data_2J3N
#
_model_server_result.job_id            112-EevTXuvk7iWVpSPX0w 
_model_server_result.datetime_utc      '2025-06-22 22:42:34' 
_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          2j3n 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":701}' 
#
_entry.id    2J3N 
#
_exptl.entry_id    2J3N 
_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    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          112.46 
_cell.angle_gamma         90 
_cell.entry_id            2J3N 
_cell.length_a            144.63 
_cell.length_b            90.64 
_cell.length_c            166.6 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2J3N 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1 21 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
PQS dimeric 2 author_and_software_defined_assembly 1 
PQS dimeric 2 author_and_software_defined_assembly 2 
PQS dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,G,H,I,J,K,L,M,X,Y 1 1 
C,D,N,O,P,Q,R,Z,AA 2 1 
E,F,S,T,U,V,W,BA,CA 3 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 L N N 
? 4 M N N 
? 4 R N N 
? 4 W 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
disulf ? disulf1 A SG CYS 79 A CYS 59 1_555 A SG CYS 84 A CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
disulf ? disulf2 B SG CYS 79 B CYS 59 1_555 B SG CYS 84 B CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf3 C SG CYS 79 C CYS 59 1_555 C SG CYS 84 C CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? 
disulf ? disulf4 D SG CYS 79 D CYS 59 1_555 D SG CYS 84 D CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 E SG CYS 79 E CYS 59 1_555 E SG CYS 84 E CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf6 E SG CYS 517 E CYS 497 1_555 E SG CYS 518 E CYS 498 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf7 F SG CYS 79 F CYS 59 1_555 F SG CYS 84 F CYS 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
#
_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 328 n n 
C1 H11 MPD sing 329 n n 
C1 H12 MPD sing 330 n n 
C1 H13 MPD sing 331 n n 
C2 O2 MPD sing 332 n n 
C2 CM MPD sing 333 n n 
C2 C3 MPD sing 334 n n 
O2 HO2 MPD sing 335 n n 
CM HM1 MPD sing 336 n n 
CM HM2 MPD sing 337 n n 
CM HM3 MPD sing 338 n n 
C3 C4 MPD sing 339 n n 
C3 H31 MPD sing 340 n n 
C3 H32 MPD sing 341 n n 
C4 O4 MPD sing 342 n n 
C4 C5 MPD sing 343 n n 
C4 H4 MPD sing 344 n n 
O4 HO4 MPD sing 345 n n 
C5 H51 MPD sing 346 n n 
C5 H52 MPD sing 347 n n 
C5 H53 MPD sing 348 n n 
#
_atom_sites.entry_id                     2J3N 
_atom_sites.fract_transf_matrix[1][1]    0.006914 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002858 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011033 
_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]    0.006495 
_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
G 2 FAD A 1 600 600 FAD FAD . 
H 3 NAP A 1 601 601 NAP NAP . 
I 4 MPD A 1 701 701 MPD MPD . 
J 2 FAD B 1 600 600 FAD FAD . 
K 3 NAP B 1 601 601 NAP NAP . 
L 4 MPD B 1 700 700 MPD MPD . 
M 4 MPD B 1 701 701 MPD MPD . 
N 2 FAD C 1 600 600 FAD FAD . 
O 3 NAP C 1 601 601 NAP NAP . 
P 2 FAD D 1 600 600 FAD FAD . 
Q 3 NAP D 1 601 601 NAP NAP . 
R 4 MPD D 1 700 700 MPD MPD . 
S 2 FAD E 1 600 600 FAD FAD . 
T 3 NAP E 1 601 601 NAP NAP . 
U 2 FAD F 1 600 600 FAD FAD . 
V 3 NAP F 1 601 601 NAP NAP . 
W 4 MPD F 1 700 700 MPD MPD . 
X 5 HOH A 1 2001 2001 HOH HOH . 
X 5 HOH A 2 2002 2002 HOH HOH . 
X 5 HOH A 3 2003 2003 HOH HOH . 
X 5 HOH A 4 2004 2004 HOH HOH . 
X 5 HOH A 5 2005 2005 HOH HOH . 
X 5 HOH A 6 2006 2006 HOH HOH . 
X 5 HOH A 7 2007 2007 HOH HOH . 
X 5 HOH A 8 2008 2008 HOH HOH . 
X 5 HOH A 9 2009 2009 HOH HOH . 
Y 5 HOH B 1 2001 2001 HOH HOH . 
Y 5 HOH B 2 2002 2002 HOH HOH . 
Y 5 HOH B 3 2003 2003 HOH HOH . 
Y 5 HOH B 4 2004 2004 HOH HOH . 
Y 5 HOH B 5 2005 2005 HOH HOH . 
Y 5 HOH B 6 2006 2006 HOH HOH . 
Y 5 HOH B 7 2007 2007 HOH HOH . 
Y 5 HOH B 8 2008 2008 HOH HOH . 
Y 5 HOH B 9 2009 2009 HOH HOH . 
Z 5 HOH C 1 2001 2001 HOH HOH . 
Z 5 HOH C 2 2002 2002 HOH HOH . 
Z 5 HOH C 3 2003 2003 HOH HOH . 
Z 5 HOH C 4 2004 2004 HOH HOH . 
Z 5 HOH C 5 2005 2005 HOH HOH . 
Z 5 HOH C 6 2006 2006 HOH HOH . 
Z 5 HOH C 7 2007 2007 HOH HOH . 
AA 5 HOH D 1 2001 2001 HOH HOH . 
AA 5 HOH D 2 2002 2002 HOH HOH . 
AA 5 HOH D 3 2003 2003 HOH HOH . 
AA 5 HOH D 4 2004 2004 HOH HOH . 
AA 5 HOH D 5 2005 2005 HOH HOH . 
AA 5 HOH D 6 2006 2006 HOH HOH . 
AA 5 HOH D 7 2007 2007 HOH HOH . 
AA 5 HOH D 8 2008 2008 HOH HOH . 
BA 5 HOH E 1 2001 2001 HOH HOH . 
BA 5 HOH E 2 2002 2002 HOH HOH . 
BA 5 HOH E 3 2003 2003 HOH HOH . 
BA 5 HOH E 4 2004 2004 HOH HOH . 
CA 5 HOH F 1 2001 2001 HOH HOH . 
CA 5 HOH F 2 2002 2002 HOH HOH . 
CA 5 HOH F 3 2003 2003 HOH HOH . 
CA 5 HOH F 4 2004 2004 HOH HOH . 
CA 5 HOH F 5 2005 2005 HOH HOH . 
CA 5 HOH F 6 2006 2006 HOH HOH . 
CA 5 HOH F 7 2007 2007 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 . . . I 4 -96.769 100.984 34.111 1 79.35 ? C1 MPD 701 A 1 
HETATM 2 C C2 MPD . . . I 4 -95.97 99.953 34.908 1 79.05 ? C2 MPD 701 A 1 
HETATM 3 O O2 MPD . . . I 4 -95.049 100.628 35.769 1 79.18 ? O2 MPD 701 A 1 
HETATM 4 C CM MPD . . . I 4 -96.929 99.1 35.736 1 77.47 ? CM MPD 701 A 1 
HETATM 5 C C3 MPD . . . I 4 -95.165 99.083 33.936 1 79.17 ? C3 MPD 701 A 1 
HETATM 6 C C4 MPD . . . I 4 -94.304 98.07 34.698 1 78.55 ? C4 MPD 701 A 1 
HETATM 7 O O4 MPD . . . I 4 -95.146 97.068 35.267 1 78.54 ? O4 MPD 701 A 1 
HETATM 8 C C5 MPD . . . I 4 -93.261 97.44 33.775 1 76.88 ? C5 MPD 701 A 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           330 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           8 
#