 1 
HETATM 6 C C4 MPD . . . J 4 -3.116 -25.039 12.767 1 34.57 ? C4 MPD 2009 A 1 
HETATM 7 O O4 MPD . . . J 4 -2.496 -25.186 11.487 1 34.9 ? O4 MPD 2009 A 1 
HETATM 8 C C5 MPD . . . J 4 -2.033 -24.78 13.813 1 35.06 ? C5 MPD 2009 A 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           8 
#