data_5VCG
#
_model_server_result.job_id            7WLqGok7wlLZpypIgWwDKQ 
_model_server_result.datetime_utc      '2024-11-08 04:37:22' 
_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          5vcg 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":605}' 
#
_entry.id    5VCG 
#
_exptl.entry_id    5VCG 
_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    4 
_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            5VCG 
_cell.length_a            76.539 
_cell.length_b            100.459 
_cell.length_c            133.679 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VCG 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        23 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'I 2 2 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 dimeric 2 author_and_software_defined_assembly 1 
PISA tetrameric 4 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,B,C,D,E,F,G,H 1 1,2 
A,B,C,D,E,F,G,H 2 1,2,3,4 
#
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_455 -x-1,-y,z -1 0 0 0 -1 0 0 0 1 -77.34 0 0 
3 'crystal symmetry operation' 3_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -77.34 0 0 
4 'crystal symmetry operation' 4_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 G N N 
#
_struct_conn.conn_type_id                   metalc 
_struct_conn.details                        ? 
_struct_conn.id                             metalc1 
_struct_conn.ptnr1_label_asym_id            A 
_struct_conn.ptnr1_label_atom_id            SG 
_struct_conn.ptnr1_label_comp_id            CYS 
_struct_conn.ptnr1_label_seq_id             422 
_struct_conn.ptnr1_auth_asym_id             A 
_struct_conn.ptnr1_auth_comp_id             CYS 
_struct_conn.ptnr1_auth_seq_id              442 
_struct_conn.ptnr1_symmetry                 1_555 
_struct_conn.ptnr2_label_asym_id            B 
_struct_conn.ptnr2_label_atom_id            FE 
_struct_conn.ptnr2_label_comp_id            HEM 
_struct_conn.ptnr2_label_seq_id             . 
_struct_conn.ptnr2_auth_asym_id             A 
_struct_conn.ptnr2_auth_comp_id             HEM 
_struct_conn.ptnr2_auth_seq_id              601 
_struct_conn.ptnr2_symmetry                 1_555 
_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                2.3 
_struct_conn.pdbx_value_order               ? 
#
_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 218 n n 
C1 C2 GOL sing 219 n n 
C1 H11 GOL sing 220 n n 
C1 H12 GOL sing 221 n n 
O1 HO1 GOL sing 222 n n 
C2 O2 GOL sing 223 n n 
C2 C3 GOL sing 224 n n 
C2 H2 GOL sing 225 n n 
O2 HO2 GOL sing 226 n n 
C3 O3 GOL sing 227 n n 
C3 H31 GOL sing 228 n n 
C3 H32 GOL sing 229 n n 
O3 HO3 GOL sing 230 n n 
#
_atom_sites.entry_id                     5VCG 
_atom_sites.fract_transf_matrix[1][1]    0.013065 
_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]    0.009954 
_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]    0.007481 
_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 HEM A 1 601 599 HEM HEM . 
C 3 08Y A 1 602 600 08Y 08Y . 
D 4 GOL A 1 603 700 GOL GOL . 
E 4 GOL A 1 604 701 GOL GOL . 
F 4 GOL A 1 605 702 GOL GOL . 
G 4 GOL A 1 606 703 GOL GOL . 
H 5 HOH A 1 701 4 HOH HOH . 
H 5 HOH A 2 702 33 HOH HOH . 
H 5 HOH A 3 703 76 HOH HOH . 
H 5 HOH A 4 704 49 HOH HOH . 
H 5 HOH A 5 705 55 HOH HOH . 
H 5 HOH A 6 706 57 HOH HOH . 
H 5 HOH A 7 707 52 HOH HOH . 
H 5 HOH A 8 708 28 HOH HOH . 
H 5 HOH A 9 709 46 HOH HOH . 
H 5 HOH A 10 710 45 HOH HOH . 
H 5 HOH A 11 711 6 HOH HOH . 
H 5 HOH A 12 712 10 HOH HOH . 
H 5 HOH A 13 713 51 HOH HOH . 
H 5 HOH A 14 714 14 HOH HOH . 
H 5 HOH A 15 715 1 HOH HOH . 
H 5 HOH A 16 716 60 HOH HOH . 
H 5 HOH A 17 717 38 HOH HOH . 
H 5 HOH A 18 718 53 HOH HOH . 
H 5 HOH A 19 719 30 HOH HOH . 
H 5 HOH A 20 720 20 HOH HOH . 
H 5 HOH A 21 721 19 HOH HOH . 
H 5 HOH A 22 722 21 HOH HOH . 
H 5 HOH A 23 723 65 HOH HOH . 
H 5 HOH A 24 724 11 HOH HOH . 
H 5 HOH A 25 725 68 HOH HOH . 
H 5 HOH A 26 726 42 HOH HOH . 
H 5 HOH A 27 727 17 HOH HOH . 
H 5 HOH A 28 728 61 HOH HOH . 
H 5 HOH A 29 729 5 HOH HOH . 
H 5 HOH A 30 730 22 HOH HOH . 
H 5 HOH A 31 731 16 HOH HOH . 
H 5 HOH A 32 732 47 HOH HOH . 
H 5 HOH A 33 733 67 HOH HOH . 
H 5 HOH A 34 734 66 HOH HOH . 
H 5 HOH A 35 735 39 HOH HOH . 
H 5 HOH A 36 736 31 HOH HOH . 
H 5 HOH A 37 737 71 HOH HOH . 
H 5 HOH A 38 738 54 HOH HOH . 
H 5 HOH A 39 739 15 HOH HOH . 
H 5 HOH A 40 740 29 HOH HOH . 
H 5 HOH A 41 741 2 HOH HOH . 
H 5 HOH A 42 742 69 HOH HOH . 
H 5 HOH A 43 743 73 HOH HOH . 
H 5 HOH A 44 744 36 HOH HOH . 
H 5 HOH A 45 745 64 HOH HOH . 
H 5 HOH A 46 746 9 HOH HOH . 
H 5 HOH A 47 747 40 HOH HOH . 
H 5 HOH A 48 748 32 HOH HOH . 
H 5 HOH A 49 749 13 HOH HOH . 
H 5 HOH A 50 750 62 HOH HOH . 
H 5 HOH A 51 751 72 HOH HOH . 
H 5 HOH A 52 752 75 HOH HOH . 
H 5 HOH A 53 753 34 HOH HOH . 
H 5 HOH A 54 754 70 HOH HOH . 
H 5 HOH A 55 755 25 HOH HOH . 
H 5 HOH A 56 756 56 HOH HOH . 
H 5 HOH A 57 757 18 HOH HOH . 
H 5 HOH A 58 758 63 HOH HOH . 
H 5 HOH A 59 759 37 HOH HOH . 
H 5 HOH A 60 760 43 HOH HOH . 
H 5 HOH A 61 761 44 HOH HOH . 
H 5 HOH A 62 762 24 HOH HOH . 
H 5 HOH A 63 763 23 HOH HOH . 
H 5 HOH A 64 764 48 HOH HOH . 
H 5 HOH A 65 765 27 HOH HOH . 
H 5 HOH A 66 766 74 HOH HOH . 
H 5 HOH A 67 767 59 HOH HOH . 
H 5 HOH A 68 768 26 HOH HOH . 
H 5 HOH A 69 769 12 HOH HOH . 
H 5 HOH A 70 770 58 HOH HOH . 
H 5 HOH A 71 771 41 HOH HOH . 
H 5 HOH A 72 772 35 HOH HOH . 
H 5 HOH A 73 773 50 HOH HOH . 
H 5 HOH A 74 774 7 HOH HOH . 
H 5 HOH A 75 775 3 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 -6.605 -16.971 -36.877 1 91.5 ? C1 GOL 605 A 1 
HETATM 2 O O1 GOL . . . F 4 -5.723 -16.632 -35.795 1 89.67 ? O1 GOL 605 A 1 
HETATM 3 C C2 GOL . . . F 4 -6.898 -18.473 -36.887 1 90.83 ? C2 GOL 605 A 1 
HETATM 4 O O2 GOL . . . F 4 -5.712 -19.193 -36.517 1 88.49 ? O2 GOL 605 A 1 
HETATM 5 C C3 GOL . . . F 4 -7.354 -18.949 -38.27 1 92.57 ? C3 GOL 605 A 1 
HETATM 6 O O3 GOL . . . F 4 -8.321 -18.058 -38.843 1 94.86 ? O3 GOL 605 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           352 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           6 
#