data_5JQ7
#
_model_server_result.job_id            MzY-xOuP-Rwgb_ybF41SPw 
_model_server_result.datetime_utc      '2024-11-25 00:21:49' 
_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          5jq7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":605}' 
#
_entry.id    5JQ7 
#
_exptl.entry_id    5JQ7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              92.094 
_entity.id                          5 
_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         120 
_cell.entry_id            5JQ7 
_cell.length_a            113.45 
_cell.length_b            113.45 
_cell.length_c            306.87 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5JQ7 
_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,G,H,I,J,K,L,M 
_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_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -56.725 98.250582 0 
3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -113.45 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 H N N 
? 5 I N N 
#
_pdbx_entity_branch.entity_id    3 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
3 ? 3 4 3 MAN BMA C1 O1 . O6 HO6 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
3 n C NAG 1 C 1 NAG D 621 NAG 
3 n C NAG 2 C 2 NAG D 622 NAG 
3 n C BMA 3 C 3 BMA D 623 BMA 
3 n C MAN 4 C 4 MAN D 624 MAN 
#
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 26 A CYS 53 1_555 B SG CYS 108 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf2 A SG CYS 81 A CYS 108 1_555 A SG CYS 108 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 A SG CYS 94 A CYS 121 1_555 A SG CYS 120 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
covale ? covale1 A ND2 ASN 201 A ASN 228 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
covale ? covale2 A ND2 ASN 211 A ASN 238 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale3 A ND2 ASN 230 A ASN 257 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale4 A ND2 ASN 241 A ASN 268 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale5 B ND2 ASN 62 B ASN 563 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale7 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale8 C O6 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
#
_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 162 n n 
C1 C2 GOL sing 163 n n 
C1 H11 GOL sing 164 n n 
C1 H12 GOL sing 165 n n 
O1 HO1 GOL sing 166 n n 
C2 O2 GOL sing 167 n n 
C2 C3 GOL sing 168 n n 
C2 H2 GOL sing 169 n n 
O2 HO2 GOL sing 170 n n 
C3 O3 GOL sing 171 n n 
C3 H31 GOL sing 172 n n 
C3 H32 GOL sing 173 n n 
O3 HO3 GOL sing 174 n n 
#
_atom_sites.entry_id                     5JQ7 
_atom_sites.fract_transf_matrix[1][1]    0.008814 
_atom_sites.fract_transf_matrix[1][2]    0.005089 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010178 
_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]    0.003259 
_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 4 NAG A 1 601 2 NAG NAG . 
E 4 NAG A 1 602 10 NAG NAG . 
F 4 NAG A 1 603 11 NAG NAG . 
G 4 NAG A 1 604 12 NAG NAG . 
H 5 GOL A 1 605 6 GOL GOL . 
I 5 GOL A 1 606 7 GOL GOL . 
J 6 DMS A 1 607 1 DMS DMS . 
K 7 T0R B 1 705 1 T0R T0R . 
L 8 HOH A 1 701 18 HOH HOH . 
L 8 HOH A 2 702 10 HOH HOH . 
L 8 HOH A 3 703 146 HOH HOH . 
L 8 HOH A 4 704 6 HOH HOH . 
L 8 HOH A 5 705 37 HOH HOH . 
L 8 HOH A 6 706 17 HOH HOH . 
L 8 HOH A 7 707 141 HOH HOH . 
L 8 HOH A 8 708 38 HOH HOH . 
L 8 HOH A 9 709 5 HOH HOH . 
L 8 HOH A 10 710 41 HOH HOH . 
L 8 HOH A 11 711 8 HOH HOH . 
L 8 HOH A 12 712 50 HOH HOH . 
L 8 HOH A 13 713 1 HOH HOH . 
L 8 HOH A 14 714 140 HOH HOH . 
L 8 HOH A 15 715 23 HOH HOH . 
L 8 HOH A 16 716 85 HOH HOH . 
L 8 HOH A 17 717 46 HOH HOH . 
L 8 HOH A 18 718 136 HOH HOH . 
L 8 HOH A 19 719 69 HOH HOH . 
L 8 HOH A 20 720 127 HOH HOH . 
L 8 HOH A 21 721 135 HOH HOH . 
L 8 HOH A 22 722 97 HOH HOH . 
L 8 HOH A 23 723 22 HOH HOH . 
L 8 HOH A 24 724 68 HOH HOH . 
L 8 HOH A 25 725 83 HOH HOH . 
L 8 HOH A 26 726 121 HOH HOH . 
L 8 HOH A 27 727 123 HOH HOH . 
L 8 HOH A 28 728 53 HOH HOH . 
L 8 HOH A 29 729 147 HOH HOH . 
L 8 HOH A 30 730 26 HOH HOH . 
L 8 HOH A 31 731 118 HOH HOH . 
L 8 HOH A 32 732 111 HOH HOH . 
M 8 HOH B 1 801 74 HOH HOH . 
M 8 HOH B 2 802 29 HOH HOH . 
M 8 HOH B 3 803 67 HOH HOH . 
M 8 HOH B 4 804 3 HOH HOH . 
M 8 HOH B 5 805 20 HOH HOH . 
M 8 HOH B 6 806 52 HOH HOH . 
M 8 HOH B 7 807 87 HOH HOH . 
M 8 HOH B 8 808 65 HOH HOH . 
M 8 HOH B 9 809 142 HOH HOH . 
M 8 HOH B 10 810 49 HOH HOH . 
M 8 HOH B 11 811 99 HOH HOH . 
M 8 HOH B 12 812 112 HOH HOH . 
M 8 HOH B 13 813 84 HOH HOH . 
M 8 HOH B 14 814 36 HOH HOH . 
M 8 HOH B 15 815 60 HOH HOH . 
M 8 HOH B 16 816 86 HOH HOH . 
M 8 HOH B 17 817 126 HOH HOH . 
M 8 HOH B 18 818 144 HOH HOH . 
M 8 HOH B 19 819 45 HOH HOH . 
M 8 HOH B 20 820 143 HOH HOH . 
M 8 HOH B 21 821 43 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 . . . H 5 -61.136 20.426 -39.332 1 91.99 ? C1 GOL 605 A 1 
HETATM 2 O O1 GOL . . . H 5 -60.75 21.619 -38.64 1 90.92 ? O1 GOL 605 A 1 
HETATM 3 C C2 GOL . . . H 5 -62.091 19.601 -38.474 1 92.02 ? C2 GOL 605 A 1 
HETATM 4 O O2 GOL . . . H 5 -61.805 19.808 -37.089 1 91.61 ? O2 GOL 605 A 1 
HETATM 5 C C3 GOL . . . H 5 -63.537 19.993 -38.762 1 96.85 ? C3 GOL 605 A 1 
HETATM 6 O O3 GOL . . . H 5 -64.426 19.303 -37.872 1 99.53 ? O3 GOL 605 A 1 
#
_model_server_stats.io_time_ms              13 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           290 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           6 
#