data_6YB2
#
_model_server_result.job_id            9L72_GI9_pfLgDp3tO5C5Q 
_model_server_result.datetime_utc      '2024-12-27 19:07:07' 
_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          6yb2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":101}' 
#
_entry.id    6YB2 
#
_exptl.entry_id    6YB2 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_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            6YB2 
_cell.length_a            31.01 
_cell.length_b            55.99 
_cell.length_c            90.63 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YB2 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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,L,M,N 
_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
? 2 G N N 
? 2 H 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 C ACE 1 A ACE 0 1_555 A N GLY 2 A GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 A C GLY 31 A GLY 30 1_555 A N NH2 32 A NH2 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? 
covale ? covale3 B C ACE 1 B ACE 0 1_555 B N GLY 2 B GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? 
covale ? covale4 B C GLY 31 B GLY 30 1_555 B N NH2 32 B NH2 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.356 ? 
covale ? covale5 C C ACE 1 C ACE 0 1_555 C N GLY 2 C GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale6 C C GLY 31 C GLY 30 1_555 C N NH2 32 C NH2 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? 
covale ? covale7 D C ACE 1 D ACE 0 1_555 D N GLY 2 D GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? 
covale ? covale8 D C GLY 31 D GLY 30 1_555 D N NH2 32 D NH2 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? 
covale ? covale9 E C ACE 1 E ACE 0 1_555 E N GLY 2 E GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? 
covale ? covale10 E C GLY 31 E GLY 30 1_555 E N NH2 32 E NH2 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? 
covale ? covale11 F C ACE 1 F ACE 0 1_555 F N GLY 2 F GLY 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? 
covale ? covale12 F C GLY 31 F GLY 30 1_555 F N NH2 32 F NH2 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
#
_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 65 n n 
C1 C2 GOL sing 66 n n 
C1 H11 GOL sing 67 n n 
C1 H12 GOL sing 68 n n 
O1 HO1 GOL sing 69 n n 
C2 O2 GOL sing 70 n n 
C2 C3 GOL sing 71 n n 
C2 H2 GOL sing 72 n n 
O2 HO2 GOL sing 73 n n 
C3 O3 GOL sing 74 n n 
C3 H31 GOL sing 75 n n 
C3 H32 GOL sing 76 n n 
O3 HO3 GOL sing 77 n n 
#
_atom_sites.entry_id                     6YB2 
_atom_sites.fract_transf_matrix[1][1]    0.032248 
_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]    0.01786 
_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]    0.011034 
_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 GOL A 1 101 1 GOL GOL . 
H 2 GOL F 1 101 0 GOL GOL . 
I 3 HOH A 1 201 3 HOH HOH . 
I 3 HOH A 2 202 28 HOH HOH . 
I 3 HOH A 3 203 99 HOH HOH . 
I 3 HOH A 4 204 42 HOH HOH . 
I 3 HOH A 5 205 117 HOH HOH . 
I 3 HOH A 6 206 115 HOH HOH . 
I 3 HOH A 7 207 127 HOH HOH . 
I 3 HOH A 8 208 9 HOH HOH . 
I 3 HOH A 9 209 140 HOH HOH . 
I 3 HOH A 10 210 23 HOH HOH . 
I 3 HOH A 11 211 49 HOH HOH . 
I 3 HOH A 12 212 4 HOH HOH . 
I 3 HOH A 13 213 136 HOH HOH . 
I 3 HOH A 14 214 120 HOH HOH . 
I 3 HOH A 15 215 124 HOH HOH . 
I 3 HOH A 16 216 57 HOH HOH . 
I 3 HOH A 17 217 73 HOH HOH . 
I 3 HOH A 18 218 104 HOH HOH . 
I 3 HOH A 19 219 116 HOH HOH . 
I 3 HOH A 20 220 123 HOH HOH . 
I 3 HOH A 21 221 12 HOH HOH . 
I 3 HOH A 22 222 34 HOH HOH . 
I 3 HOH A 23 223 121 HOH HOH . 
I 3 HOH A 24 224 66 HOH HOH . 
I 3 HOH A 25 225 130 HOH HOH . 
J 3 HOH B 1 101 46 HOH HOH . 
J 3 HOH B 2 102 37 HOH HOH . 
J 3 HOH B 3 103 100 HOH HOH . 
J 3 HOH B 4 104 93 HOH HOH . 
J 3 HOH B 5 105 22 HOH HOH . 
J 3 HOH B 6 106 7 HOH HOH . 
J 3 HOH B 7 107 60 HOH HOH . 
J 3 HOH B 8 108 13 HOH HOH . 
J 3 HOH B 9 109 10 HOH HOH . 
J 3 HOH B 10 110 30 HOH HOH . 
J 3 HOH B 11 111 15 HOH HOH . 
J 3 HOH B 12 112 58 HOH HOH . 
J 3 HOH B 13 113 47 HOH HOH . 
J 3 HOH B 14 114 114 HOH HOH . 
J 3 HOH B 15 115 132 HOH HOH . 
J 3 HOH B 16 116 41 HOH HOH . 
J 3 HOH B 17 117 83 HOH HOH . 
J 3 HOH B 18 118 103 HOH HOH . 
J 3 HOH B 19 119 118 HOH HOH . 
J 3 HOH B 20 120 94 HOH HOH . 
J 3 HOH B 21 121 101 HOH HOH . 
J 3 HOH B 22 122 50 HOH HOH . 
K 3 HOH C 1 101 69 HOH HOH . 
K 3 HOH C 2 102 24 HOH HOH . 
K 3 HOH C 3 103 63 HOH HOH . 
K 3 HOH C 4 104 35 HOH HOH . 
K 3 HOH C 5 105 38 HOH HOH . 
K 3 HOH C 6 106 21 HOH HOH . 
K 3 HOH C 7 107 18 HOH HOH . 
K 3 HOH C 8 108 2 HOH HOH . 
K 3 HOH C 9 109 89 HOH HOH . 
K 3 HOH C 10 110 32 HOH HOH . 
K 3 HOH C 11 111 74 HOH HOH . 
K 3 HOH C 12 112 79 HOH HOH . 
K 3 HOH C 13 113 6 HOH HOH . 
K 3 HOH C 14 114 8 HOH HOH . 
K 3 HOH C 15 115 29 HOH HOH . 
K 3 HOH C 16 116 1 HOH HOH . 
K 3 HOH C 17 117 137 HOH HOH . 
K 3 HOH C 18 118 16 HOH HOH . 
K 3 HOH C 19 119 133 HOH HOH . 
K 3 HOH C 20 120 113 HOH HOH . 
K 3 HOH C 21 121 84 HOH HOH . 
K 3 HOH C 22 122 72 HOH HOH . 
K 3 HOH C 23 123 54 HOH HOH . 
K 3 HOH C 24 124 26 HOH HOH . 
K 3 HOH C 25 125 88 HOH HOH . 
K 3 HOH C 26 126 55 HOH HOH . 
K 3 HOH C 27 127 56 HOH HOH . 
K 3 HOH C 28 128 52 HOH HOH . 
K 3 HOH C 29 129 59 HOH HOH . 
K 3 HOH C 30 130 92 HOH HOH . 
K 3 HOH C 31 131 85 HOH HOH . 
K 3 HOH C 32 132 45 HOH HOH . 
K 3 HOH C 33 133 25 HOH HOH . 
K 3 HOH C 34 134 131 HOH HOH . 
K 3 HOH C 35 135 82 HOH HOH . 
L 3 HOH D 1 101 36 HOH HOH . 
L 3 HOH D 2 102 27 HOH HOH . 
L 3 HOH D 3 103 98 HOH HOH . 
L 3 HOH D 4 104 95 HOH HOH . 
L 3 HOH D 5 105 44 HOH HOH . 
L 3 HOH D 6 106 5 HOH HOH . 
L 3 HOH D 7 107 33 HOH HOH . 
L 3 HOH D 8 108 61 HOH HOH . 
L 3 HOH D 9 109 134 HOH HOH . 
L 3 HOH D 10 110 112 HOH HOH . 
L 3 HOH D 11 111 11 HOH HOH . 
L 3 HOH D 12 112 75 HOH HOH . 
L 3 HOH D 13 113 90 HOH HOH . 
L 3 HOH D 14 114 96 HOH HOH . 
L 3 HOH D 15 115 76 HOH HOH . 
L 3 HOH D 16 116 65 HOH HOH . 
L 3 HOH D 17 117 80 HOH HOH . 
L 3 HOH D 18 118 43 HOH HOH . 
L 3 HOH D 19 119 139 HOH HOH . 
L 3 HOH D 20 120 125 HOH HOH . 
L 3 HOH D 21 121 86 HOH HOH . 
L 3 HOH D 22 122 71 HOH HOH . 
L 3 HOH D 23 123 77 HOH HOH . 
L 3 HOH D 24 124 128 HOH HOH . 
M 3 HOH E 1 101 68 HOH HOH . 
M 3 HOH E 2 102 51 HOH HOH . 
M 3 HOH E 3 103 109 HOH HOH . 
M 3 HOH E 4 104 105 HOH HOH . 
M 3 HOH E 5 105 97 HOH HOH . 
M 3 HOH E 6 106 91 HOH HOH . 
M 3 HOH E 7 107 78 HOH HOH . 
M 3 HOH E 8 108 14 HOH HOH . 
M 3 HOH E 9 109 87 HOH HOH . 
M 3 HOH E 10 110 111 HOH HOH . 
M 3 HOH E 11 111 20 HOH HOH . 
M 3 HOH E 12 112 138 HOH HOH . 
M 3 HOH E 13 113 126 HOH HOH . 
M 3 HOH E 14 114 107 HOH HOH . 
M 3 HOH E 15 115 108 HOH HOH . 
M 3 HOH E 16 116 141 HOH HOH . 
M 3 HOH E 17 117 81 HOH HOH . 
N 3 HOH F 1 201 31 HOH HOH . 
N 3 HOH F 2 202 19 HOH HOH . 
N 3 HOH F 3 203 135 HOH HOH . 
N 3 HOH F 4 204 70 HOH HOH . 
N 3 HOH F 5 205 17 HOH HOH . 
N 3 HOH F 6 206 122 HOH HOH . 
N 3 HOH F 7 207 67 HOH HOH . 
N 3 HOH F 8 208 64 HOH HOH . 
N 3 HOH F 9 209 62 HOH HOH . 
N 3 HOH F 10 210 53 HOH HOH . 
N 3 HOH F 11 211 110 HOH HOH . 
N 3 HOH F 12 212 119 HOH HOH . 
N 3 HOH F 13 213 39 HOH HOH . 
N 3 HOH F 14 214 102 HOH HOH . 
N 3 HOH F 15 215 48 HOH HOH . 
N 3 HOH F 16 216 40 HOH HOH . 
N 3 HOH F 17 217 129 HOH HOH . 
N 3 HOH F 18 218 106 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 . . . G 2 5.39 -3.041 -21.553 1 58.63 ? C1 GOL 101 A 1 
HETATM 2 O O1 GOL . . . G 2 5.145 -2.18 -20.465 1 91.32 ? O1 GOL 101 A 1 
HETATM 3 C C2 GOL . . . G 2 4.287 -4.088 -21.637 1 47.43 ? C2 GOL 101 A 1 
HETATM 4 O O2 GOL . . . G 2 3.137 -3.628 -20.964 1 189.01 ? O2 GOL 101 A 1 
HETATM 5 C C3 GOL . . . G 2 3.965 -4.367 -23.099 1 71.8 ? C3 GOL 101 A 1 
HETATM 6 O O3 GOL . . . G 2 3.065 -5.447 -23.197 1 58.96 ? O3 GOL 101 A 1 
HETATM 7 H H11 GOL . . . G 2 6.354 -3.532 -21.424 1 70.35 ? H11 GOL 101 A 1 
HETATM 8 H H12 GOL . . . G 2 5.422 -2.466 -22.478 1 70.35 ? H12 GOL 101 A 1 
HETATM 9 H HO1 GOL . . . G 2 5.889 -1.549 -20.374 1 109.58 ? HO1 GOL 101 A 1 
HETATM 10 H H2 GOL . . . G 2 4.643 -5.009 -21.175 1 56.92 ? H2 GOL 101 A 1 
HETATM 11 H HO2 GOL . . . G 2 2.813 -2.809 -21.393 1 226.81 ? HO2 GOL 101 A 1 
HETATM 12 H H31 GOL . . . G 2 4.883 -4.604 -23.638 1 86.17 ? H31 GOL 101 A 1 
HETATM 13 H H32 GOL . . . G 2 3.525 -3.48 -23.554 1 86.17 ? H32 GOL 101 A 1 
HETATM 14 H HO3 GOL . . . G 2 2.779 -5.55 -24.129 1 70.75 ? HO3 GOL 101 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           316 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#