data_3TY9
#
_model_server_result.job_id            7enmt-TwhjZgRUF0V25_mA 
_model_server_result.datetime_utc      '2025-04-04 14:30:07' 
_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          3ty9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":907}' 
#
_entry.id    3TY9 
#
_exptl.entry_id    3TY9 
_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    10 
_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            3TY9 
_cell.length_a            95.5 
_cell.length_b            132.76 
_cell.length_c            162.77 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3TY9 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 dimeric 2 software_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 software_defined_assembly 3 
PISA dimeric 2 software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,G,H,I,J,K,L,DA 1 1 
C,S,T,U,V,W,FA 1 2 
A,B,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,DA,EA 2 1 
B,M,N,O,P,Q,R,EA 3 1 
D,X,Y,Z,AA,BA,CA,GA 3 3 
C,D,S,T,U,V,W,X,Y,Z,AA,BA,CA,FA,GA 4 1 
#
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' 3_655 -x+1,y+1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 95.5 66.38 81.385 
3 'crystal symmetry operation' 3_545 -x,y-1/2,-z+1/2 -1 0 0 0 1 0 0 0 -1 0 -66.38 81.385 
#
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 G N N 
? 3 H N N 
? 3 N N N 
? 3 T N N 
? 3 U N N 
? 3 V N N 
? 3 Y N N 
? 3 Z N N 
? 3 AA 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
covale ? covale1 A NZ LYS 54 A LYS 531 1_555 E P AMP . A AMP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.504 ? 
covale ? covale2 B NZ LYS 54 B LYS 531 1_555 M P AMP . B AMP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.504 ? 
covale ? covale3 C NZ LYS 54 C LYS 531 1_555 S P AMP . C AMP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? 
covale ? covale4 D NZ LYS 54 D LYS 531 1_555 X P AMP . D AMP 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.501 ? 
metalc ? metalc1 A O THR 254 A THR 731 1_555 L MG MG . A MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? 
metalc ? metalc2 A O ASP 257 A ASP 734 1_555 L MG MG . A MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? 
metalc ? metalc3 A O ILE 260 A ILE 737 1_555 L MG MG . A MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.868 ? 
metalc ? metalc4 B O THR 254 B THR 731 1_555 R MG MG . B MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.732 ? 
metalc ? metalc5 B O ASP 257 B ASP 734 1_555 R MG MG . B MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? 
metalc ? metalc6 B O ILE 260 B ILE 737 1_555 R MG MG . B MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? 
metalc ? metalc7 C O THR 254 C THR 731 1_555 W MG MG . C MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.815 ? 
metalc ? metalc8 C O ASP 257 C ASP 734 1_555 W MG MG . C MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.59 ? 
metalc ? metalc9 C O ILE 260 C ILE 737 1_555 W MG MG . C MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? 
metalc ? metalc10 D O THR 254 D THR 731 1_555 CA MG MG . D MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? 
metalc ? metalc11 D O ASP 257 D ASP 734 1_555 CA MG MG . D MG 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? 
#
_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 289 n n 
C1 H11 MPD sing 290 n n 
C1 H12 MPD sing 291 n n 
C1 H13 MPD sing 292 n n 
C2 O2 MPD sing 293 n n 
C2 CM MPD sing 294 n n 
C2 C3 MPD sing 295 n n 
O2 HO2 MPD sing 296 n n 
CM HM1 MPD sing 297 n n 
CM HM2 MPD sing 298 n n 
CM HM3 MPD sing 299 n n 
C3 C4 MPD sing 300 n n 
C3 H31 MPD sing 301 n n 
C3 H32 MPD sing 302 n n 
C4 O4 MPD sing 303 n n 
C4 C5 MPD sing 304 n n 
C4 H4 MPD sing 305 n n 
O4 HO4 MPD sing 306 n n 
C5 H51 MPD sing 307 n n 
C5 H52 MPD sing 308 n n 
C5 H53 MPD sing 309 n n 
#
_atom_sites.entry_id                     3TY9 
_atom_sites.fract_transf_matrix[1][1]    0.010471 
_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]    0.007532 
_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]    0.006144 
_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
E 2 AMP A 1 900 900 AMP AMP . 
F 3 MPD A 1 905 905 MPD MPD . 
G 3 MPD A 1 906 906 MPD MPD . 
H 3 MPD A 1 907 907 MPD MPD . 
I 4 MRD A 1 908 908 MRD MPD . 
J 4 MRD A 1 909 909 MRD MPD . 
K 5 GOL A 1 910 910 GOL GOL . 
L 6 MG A 1 1000 1000 MG MG . 
M 2 AMP B 1 900 900 AMP AMP . 
N 3 MPD B 1 905 905 MPD MPD . 
O 4 MRD B 1 906 906 MRD MPD . 
P 4 MRD B 1 907 907 MRD MPD . 
Q 4 MRD B 1 908 908 MRD MPD . 
R 6 MG B 1 1000 1000 MG MG . 
S 2 AMP C 1 900 900 AMP AMP . 
T 3 MPD C 1 905 905 MPD MPD . 
U 3 MPD C 1 906 906 MPD MPD . 
V 3 MPD C 1 907 907 MPD MPD . 
W 6 MG C 1 1000 1000 MG MG . 
X 2 AMP D 1 900 900 AMP AMP . 
Y 3 MPD D 1 905 905 MPD MPD . 
Z 3 MPD D 1 906 906 MPD MPD . 
AA 3 MPD D 1 907 907 MPD MPD . 
BA 4 MRD D 1 908 908 MRD MPD . 
CA 6 MG D 1 1000 1000 MG MG . 
DA 7 HOH A 1 1 1 HOH HOH . 
DA 7 HOH A 2 2 2 HOH HOH . 
DA 7 HOH A 3 3 3 HOH HOH . 
DA 7 HOH A 4 11 11 HOH HOH . 
DA 7 HOH A 5 14 14 HOH HOH . 
DA 7 HOH A 6 15 15 HOH HOH . 
DA 7 HOH A 7 22 22 HOH HOH . 
DA 7 HOH A 8 25 25 HOH HOH . 
DA 7 HOH A 9 26 26 HOH HOH . 
DA 7 HOH A 10 27 27 HOH HOH . 
DA 7 HOH A 11 28 28 HOH HOH . 
DA 7 HOH A 12 29 29 HOH HOH . 
DA 7 HOH A 13 32 32 HOH HOH . 
DA 7 HOH A 14 35 35 HOH HOH . 
DA 7 HOH A 15 36 36 HOH HOH . 
DA 7 HOH A 16 38 38 HOH HOH . 
DA 7 HOH A 17 40 40 HOH HOH . 
DA 7 HOH A 18 41 41 HOH HOH . 
DA 7 HOH A 19 43 43 HOH HOH . 
DA 7 HOH A 20 44 44 HOH HOH . 
DA 7 HOH A 21 45 45 HOH HOH . 
DA 7 HOH A 22 52 52 HOH HOH . 
EA 7 HOH B 1 10 10 HOH HOH . 
EA 7 HOH B 2 12 12 HOH HOH . 
EA 7 HOH B 3 18 18 HOH HOH . 
EA 7 HOH B 4 24 24 HOH HOH . 
EA 7 HOH B 5 30 30 HOH HOH . 
EA 7 HOH B 6 31 31 HOH HOH . 
EA 7 HOH B 7 39 39 HOH HOH . 
EA 7 HOH B 8 48 48 HOH HOH . 
FA 7 HOH C 1 4 4 HOH HOH . 
FA 7 HOH C 2 5 5 HOH HOH . 
FA 7 HOH C 3 6 6 HOH HOH . 
FA 7 HOH C 4 8 8 HOH HOH . 
FA 7 HOH C 5 16 16 HOH HOH . 
FA 7 HOH C 6 17 17 HOH HOH . 
FA 7 HOH C 7 19 19 HOH HOH . 
FA 7 HOH C 8 20 20 HOH HOH . 
FA 7 HOH C 9 21 21 HOH HOH . 
FA 7 HOH C 10 42 42 HOH HOH . 
FA 7 HOH C 11 46 46 HOH HOH . 
FA 7 HOH C 12 47 47 HOH HOH . 
FA 7 HOH C 13 49 49 HOH HOH . 
GA 7 HOH D 1 7 7 HOH HOH . 
GA 7 HOH D 2 9 9 HOH HOH . 
GA 7 HOH D 3 13 13 HOH HOH . 
GA 7 HOH D 4 23 23 HOH HOH . 
GA 7 HOH D 5 33 33 HOH HOH . 
GA 7 HOH D 6 34 34 HOH HOH . 
GA 7 HOH D 7 37 37 HOH HOH . 
GA 7 HOH D 8 50 50 HOH HOH . 
GA 7 HOH D 9 51 51 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 . . . H 3 5.207 9.712 5.105 1 93.73 ? C1 MPD 907 A 1 
HETATM 2 C C2 MPD . . . H 3 5.767 10.365 3.84 1 99.16 ? C2 MPD 907 A 1 
HETATM 3 O O2 MPD . . . H 3 6.419 9.368 3 1 85.71 ? O2 MPD 907 A 1 
HETATM 4 C CM MPD . . . H 3 4.623 10.978 3.035 1 94.69 ? CM MPD 907 A 1 
HETATM 5 C C3 MPD . . . H 3 6.785 11.441 4.236 1 97.85 ? C3 MPD 907 A 1 
HETATM 6 C C4 MPD . . . H 3 8.198 10.88 4.436 1 96.79 ? C4 MPD 907 A 1 
HETATM 7 O O4 MPD . . . H 3 9.167 11.824 4.001 1 76.66 ? O4 MPD 907 A 1 
HETATM 8 C C5 MPD . . . H 3 8.44 10.467 5.895 1 90.99 ? C5 MPD 907 A 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           291 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           8 
#