data_5DF0
#
_model_server_result.job_id            fgzcfNo3JzA5YKKH4jcilQ 
_model_server_result.datetime_utc      '2024-10-10 07:21:01' 
_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          5df0 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"P","auth_seq_id":605}' 
#
_entry.id    5DF0 
#
_exptl.entry_id    5DF0 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.274 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            (2R,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methylhexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol 
_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         90 
_cell.entry_id            5DF0 
_cell.length_a            96.712 
_cell.length_b            112.766 
_cell.length_c            129.591 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5DF0 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,E,F,G,H,I,J,K,S 1 1 
B,L,M,N,O,P,Q,R,T 2 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
? 4 G N N 
? 4 P 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 106 A CYS 106 1_555 A SG CYS 111 A CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 185 A CYS 185 1_555 A SG CYS 208 A CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 B SG CYS 106 B CYS 106 1_555 B SG CYS 111 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf4 B SG CYS 185 B CYS 185 1_555 B SG CYS 208 B CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale1 F C1 SN5 . A SN5 604 1_555 G O4 58Y . A 58Y 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale2 B ND2 ASN 444 B ASN 444 1_555 N C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale3 O C1 SN5 . B SN5 604 1_555 P O4 58Y . B 58Y 605 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
#
_chem_comp.formula           'C8 H15 N O4 S' 
_chem_comp.formula_weight    221.274 
_chem_comp.id                58Y 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              (2R,3aR,5R,6R,7R,7aR)-5-(hydroxymethyl)-2-methylhexahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
C8 C7 58Y sing 1 n n 
C7 S1 58Y sing 2 n n 
C7 N2 58Y sing 3 n n 
S1 C1 58Y sing 4 n n 
N2 C2 58Y sing 5 n n 
C1 C2 58Y sing 6 n n 
C1 O5 58Y sing 7 n n 
C2 C3 58Y sing 8 n n 
O5 C5 58Y sing 9 n n 
C5 C4 58Y sing 10 n n 
C5 C6 58Y sing 11 n n 
C3 C4 58Y sing 12 n n 
C3 O3 58Y sing 13 n n 
C4 O4 58Y sing 14 n n 
C6 O6 58Y sing 15 n n 
C1 H1 58Y sing 16 n n 
C2 H2 58Y sing 17 n n 
C3 H3 58Y sing 18 n n 
C4 H4 58Y sing 19 n n 
C5 H5 58Y sing 20 n n 
C6 H6 58Y sing 21 n n 
C6 H7 58Y sing 22 n n 
C7 H8 58Y sing 23 n n 
C8 H9 58Y sing 24 n n 
C8 H10 58Y sing 25 n n 
C8 H11 58Y sing 26 n n 
N2 H12 58Y sing 27 n n 
O3 H14 58Y sing 28 n n 
O4 H15 58Y sing 29 n n 
O6 H16 58Y sing 30 n n 
#
_atom_sites.entry_id                     5DF0 
_atom_sites.fract_transf_matrix[1][1]    0.01034 
_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]    0.008868 
_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]    0.007717 
_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 2 NAG A 1 601 546 NAG NAG . 
D 2 NAG A 1 602 547 NAG NAG . 
E 2 NAG A 1 603 550 NAG NAG . 
F 3 SN5 A 1 604 561 SN5 SN5 . 
G 4 58Y A 1 605 560 58Y NGT . 
H 5 CL A 1 606 554 CL CL . 
I 6 SO4 A 1 607 766 SO4 SO4 . 
J 6 SO4 A 1 608 767 SO4 SO4 . 
K 6 SO4 A 1 609 768 SO4 SO4 . 
L 2 NAG B 1 601 550 NAG NAG . 
M 2 NAG B 1 602 552 NAG NAG . 
N 2 NAG B 1 603 553 NAG NAG . 
O 3 SN5 B 1 604 561 SN5 SN5 . 
P 4 58Y B 1 605 560 58Y NGT . 
Q 6 SO4 B 1 606 901 SO4 SO4 . 
R 6 SO4 B 1 607 902 SO4 SO4 . 
S 7 HOH A 1 701 616 HOH HOH . 
S 7 HOH A 2 702 609 HOH HOH . 
S 7 HOH A 3 703 717 HOH HOH . 
S 7 HOH A 4 704 765 HOH HOH . 
T 7 HOH B 1 701 565 HOH HOH . 
T 7 HOH B 2 702 577 HOH HOH . 
T 7 HOH B 3 703 900 HOH HOH . 
T 7 HOH B 4 704 684 HOH HOH . 
T 7 HOH B 5 705 774 HOH HOH . 
T 7 HOH B 6 706 639 HOH HOH . 
T 7 HOH B 7 707 750 HOH HOH . 
T 7 HOH B 8 708 877 HOH HOH . 
T 7 HOH B 9 709 736 HOH HOH . 
T 7 HOH B 10 710 702 HOH HOH . 
T 7 HOH B 11 711 641 HOH HOH . 
T 7 HOH B 12 712 854 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 58Y . . . P 4 -55.441 -11.478 276.85 1 24.11 ? C1 58Y 605 B 1 
HETATM 2 C C2 58Y . . . P 4 -56.396 -12.139 276.027 1 24.99 ? C2 58Y 605 B 1 
HETATM 3 C C3 58Y . . . P 4 -57.688 -12.309 276.704 1 28.26 ? C3 58Y 605 B 1 
HETATM 4 C C4 58Y . . . P 4 -57.608 -12.858 278.134 1 29.53 ? C4 58Y 605 B 1 
HETATM 5 C C5 58Y . . . P 4 -56.44 -12.305 278.964 1 29.98 ? C5 58Y 605 B 1 
HETATM 6 C C6 58Y . . . P 4 -56.203 -13.215 280.211 1 30.26 ? C6 58Y 605 B 1 
HETATM 7 C C7 58Y . . . P 4 -56.345 -9.753 275.271 1 21.55 ? C7 58Y 605 B 1 
HETATM 8 C C8 58Y . . . P 4 -57.496 -8.728 275.142 1 19.23 ? C8 58Y 605 B 1 
HETATM 9 N N2 58Y . . . P 4 -56.788 -11.075 274.845 1 23.74 ? N2 58Y 605 B 1 
HETATM 10 S S1 58Y . . . P 4 -55.908 -9.929 276.817 1 29.14 ? S1 58Y 605 B 1 
HETATM 11 O O3 58Y . . . P 4 -58.497 -13.2 275.902 1 40.19 ? O3 58Y 605 B 1 
HETATM 12 O O4 58Y . . . P 4 -57.592 -14.274 278.118 1 30.81 ? O4 58Y 605 B 1 
HETATM 13 O O5 58Y . . . P 4 -55.283 -12.222 278.301 1 26 ? O5 58Y 605 B 1 
HETATM 14 O O6 58Y . . . P 4 -54.921 -13.788 280.085 1 30.67 ? O6 58Y 605 B 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           26 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           266 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#