data_5XIT
#
_model_server_result.job_id            nJWK77zvzK4MVw23VPfYPg 
_model_server_result.datetime_utc      '2024-12-04 21:55:27' 
_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          5xit 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":202}' 
#
_entry.id    5XIT 
#
_exptl.entry_id    5XIT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         73.49 
_cell.angle_beta          69.69 
_cell.angle_gamma         73.82 
_cell.entry_id            5XIT 
_cell.length_a            45.372 
_cell.length_b            50.019 
_cell.length_c            64.407 
_cell.Z_PDB               2 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5XIT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,G,L,M,N,O,R,S 1 1 
B,C,F,H,I,J,K,P,Q,T 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
? 4 G N N 
? 4 K N N 
? 4 L N N 
? 4 M N N 
? 4 N 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 H PR PR . E PR 201 1_555 P O HOH . E HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? 
metalc ? metalc2 H PR PR . E PR 201 1_555 P O HOH . E HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.099 ? 
metalc ? metalc3 H PR PR . E PR 201 1_555 Q O HOH . H HOH 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? 
metalc ? metalc4 H PR PR . E PR 201 1_555 R O HOH . A HOH 314 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? 
metalc ? metalc5 H PR PR . E PR 201 1_555 R O HOH . A HOH 318 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 3.255 ? 
metalc ? metalc6 H PR PR . E PR 201 1_555 R O HOH . A HOH 319 1_455 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? 
metalc ? metalc7 J PR PR . E PR 203 1_655 D NH2 ARG 10 A ARG 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.152 ? 
metalc ? metalc8 J PR PR . E PR 203 1_655 D NE ARG 11 A ARG 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.495 ? 
metalc ? metalc9 J PR PR . E PR 203 1_655 D NH2 ARG 11 A ARG 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.079 ? 
#
_chem_comp.formula           'C3 H8 O3' 
_chem_comp.formula_weight    92.094 
_chem_comp.id                GOL 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              GLYCEROL 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     GLYCERIN;PROPANE-1,2,3-TRIOL 
#
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 O1 GOL sing 116 n n 
C1 C2 GOL sing 117 n n 
C1 H11 GOL sing 118 n n 
C1 H12 GOL sing 119 n n 
O1 HO1 GOL sing 120 n n 
C2 O2 GOL sing 121 n n 
C2 C3 GOL sing 122 n n 
C2 H2 GOL sing 123 n n 
O2 HO2 GOL sing 124 n n 
C3 O3 GOL sing 125 n n 
C3 H31 GOL sing 126 n n 
C3 H32 GOL sing 127 n n 
O3 HO3 GOL sing 128 n n 
#
_atom_sites.entry_id                     5XIT 
_atom_sites.fract_transf_matrix[1][1]    0.02204 
_atom_sites.fract_transf_matrix[1][2]    -0.006396 
_atom_sites.fract_transf_matrix[1][3]    -0.006979 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020817 
_atom_sites.fract_transf_matrix[2][3]    -0.004429 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.016926 
_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 4 GOL D 1 101 3 GOL GOL . 
H 5 PR E 1 201 1 PR PR . 
I 5 PR E 1 202 2 PR PR . 
J 5 PR E 1 203 3 PR PR . 
K 4 GOL E 1 204 6 GOL GOL . 
L 4 GOL A 1 201 4 GOL GOL . 
M 4 GOL A 1 202 5 GOL GOL . 
N 4 GOL A 1 203 7 GOL GOL . 
O 6 HOH D 1 201 32 HOH HOH . 
O 6 HOH D 2 202 29 HOH HOH . 
O 6 HOH D 3 203 15 HOH HOH . 
O 6 HOH D 4 204 56 HOH HOH . 
O 6 HOH D 5 205 2 HOH HOH . 
P 6 HOH E 1 301 33 HOH HOH . 
P 6 HOH E 2 302 47 HOH HOH . 
P 6 HOH E 3 303 6 HOH HOH . 
P 6 HOH E 4 304 23 HOH HOH . 
P 6 HOH E 5 305 39 HOH HOH . 
P 6 HOH E 6 306 19 HOH HOH . 
P 6 HOH E 7 307 54 HOH HOH . 
P 6 HOH E 8 308 31 HOH HOH . 
Q 6 HOH H 1 101 10 HOH HOH . 
Q 6 HOH H 2 102 21 HOH HOH . 
Q 6 HOH H 3 103 22 HOH HOH . 
Q 6 HOH H 4 104 18 HOH HOH . 
R 6 HOH A 1 301 46 HOH HOH . 
R 6 HOH A 2 302 25 HOH HOH . 
R 6 HOH A 3 303 26 HOH HOH . 
R 6 HOH A 4 304 20 HOH HOH . 
R 6 HOH A 5 305 7 HOH HOH . 
R 6 HOH A 6 306 55 HOH HOH . 
R 6 HOH A 7 307 13 HOH HOH . 
R 6 HOH A 8 308 58 HOH HOH . 
R 6 HOH A 9 309 5 HOH HOH . 
R 6 HOH A 10 310 17 HOH HOH . 
R 6 HOH A 11 311 34 HOH HOH . 
R 6 HOH A 12 312 27 HOH HOH . 
R 6 HOH A 13 313 24 HOH HOH . 
R 6 HOH A 14 314 4 HOH HOH . 
R 6 HOH A 15 315 8 HOH HOH . 
R 6 HOH A 16 316 37 HOH HOH . 
R 6 HOH A 17 317 40 HOH HOH . 
R 6 HOH A 18 318 30 HOH HOH . 
R 6 HOH A 19 319 14 HOH HOH . 
S 6 HOH B 1 101 16 HOH HOH . 
S 6 HOH B 2 102 57 HOH HOH . 
S 6 HOH B 3 103 52 HOH HOH . 
S 6 HOH B 4 104 3 HOH HOH . 
S 6 HOH B 5 105 44 HOH HOH . 
S 6 HOH B 6 106 11 HOH HOH . 
S 6 HOH B 7 107 9 HOH HOH . 
S 6 HOH B 8 108 48 HOH HOH . 
S 6 HOH B 9 109 50 HOH HOH . 
S 6 HOH B 10 110 35 HOH HOH . 
T 6 HOH F 1 101 41 HOH HOH . 
T 6 HOH F 2 102 12 HOH HOH . 
T 6 HOH F 3 103 38 HOH HOH . 
T 6 HOH F 4 104 53 HOH HOH . 
T 6 HOH F 5 105 36 HOH HOH . 
T 6 HOH F 6 106 49 HOH HOH . 
T 6 HOH F 7 107 51 HOH HOH . 
T 6 HOH F 8 108 28 HOH HOH . 
T 6 HOH F 9 109 45 HOH HOH . 
T 6 HOH F 10 110 42 HOH HOH . 
T 6 HOH F 11 111 43 HOH HOH . 
T 6 HOH F 12 112 1 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 GOL . . . M 4 13.965 -8.282 12.094 1 74.93 ? C1 GOL 202 A 1 
HETATM 2 O O1 GOL . . . M 4 13.233 -9.425 11.744 1 74.38 ? O1 GOL 202 A 1 
HETATM 3 C C2 GOL . . . M 4 12.949 -7.17 12.321 1 78.05 ? C2 GOL 202 A 1 
HETATM 4 O O2 GOL . . . M 4 13.328 -6.387 13.426 1 90.32 ? O2 GOL 202 A 1 
HETATM 5 C C3 GOL . . . M 4 12.905 -6.29 11.074 1 72.92 ? C3 GOL 202 A 1 
HETATM 6 O O3 GOL . . . M 4 13.151 -4.966 11.473 1 77.09 ? O3 GOL 202 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           48 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           1203 
_model_server_stats.encode_time_ms          14 
_model_server_stats.element_count           6 
#