data_5YV9
#
_model_server_result.job_id            F9hh75EiRhIRA41V1Sdx0w 
_model_server_result.datetime_utc      '2024-12-02 07:44:02' 
_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          5yv9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":503}' 
#
_entry.id    5YV9 
#
_exptl.entry_id    5YV9 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          3 
_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            5YV9 
_cell.length_a            66.823 
_cell.length_b            78.017 
_cell.length_c            83.71 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YV9 
_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        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_pdbx_struct_assembly.details               author_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
_pdbx_struct_assembly_gen.asym_id_list       A,B,C,D,E,F 
_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
? 3 C N N 
? 3 D 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 MET 246 A MET 396 1_555 A N CAS 247 A CAS 397 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
covale ? covale2 A C CAS 247 A CAS 397 1_555 A N LEU 248 A LEU 398 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? 
#
_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 192 n n 
C1 C2 GOL sing 193 n n 
C1 H11 GOL sing 194 n n 
C1 H12 GOL sing 195 n n 
O1 HO1 GOL sing 196 n n 
C2 O2 GOL sing 197 n n 
C2 C3 GOL sing 198 n n 
C2 H2 GOL sing 199 n n 
O2 HO2 GOL sing 200 n n 
C3 O3 GOL sing 201 n n 
C3 H31 GOL sing 202 n n 
C3 H32 GOL sing 203 n n 
O3 HO3 GOL sing 204 n n 
#
_atom_sites.entry_id                     5YV9 
_atom_sites.fract_transf_matrix[1][1]    0.014965 
_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]    0.012818 
_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]    0.011946 
_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
B 2 91O A 1 501 501 91O CK9 . 
C 3 GOL A 1 502 601 GOL GOL . 
D 3 GOL A 1 503 602 GOL GOL . 
E 4 CL A 1 504 701 CL CL . 
F 5 HOH A 1 601 80 HOH HOH . 
F 5 HOH A 2 602 39 HOH HOH . 
F 5 HOH A 3 603 9 HOH HOH . 
F 5 HOH A 4 604 41 HOH HOH . 
F 5 HOH A 5 605 49 HOH HOH . 
F 5 HOH A 6 606 68 HOH HOH . 
F 5 HOH A 7 607 13 HOH HOH . 
F 5 HOH A 8 608 30 HOH HOH . 
F 5 HOH A 9 609 1 HOH HOH . 
F 5 HOH A 10 610 38 HOH HOH . 
F 5 HOH A 11 611 63 HOH HOH . 
F 5 HOH A 12 612 12 HOH HOH . 
F 5 HOH A 13 613 18 HOH HOH . 
F 5 HOH A 14 614 65 HOH HOH . 
F 5 HOH A 15 615 24 HOH HOH . 
F 5 HOH A 16 616 61 HOH HOH . 
F 5 HOH A 17 617 43 HOH HOH . 
F 5 HOH A 18 618 16 HOH HOH . 
F 5 HOH A 19 619 44 HOH HOH . 
F 5 HOH A 20 620 15 HOH HOH . 
F 5 HOH A 21 621 31 HOH HOH . 
F 5 HOH A 22 622 7 HOH HOH . 
F 5 HOH A 23 623 70 HOH HOH . 
F 5 HOH A 24 624 66 HOH HOH . 
F 5 HOH A 25 625 59 HOH HOH . 
F 5 HOH A 26 626 2 HOH HOH . 
F 5 HOH A 27 627 5 HOH HOH . 
F 5 HOH A 28 628 69 HOH HOH . 
F 5 HOH A 29 629 33 HOH HOH . 
F 5 HOH A 30 630 57 HOH HOH . 
F 5 HOH A 31 631 4 HOH HOH . 
F 5 HOH A 32 632 73 HOH HOH . 
F 5 HOH A 33 633 60 HOH HOH . 
F 5 HOH A 34 634 34 HOH HOH . 
F 5 HOH A 35 635 10 HOH HOH . 
F 5 HOH A 36 636 75 HOH HOH . 
F 5 HOH A 37 637 3 HOH HOH . 
F 5 HOH A 38 638 84 HOH HOH . 
F 5 HOH A 39 639 83 HOH HOH . 
F 5 HOH A 40 640 11 HOH HOH . 
F 5 HOH A 41 641 42 HOH HOH . 
F 5 HOH A 42 642 6 HOH HOH . 
F 5 HOH A 43 643 26 HOH HOH . 
F 5 HOH A 44 644 55 HOH HOH . 
F 5 HOH A 45 645 29 HOH HOH . 
F 5 HOH A 46 646 25 HOH HOH . 
F 5 HOH A 47 647 40 HOH HOH . 
F 5 HOH A 48 648 23 HOH HOH . 
F 5 HOH A 49 649 32 HOH HOH . 
F 5 HOH A 50 650 37 HOH HOH . 
F 5 HOH A 51 651 20 HOH HOH . 
F 5 HOH A 52 652 45 HOH HOH . 
F 5 HOH A 53 653 50 HOH HOH . 
F 5 HOH A 54 654 28 HOH HOH . 
F 5 HOH A 55 655 76 HOH HOH . 
F 5 HOH A 56 656 14 HOH HOH . 
F 5 HOH A 57 657 48 HOH HOH . 
F 5 HOH A 58 658 62 HOH HOH . 
F 5 HOH A 59 659 47 HOH HOH . 
F 5 HOH A 60 660 51 HOH HOH . 
F 5 HOH A 61 661 27 HOH HOH . 
F 5 HOH A 62 662 21 HOH HOH . 
F 5 HOH A 63 663 71 HOH HOH . 
F 5 HOH A 64 664 74 HOH HOH . 
F 5 HOH A 65 665 79 HOH HOH . 
F 5 HOH A 66 666 81 HOH HOH . 
F 5 HOH A 67 667 46 HOH HOH . 
F 5 HOH A 68 668 77 HOH HOH . 
F 5 HOH A 69 669 82 HOH HOH . 
F 5 HOH A 70 670 52 HOH HOH . 
F 5 HOH A 71 671 8 HOH HOH . 
F 5 HOH A 72 672 19 HOH HOH . 
F 5 HOH A 73 673 78 HOH HOH . 
F 5 HOH A 74 674 56 HOH HOH . 
F 5 HOH A 75 675 22 HOH HOH . 
F 5 HOH A 76 676 35 HOH HOH . 
F 5 HOH A 77 677 17 HOH HOH . 
F 5 HOH A 78 678 54 HOH HOH . 
F 5 HOH A 79 679 36 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 . . . D 3 -5.09 -27.732 -0.273 1 83.46 ? C1 GOL 503 A 1 
HETATM 2 O O1 GOL . . . D 3 -4.743 -27.64 -1.616 1 81.11 ? O1 GOL 503 A 1 
HETATM 3 C C2 GOL . . . D 3 -5.845 -26.425 0.065 1 86.03 ? C2 GOL 503 A 1 
HETATM 4 O O2 GOL . . . D 3 -7.201 -26.653 0.338 1 87.54 ? O2 GOL 503 A 1 
HETATM 5 C C3 GOL . . . D 3 -5.07 -25.778 1.257 1 82.22 ? C3 GOL 503 A 1 
HETATM 6 O O3 GOL . . . D 3 -5.289 -24.398 1.142 1 72.89 ? O3 GOL 503 A 1 
#
_model_server_stats.io_time_ms              74 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#