data_3BY0
#
_model_server_result.job_id            CVUJEdLfocyRAYLQRHGkyA 
_model_server_result.datetime_utc      '2024-10-18 08:31:01' 
_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          3by0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":602}' 
#
_entry.id    3BY0 
#
_exptl.entry_id    3BY0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          6 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            GLYCEROL 
_entity.pdbx_number_of_molecules    3 
_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            3BY0 
_cell.length_a            114.358 
_cell.length_b            114.358 
_cell.length_c            119.042 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3BY0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I,S 1 1 
B,J,K,T 2 1 
C,L,M,N,O,P,Q,R,U 3 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
? 6 I N N 
? 6 Q N N 
? 6 R 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 96 A CYS 76 1_555 A SG CYS 195 A CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf2 B SG CYS 96 B CYS 76 1_555 B SG CYS 195 B CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf3 C SG CYS 96 C CYS 76 1_555 C SG CYS 195 C CYS 175 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
metalc ? metalc1 F O4 DBS . A DBS 191 1_555 D FE FE . A FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? 
metalc ? metalc2 F O1 DBS . A DBS 191 1_555 D FE FE . A FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? 
metalc ? metalc3 G O6 DBH . A DBH 192 1_555 D FE FE . A FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
metalc ? metalc4 H O3 DBH . A DBH 193 1_555 D FE FE . A FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.736 ? 
metalc ? metalc5 K O3 DBH . B DBH 201 1_555 J FE FE . B FE 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc6 K O6 DBH . B DBH 201 1_555 J FE FE . B FE 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.416 ? 
metalc ? metalc7 N O1 DBS . C DBS 301 1_555 L FE FE . C FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
metalc ? metalc8 N O4 DBS . C DBS 301 1_555 L FE FE . C FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? 
metalc ? metalc9 O O1 DBS . C DBS 302 1_555 L FE FE . C FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.759 ? 
metalc ? metalc10 O O4 DBS . C DBS 302 1_555 L FE FE . C FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? 
metalc ? metalc11 P O3 DBH . C DBH 303 1_555 L FE FE . C FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? 
metalc ? metalc12 P O6 DBH . C DBH 303 1_555 L FE FE . C FE 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
#
_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 174 n n 
C1 C2 GOL sing 175 n n 
C1 H11 GOL sing 176 n n 
C1 H12 GOL sing 177 n n 
O1 HO1 GOL sing 178 n n 
C2 O2 GOL sing 179 n n 
C2 C3 GOL sing 180 n n 
C2 H2 GOL sing 181 n n 
O2 HO2 GOL sing 182 n n 
C3 O3 GOL sing 183 n n 
C3 H31 GOL sing 184 n n 
C3 H32 GOL sing 185 n n 
O3 HO3 GOL sing 186 n n 
#
_atom_sites.entry_id                     3BY0 
_atom_sites.fract_transf_matrix[1][1]    0.008744 
_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]    0.008744 
_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]    0.0084 
_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
D 2 FE A 1 401 401 FE FE . 
E 3 SO4 A 1 531 531 SO4 SO4 . 
F 4 DBS A 1 191 191 DBS DBS . 
G 5 DBH A 1 192 192 DBH DBH . 
H 5 DBH A 1 193 193 DBH DBH . 
I 6 GOL A 1 601 601 GOL GOL . 
J 2 FE B 1 402 402 FE FE . 
K 5 DBH B 1 201 201 DBH DBH . 
L 2 FE C 1 403 403 FE FE . 
M 3 SO4 C 1 532 532 SO4 SO4 . 
N 4 DBS C 1 301 301 DBS DBS . 
O 4 DBS C 1 302 302 DBS DBS . 
P 5 DBH C 1 303 303 DBH DBH . 
Q 6 GOL C 1 602 602 GOL GOL . 
R 6 GOL C 1 603 603 GOL GOL . 
S 7 HOH A 1 602 703 HOH HOH . 
S 7 HOH A 2 603 705 HOH HOH . 
S 7 HOH A 3 604 709 HOH HOH . 
S 7 HOH A 4 605 714 HOH HOH . 
S 7 HOH A 5 606 715 HOH HOH . 
S 7 HOH A 6 607 720 HOH HOH . 
S 7 HOH A 7 608 721 HOH HOH . 
S 7 HOH A 8 609 727 HOH HOH . 
S 7 HOH A 9 610 729 HOH HOH . 
S 7 HOH A 10 611 730 HOH HOH . 
S 7 HOH A 11 612 732 HOH HOH . 
S 7 HOH A 12 613 745 HOH HOH . 
S 7 HOH A 13 614 747 HOH HOH . 
S 7 HOH A 14 615 750 HOH HOH . 
S 7 HOH A 15 616 751 HOH HOH . 
S 7 HOH A 16 617 754 HOH HOH . 
S 7 HOH A 17 618 757 HOH HOH . 
S 7 HOH A 18 619 759 HOH HOH . 
S 7 HOH A 19 620 762 HOH HOH . 
S 7 HOH A 20 621 765 HOH HOH . 
S 7 HOH A 21 622 771 HOH HOH . 
S 7 HOH A 22 623 772 HOH HOH . 
S 7 HOH A 23 624 773 HOH HOH . 
S 7 HOH A 24 625 774 HOH HOH . 
S 7 HOH A 25 626 777 HOH HOH . 
S 7 HOH A 26 627 779 HOH HOH . 
S 7 HOH A 27 628 783 HOH HOH . 
S 7 HOH A 28 629 784 HOH HOH . 
S 7 HOH A 29 630 786 HOH HOH . 
S 7 HOH A 30 631 787 HOH HOH . 
S 7 HOH A 31 632 788 HOH HOH . 
T 7 HOH B 1 403 734 HOH HOH . 
U 7 HOH C 1 604 701 HOH HOH . 
U 7 HOH C 2 605 702 HOH HOH . 
U 7 HOH C 3 606 704 HOH HOH . 
U 7 HOH C 4 607 706 HOH HOH . 
U 7 HOH C 5 608 707 HOH HOH . 
U 7 HOH C 6 609 708 HOH HOH . 
U 7 HOH C 7 610 710 HOH HOH . 
U 7 HOH C 8 611 711 HOH HOH . 
U 7 HOH C 9 612 712 HOH HOH . 
U 7 HOH C 10 613 716 HOH HOH . 
U 7 HOH C 11 614 717 HOH HOH . 
U 7 HOH C 12 615 718 HOH HOH . 
U 7 HOH C 13 616 719 HOH HOH . 
U 7 HOH C 14 617 722 HOH HOH . 
U 7 HOH C 15 618 723 HOH HOH . 
U 7 HOH C 16 619 724 HOH HOH . 
U 7 HOH C 17 620 725 HOH HOH . 
U 7 HOH C 18 621 726 HOH HOH . 
U 7 HOH C 19 622 728 HOH HOH . 
U 7 HOH C 20 623 731 HOH HOH . 
U 7 HOH C 21 624 733 HOH HOH . 
U 7 HOH C 22 625 735 HOH HOH . 
U 7 HOH C 23 626 738 HOH HOH . 
U 7 HOH C 24 627 739 HOH HOH . 
U 7 HOH C 25 628 740 HOH HOH . 
U 7 HOH C 26 629 741 HOH HOH . 
U 7 HOH C 27 630 742 HOH HOH . 
U 7 HOH C 28 631 743 HOH HOH . 
U 7 HOH C 29 632 744 HOH HOH . 
U 7 HOH C 30 633 746 HOH HOH . 
U 7 HOH C 31 634 748 HOH HOH . 
U 7 HOH C 32 635 749 HOH HOH . 
U 7 HOH C 33 636 752 HOH HOH . 
U 7 HOH C 34 637 755 HOH HOH . 
U 7 HOH C 35 638 756 HOH HOH . 
U 7 HOH C 36 639 758 HOH HOH . 
U 7 HOH C 37 640 761 HOH HOH . 
U 7 HOH C 38 641 763 HOH HOH . 
U 7 HOH C 39 642 764 HOH HOH . 
U 7 HOH C 40 643 766 HOH HOH . 
U 7 HOH C 41 644 767 HOH HOH . 
U 7 HOH C 42 645 769 HOH HOH . 
U 7 HOH C 43 646 770 HOH HOH . 
U 7 HOH C 44 647 775 HOH HOH . 
U 7 HOH C 45 648 776 HOH HOH . 
U 7 HOH C 46 649 781 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 . . . Q 6 47.502 39.003 56.682 1 64.78 ? C1 GOL 602 C 1 
HETATM 2 O O1 GOL . . . Q 6 47.443 39.24 55.291 1 64.4 ? O1 GOL 602 C 1 
HETATM 3 C C2 GOL . . . Q 6 48.94 39.104 57.176 1 64.8 ? C2 GOL 602 C 1 
HETATM 4 O O2 GOL . . . Q 6 48.98 38.774 58.546 1 64.81 ? O2 GOL 602 C 1 
HETATM 5 C C3 GOL . . . Q 6 49.469 40.526 56.99 1 64.88 ? C3 GOL 602 C 1 
HETATM 6 O O3 GOL . . . Q 6 50.315 40.618 55.87 1 64.99 ? O3 GOL 602 C 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#