data_5KND
#
_model_server_result.job_id            aUSidQxXPCHrnE4PN5Wc2Q 
_model_server_result.datetime_utc      '2024-12-03 18:53:21' 
_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          5knd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":301}' 
#
_entry.id    5KND 
#
_exptl.entry_id    5KND 
_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            5KND 
_cell.length_a            128.22 
_cell.length_b            128.352 
_cell.length_c            228.033 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5KND 
_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        PISA 
_pdbx_struct_assembly.oligomeric_details    octameric 
_pdbx_struct_assembly.oligomeric_count      8 
_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,N,O,P,Q,R,S,T,U,V 
_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
? 6 J N N 
? 6 L N N 
? 6 N 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
metalc ? metalc1 C OG1 THR 246 C THR 239 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? 
metalc ? metalc2 I MG MG . C MG 601 1_555 K O4 PO4 . C PO4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
metalc ? metalc3 I MG MG . C MG 601 1_555 Q O HOH . C HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc4 I MG MG . C MG 601 1_555 Q O HOH . C HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? 
metalc ? metalc5 I MG MG . C MG 601 1_555 Q O HOH . C HOH 712 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.614 ? 
#
_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 173 n n 
C1 C2 GOL sing 174 n n 
C1 H11 GOL sing 175 n n 
C1 H12 GOL sing 176 n n 
O1 HO1 GOL sing 177 n n 
C2 O2 GOL sing 178 n n 
C2 C3 GOL sing 179 n n 
C2 H2 GOL sing 180 n n 
O2 HO2 GOL sing 181 n n 
C3 O3 GOL sing 182 n n 
C3 H31 GOL sing 183 n n 
C3 H32 GOL sing 184 n n 
O3 HO3 GOL sing 185 n n 
#
_atom_sites.entry_id                     5KND 
_atom_sites.fract_transf_matrix[1][1]    0.007799 
_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]    0.007791 
_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]    0.004385 
_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
I 5 MG C 1 601 601 MG MG . 
J 6 GOL C 1 602 602 GOL GOL . 
K 7 PO4 C 1 603 603 PO4 PO4 . 
L 6 GOL F 1 501 501 GOL GOL . 
M 8 B3P F 1 502 502 B3P B3P . 
N 6 GOL G 1 301 301 GOL GOL . 
O 9 HOH A 1 601 601 HOH HOH . 
O 9 HOH A 2 602 602 HOH HOH . 
O 9 HOH A 3 603 603 HOH HOH . 
O 9 HOH A 4 604 604 HOH HOH . 
O 9 HOH A 5 605 605 HOH HOH . 
O 9 HOH A 6 606 606 HOH HOH . 
O 9 HOH A 7 607 607 HOH HOH . 
O 9 HOH A 8 608 608 HOH HOH . 
O 9 HOH A 9 609 609 HOH HOH . 
O 9 HOH A 10 610 610 HOH HOH . 
O 9 HOH A 11 611 611 HOH HOH . 
O 9 HOH A 12 612 612 HOH HOH . 
O 9 HOH A 13 613 613 HOH HOH . 
O 9 HOH A 14 614 614 HOH HOH . 
P 9 HOH B 1 601 601 HOH HOH . 
P 9 HOH B 2 602 602 HOH HOH . 
P 9 HOH B 3 603 603 HOH HOH . 
P 9 HOH B 4 604 604 HOH HOH . 
P 9 HOH B 5 605 605 HOH HOH . 
P 9 HOH B 6 606 606 HOH HOH . 
P 9 HOH B 7 607 607 HOH HOH . 
P 9 HOH B 8 608 608 HOH HOH . 
P 9 HOH B 9 609 609 HOH HOH . 
P 9 HOH B 10 610 610 HOH HOH . 
P 9 HOH B 11 611 611 HOH HOH . 
P 9 HOH B 12 612 612 HOH HOH . 
P 9 HOH B 13 613 613 HOH HOH . 
P 9 HOH B 14 614 614 HOH HOH . 
Q 9 HOH C 1 701 701 HOH HOH . 
Q 9 HOH C 2 702 702 HOH HOH . 
Q 9 HOH C 3 703 703 HOH HOH . 
Q 9 HOH C 4 704 704 HOH HOH . 
Q 9 HOH C 5 705 705 HOH HOH . 
Q 9 HOH C 6 706 706 HOH HOH . 
Q 9 HOH C 7 707 707 HOH HOH . 
Q 9 HOH C 8 708 708 HOH HOH . 
Q 9 HOH C 9 709 709 HOH HOH . 
Q 9 HOH C 10 710 710 HOH HOH . 
Q 9 HOH C 11 711 711 HOH HOH . 
Q 9 HOH C 12 712 712 HOH HOH . 
Q 9 HOH C 13 713 713 HOH HOH . 
Q 9 HOH C 14 714 714 HOH HOH . 
Q 9 HOH C 15 715 715 HOH HOH . 
Q 9 HOH C 16 716 716 HOH HOH . 
Q 9 HOH C 17 717 717 HOH HOH . 
Q 9 HOH C 18 718 718 HOH HOH . 
R 9 HOH D 1 501 501 HOH HOH . 
R 9 HOH D 2 502 502 HOH HOH . 
S 9 HOH E 1 501 501 HOH HOH . 
S 9 HOH E 2 502 502 HOH HOH . 
S 9 HOH E 3 503 503 HOH HOH . 
S 9 HOH E 4 504 504 HOH HOH . 
S 9 HOH E 5 505 505 HOH HOH . 
S 9 HOH E 6 506 506 HOH HOH . 
S 9 HOH E 7 507 507 HOH HOH . 
S 9 HOH E 8 508 508 HOH HOH . 
T 9 HOH F 1 601 601 HOH HOH . 
T 9 HOH F 2 602 602 HOH HOH . 
T 9 HOH F 3 603 603 HOH HOH . 
T 9 HOH F 4 604 604 HOH HOH . 
T 9 HOH F 5 605 605 HOH HOH . 
U 9 HOH G 1 401 401 HOH HOH . 
U 9 HOH G 2 402 402 HOH HOH . 
V 9 HOH H 1 201 201 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 . . . N 6 26.319 8.887 37.73 1 70.53 ? C1 GOL 301 G 1 
HETATM 2 O O1 GOL . . . N 6 25.671 8.481 36.544 1 69.72 ? O1 GOL 301 G 1 
HETATM 3 C C2 GOL . . . N 6 27.608 8.092 37.916 1 71.3 ? C2 GOL 301 G 1 
HETATM 4 O O2 GOL . . . N 6 28.692 8.975 38.103 1 71.37 ? O2 GOL 301 G 1 
HETATM 5 C C3 GOL . . . N 6 27.487 7.17 39.126 1 71.63 ? C3 GOL 301 G 1 
HETATM 6 O O3 GOL . . . N 6 27.304 7.935 40.296 1 72.04 ? O3 GOL 301 G 1 
#
_model_server_stats.io_time_ms              77 
_model_server_stats.parse_time_ms           235 
_model_server_stats.create_model_time_ms    241 
_model_server_stats.query_time_ms           419 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           6 
#