data_3VGX
#
_model_server_result.job_id            p1svXqwFCYELBQg6A8ZFZA 
_model_server_result.datetime_utc      '2025-03-04 06:15:50' 
_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          3vgx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":602}' 
#
_entry.id    3VGX 
#
_exptl.entry_id    3VGX 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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         120 
_cell.entry_id            3VGX 
_cell.length_a            44.967 
_cell.length_b            44.967 
_cell.length_c            209.237 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3VGX 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        155 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'H 3 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 22.4835 -38.942564 0 
3 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 44.967 0 0 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             D 
_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 A C ACE 1 C ACE 552 1_555 A N ASN 2 C ASN 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? 
covale ? covale2 A C GLN 39 C GLN 590 1_555 A N NH2 40 C NH2 591 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 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                     3VGX 
_atom_sites.fract_transf_matrix[1][1]    0.022239 
_atom_sites.fract_transf_matrix[1][2]    0.012839 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.025679 
_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]    0.004779 
_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
C 3 ACY C 1 601 1 ACY ACY . 
D 4 GOL C 1 602 1 GOL GOL . 
E 5 HOH C 1 701 1 HOH HOH . 
E 5 HOH C 2 702 2 HOH HOH . 
E 5 HOH C 3 703 3 HOH HOH . 
E 5 HOH C 4 704 4 HOH HOH . 
E 5 HOH C 5 705 5 HOH HOH . 
E 5 HOH C 6 706 6 HOH HOH . 
E 5 HOH C 7 707 7 HOH HOH . 
E 5 HOH C 8 708 8 HOH HOH . 
E 5 HOH C 9 709 9 HOH HOH . 
E 5 HOH C 10 710 10 HOH HOH . 
E 5 HOH C 11 711 11 HOH HOH . 
E 5 HOH C 12 712 12 HOH HOH . 
E 5 HOH C 13 713 13 HOH HOH . 
E 5 HOH C 14 714 16 HOH HOH . 
E 5 HOH C 15 715 17 HOH HOH . 
E 5 HOH C 16 716 18 HOH HOH . 
E 5 HOH C 17 717 19 HOH HOH . 
E 5 HOH C 18 718 20 HOH HOH . 
E 5 HOH C 19 719 21 HOH HOH . 
E 5 HOH C 20 720 22 HOH HOH . 
E 5 HOH C 21 721 24 HOH HOH . 
E 5 HOH C 22 722 25 HOH HOH . 
E 5 HOH C 23 723 26 HOH HOH . 
E 5 HOH C 24 724 27 HOH HOH . 
E 5 HOH C 25 725 28 HOH HOH . 
E 5 HOH C 26 726 29 HOH HOH . 
E 5 HOH C 27 727 30 HOH HOH . 
E 5 HOH C 28 728 32 HOH HOH . 
E 5 HOH C 29 729 34 HOH HOH . 
E 5 HOH C 30 730 36 HOH HOH . 
E 5 HOH C 31 731 37 HOH HOH . 
E 5 HOH C 32 732 38 HOH HOH . 
E 5 HOH C 33 733 39 HOH HOH . 
E 5 HOH C 34 734 40 HOH HOH . 
E 5 HOH C 35 735 41 HOH HOH . 
E 5 HOH C 36 736 44 HOH HOH . 
E 5 HOH C 37 737 46 HOH HOH . 
E 5 HOH C 38 738 47 HOH HOH . 
E 5 HOH C 39 739 48 HOH HOH . 
E 5 HOH C 40 740 49 HOH HOH . 
E 5 HOH C 41 741 51 HOH HOH . 
E 5 HOH C 42 742 52 HOH HOH . 
E 5 HOH C 43 743 53 HOH HOH . 
E 5 HOH C 44 744 54 HOH HOH . 
E 5 HOH C 45 745 55 HOH HOH . 
E 5 HOH C 46 746 56 HOH HOH . 
E 5 HOH C 47 747 57 HOH HOH . 
E 5 HOH C 48 748 58 HOH HOH . 
E 5 HOH C 49 749 59 HOH HOH . 
E 5 HOH C 50 750 60 HOH HOH . 
E 5 HOH C 51 751 61 HOH HOH . 
E 5 HOH C 52 752 62 HOH HOH . 
E 5 HOH C 53 753 66 HOH HOH . 
E 5 HOH C 54 754 69 HOH HOH . 
E 5 HOH C 55 755 72 HOH HOH . 
E 5 HOH C 56 756 74 HOH HOH . 
E 5 HOH C 57 757 76 HOH HOH . 
E 5 HOH C 58 758 77 HOH HOH . 
E 5 HOH C 59 759 82 HOH HOH . 
E 5 HOH C 60 760 83 HOH HOH . 
E 5 HOH C 61 761 84 HOH HOH . 
E 5 HOH C 62 762 85 HOH HOH . 
F 5 HOH D 1 701 14 HOH HOH . 
F 5 HOH D 2 702 15 HOH HOH . 
F 5 HOH D 3 703 23 HOH HOH . 
F 5 HOH D 4 704 31 HOH HOH . 
F 5 HOH D 5 705 33 HOH HOH . 
F 5 HOH D 6 706 35 HOH HOH . 
F 5 HOH D 7 707 42 HOH HOH . 
F 5 HOH D 8 708 43 HOH HOH . 
F 5 HOH D 9 709 45 HOH HOH . 
F 5 HOH D 10 710 50 HOH HOH . 
F 5 HOH D 11 711 63 HOH HOH . 
F 5 HOH D 12 712 64 HOH HOH . 
F 5 HOH D 13 713 65 HOH HOH . 
F 5 HOH D 14 714 67 HOH HOH . 
F 5 HOH D 15 715 68 HOH HOH . 
F 5 HOH D 16 716 70 HOH HOH . 
F 5 HOH D 17 717 71 HOH HOH . 
F 5 HOH D 18 718 73 HOH HOH . 
F 5 HOH D 19 719 75 HOH HOH . 
F 5 HOH D 20 720 78 HOH HOH . 
F 5 HOH D 21 721 79 HOH HOH . 
F 5 HOH D 22 722 80 HOH HOH . 
F 5 HOH D 23 723 81 HOH HOH . 
F 5 HOH D 24 724 86 HOH HOH . 
F 5 HOH D 25 725 87 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 4 16.315 -17.654 -36.596 1 45.91 ? C1 GOL 602 C 1 
HETATM 2 O O1 GOL . . . D 4 17.564 -17.833 -37.229 1 45.24 ? O1 GOL 602 C 1 
HETATM 3 C C2 GOL . . . D 4 16.401 -18.18 -35.167 1 39.27 ? C2 GOL 602 C 1 
HETATM 4 O O2 GOL . . . D 4 17.37 -19.198 -35.119 1 39.54 ? O2 GOL 602 C 1 
HETATM 5 C C3 GOL . . . D 4 15.06 -18.733 -34.685 1 40.41 ? C3 GOL 602 C 1 
HETATM 6 O O3 GOL . . . D 4 14.1 -17.7 -34.621 1 46.15 ? O3 GOL 602 C 1 
HETATM 7 H H11 GOL . . . D 4 16.053 -16.596 -36.586 1 55.02 ? H11 GOL 602 C 1 
HETATM 8 H H12 GOL . . . D 4 15.542 -18.193 -37.143 1 55.02 ? H12 GOL 602 C 1 
HETATM 9 H HO1 GOL . . . D 4 17.497 -17.558 -38.167 1 54.21 ? HO1 GOL 602 C 1 
HETATM 10 H H2 GOL . . . D 4 16.695 -17.36 -34.511 1 47.05 ? H2 GOL 602 C 1 
HETATM 11 H HO2 GOL . . . D 4 17.453 -19.528 -34.2 1 47.37 ? HO2 GOL 602 C 1 
HETATM 12 H H31 GOL . . . D 4 14.717 -19.509 -35.369 1 48.41 ? H31 GOL 602 C 1 
HETATM 13 H H32 GOL . . . D 4 15.182 -19.181 -33.699 1 48.41 ? H32 GOL 602 C 1 
HETATM 14 H HO3 GOL . . . D 4 14.102 -17.199 -35.463 1 55.3 ? HO3 GOL 602 C 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           14 
#