data_2Y56
#
_model_server_result.job_id            klZgKkH9YNtBFslLGnqwQA 
_model_server_result.datetime_utc      '2024-11-27 03:03:59' 
_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          2y56 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Z","auth_seq_id":702}' 
#
_entry.id    2Y56 
#
_exptl.entry_id    2Y56 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    8 
_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            2Y56 
_cell.length_a            218.93 
_cell.length_b            218.93 
_cell.length_c            218.93 
_cell.Z_PDB               120 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2Y56 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        197 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    pentameric 
_pdbx_struct_assembly.oligomeric_count      5 
_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,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA,LA,MA,NA,OA,PA,QA,RA 
_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
? 5 K N N 
? 5 L N N 
? 5 S N N 
? 5 Y N N 
? 5 Z N N 
? 5 HA N N 
? 5 IA N N 
? 5 JA 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 125 A CYS 125 1_555 A SG CYS 138 A CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 A SG CYS 188 A CYS 188 1_555 A SG CYS 189 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf3 B SG CYS 125 B CYS 125 1_555 B SG CYS 138 B CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf4 B SG CYS 188 B CYS 188 1_555 B SG CYS 189 B CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
disulf ? disulf5 C SG CYS 125 C CYS 125 1_555 C SG CYS 138 C CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf6 C SG CYS 188 C CYS 188 1_555 C SG CYS 189 C CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf7 D SG CYS 125 D CYS 125 1_555 D SG CYS 138 D CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf8 D SG CYS 188 D CYS 188 1_555 D SG CYS 189 D CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf9 E SG CYS 125 E CYS 125 1_555 E SG CYS 138 E CYS 138 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf10 E SG CYS 188 E CYS 188 1_555 E SG CYS 189 E CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
#
_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 129 n n 
C1 C2 GOL sing 130 n n 
C1 H11 GOL sing 131 n n 
C1 H12 GOL sing 132 n n 
O1 HO1 GOL sing 133 n n 
C2 O2 GOL sing 134 n n 
C2 C3 GOL sing 135 n n 
C2 H2 GOL sing 136 n n 
O2 HO2 GOL sing 137 n n 
C3 O3 GOL sing 138 n n 
C3 H31 GOL sing 139 n n 
C3 H32 GOL sing 140 n n 
O3 HO3 GOL sing 141 n n 
#
_atom_sites.entry_id                     2Y56 
_atom_sites.fract_transf_matrix[1][1]    0.004568 
_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]    0.004568 
_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]    0.004568 
_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
F 2 V11 A 1 301 301 V11 V11 . 
G 3 CL A 1 501 501 CL CL . 
H 3 CL A 1 502 502 CL CL . 
I 4 SO4 A 1 601 601 SO4 SO4 . 
J 4 SO4 A 1 602 602 SO4 SO4 . 
K 5 GOL A 1 701 701 GOL GOL . 
L 5 GOL A 1 702 702 GOL GOL . 
M 2 V11 B 1 301 301 V11 V11 . 
N 3 CL B 1 501 501 CL CL . 
O 3 CL B 1 502 502 CL CL . 
P 3 CL B 1 503 503 CL CL . 
Q 4 SO4 B 1 601 601 SO4 SO4 . 
R 4 SO4 B 1 602 602 SO4 SO4 . 
S 5 GOL B 1 701 701 GOL GOL . 
T 2 V11 C 1 301 301 V11 V11 . 
U 3 CL C 1 501 501 CL CL . 
V 3 CL C 1 502 502 CL CL . 
W 4 SO4 C 1 601 601 SO4 SO4 . 
X 4 SO4 C 1 602 602 SO4 SO4 . 
Y 5 GOL C 1 701 701 GOL GOL . 
Z 5 GOL C 1 702 702 GOL GOL . 
AA 2 V11 D 1 301 301 V11 V11 . 
BA 3 CL D 1 501 501 CL CL . 
CA 3 CL D 1 502 502 CL CL . 
DA 3 CL D 1 503 503 CL CL . 
EA 4 SO4 D 1 601 601 SO4 SO4 . 
FA 4 SO4 D 1 602 602 SO4 SO4 . 
GA 4 SO4 D 1 603 603 SO4 SO4 . 
HA 5 GOL D 1 701 701 GOL GOL . 
IA 5 GOL D 1 702 702 GOL GOL . 
JA 5 GOL D 1 703 703 GOL GOL . 
KA 2 V11 E 1 301 301 V11 V11 . 
LA 3 CL E 1 501 501 CL CL . 
MA 3 CL E 1 502 502 CL CL . 
NA 4 SO4 E 1 601 601 SO4 SO4 . 
OA 4 SO4 E 1 602 602 SO4 SO4 . 
PA 4 SO4 E 1 603 603 SO4 SO4 . 
QA 4 SO4 E 1 604 604 SO4 SO4 . 
RA 4 SO4 E 1 605 605 SO4 SO4 . 
#
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 . . . Z 5 59.587 15.779 -46.044 1 106.6 ? C1 GOL 702 C 1 
HETATM 2 O O1 GOL . . . Z 5 60.501 15.143 -45.155 1 105.69 ? O1 GOL 702 C 1 
HETATM 3 C C2 GOL . . . Z 5 60.092 17.193 -46.429 1 106.81 ? C2 GOL 702 C 1 
HETATM 4 O O2 GOL . . . Z 5 61.526 17.241 -46.633 1 107.62 ? O2 GOL 702 C 1 
HETATM 5 C C3 GOL . . . Z 5 59.199 17.941 -47.5 1 107.1 ? C3 GOL 702 C 1 
HETATM 6 O O3 GOL . . . Z 5 59.694 18.012 -48.868 1 106.05 ? O3 GOL 702 C 1 
#
_model_server_stats.io_time_ms              17 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           235 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#