data_3D9L
#
_model_server_result.job_id            oG1BoayCXiDZtXwkWb0T_Q 
_model_server_result.datetime_utc      '2024-10-12 17:22:07' 
_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          3d9l 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":503}' 
#
_entry.id    3D9L 
#
_exptl.entry_id    3D9L 
_exptl.method      'X-RAY DIFFRACTION' 
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_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    1 
_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            3D9L 
_cell.length_a            56.296 
_cell.length_b            56.296 
_cell.length_c            106.739 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D9L 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
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 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,E,G,I 1 1 
B,D,F,H 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             F 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 C C11 BTN 1 Y BTN 0 1_555 C N TYR 2 Y TYR 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.262 ? 
covale ? covale2 C C TYR 2 Y TYR 1 1_555 C N SEP 3 Y SEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale3 C C SEP 3 Y SEP 2 1_555 C N PRO 4 Y PRO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? 
covale ? covale4 C C TYR 9 Y TYR 8 1_555 C N SEP 10 Y SEP 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale5 C C SEP 10 Y SEP 9 1_555 C N PRO 11 Y PRO 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? 
covale ? covale6 D C TYR 9 Z TYR 1 1_555 D N SEP 10 Z SEP 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale7 D C SEP 10 Z SEP 2 1_555 D N PRO 11 Z PRO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? 
#
_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 168 n n 
C1 C2 GOL sing 169 n n 
C1 H11 GOL sing 170 n n 
C1 H12 GOL sing 171 n n 
O1 HO1 GOL sing 172 n n 
C2 O2 GOL sing 173 n n 
C2 C3 GOL sing 174 n n 
C2 H2 GOL sing 175 n n 
O2 HO2 GOL sing 176 n n 
C3 O3 GOL sing 177 n n 
C3 H31 GOL sing 178 n n 
C3 H32 GOL sing 179 n n 
O3 HO3 GOL sing 180 n n 
#
_atom_sites.entry_id                     3D9L 
_atom_sites.fract_transf_matrix[1][1]    0.017763 
_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]    0.017763 
_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]    0.009369 
_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 3 ACT A 1 501 501 ACT ACT . 
F 4 GOL B 1 503 503 GOL GOL . 
G 5 HOH A 1 502 502 HOH HOH . 
G 5 HOH A 2 503 503 HOH HOH . 
G 5 HOH A 3 504 504 HOH HOH . 
G 5 HOH A 4 505 505 HOH HOH . 
G 5 HOH A 5 506 506 HOH HOH . 
G 5 HOH A 6 507 507 HOH HOH . 
G 5 HOH A 7 508 508 HOH HOH . 
G 5 HOH A 8 509 509 HOH HOH . 
G 5 HOH A 9 510 510 HOH HOH . 
G 5 HOH A 10 511 511 HOH HOH . 
G 5 HOH A 11 512 512 HOH HOH . 
G 5 HOH A 12 513 513 HOH HOH . 
G 5 HOH A 13 514 514 HOH HOH . 
G 5 HOH A 14 515 515 HOH HOH . 
G 5 HOH A 15 516 516 HOH HOH . 
G 5 HOH A 16 517 517 HOH HOH . 
G 5 HOH A 17 518 518 HOH HOH . 
G 5 HOH A 18 519 519 HOH HOH . 
G 5 HOH A 19 520 520 HOH HOH . 
G 5 HOH A 20 521 521 HOH HOH . 
G 5 HOH A 21 522 522 HOH HOH . 
G 5 HOH A 22 523 523 HOH HOH . 
G 5 HOH A 23 524 524 HOH HOH . 
G 5 HOH A 24 525 525 HOH HOH . 
G 5 HOH A 25 526 526 HOH HOH . 
H 5 HOH B 1 504 504 HOH HOH . 
H 5 HOH B 2 505 505 HOH HOH . 
H 5 HOH B 3 506 506 HOH HOH . 
H 5 HOH B 4 507 507 HOH HOH . 
H 5 HOH B 5 508 508 HOH HOH . 
H 5 HOH B 6 509 509 HOH HOH . 
H 5 HOH B 7 510 510 HOH HOH . 
H 5 HOH B 8 511 511 HOH HOH . 
H 5 HOH B 9 512 512 HOH HOH . 
H 5 HOH B 10 513 513 HOH HOH . 
H 5 HOH B 11 514 514 HOH HOH . 
H 5 HOH B 12 515 515 HOH HOH . 
H 5 HOH B 13 516 516 HOH HOH . 
H 5 HOH B 14 517 517 HOH HOH . 
H 5 HOH B 15 518 518 HOH HOH . 
H 5 HOH B 16 519 519 HOH HOH . 
H 5 HOH B 17 520 520 HOH HOH . 
H 5 HOH B 18 521 521 HOH HOH . 
H 5 HOH B 19 522 522 HOH HOH . 
H 5 HOH B 20 523 523 HOH HOH . 
H 5 HOH B 21 524 524 HOH HOH . 
H 5 HOH B 22 525 525 HOH HOH . 
H 5 HOH B 23 526 526 HOH HOH . 
H 5 HOH B 24 527 527 HOH HOH . 
H 5 HOH B 25 528 528 HOH HOH . 
H 5 HOH B 26 529 529 HOH HOH . 
H 5 HOH B 27 530 530 HOH HOH . 
H 5 HOH B 28 531 531 HOH HOH . 
H 5 HOH B 29 532 532 HOH HOH . 
H 5 HOH B 30 533 533 HOH HOH . 
I 5 HOH Y 1 65 65 HOH HOH . 
I 5 HOH Y 2 109 109 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 . . . F 4 27.121 29.991 -11.075 1 62.04 ? C1 GOL 503 B 1 
HETATM 2 O O1 GOL . . . F 4 28.145 29.577 -11.963 1 61.87 ? O1 GOL 503 B 1 
HETATM 3 C C2 GOL . . . F 4 25.739 29.618 -11.62 1 61.57 ? C2 GOL 503 B 1 
HETATM 4 O O2 GOL . . . F 4 25.865 29.057 -12.908 1 62.04 ? O2 GOL 503 B 1 
HETATM 5 C C3 GOL . . . F 4 25.054 28.619 -10.69 1 60.83 ? C3 GOL 503 B 1 
HETATM 6 O O3 GOL . . . F 4 23.703 28.94 -10.425 1 58.21 ? O3 GOL 503 B 1 
#
_model_server_stats.io_time_ms              69 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           329 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           6 
#