data_4D11
#
_model_server_result.job_id            2SZKXl-ytKZJUagfQRj8VQ 
_model_server_result.datetime_utc      '2024-11-08 22:24:53' 
_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          4d11 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1571}' 
#
_entry.id    4D11 
#
_exptl.entry_id    4D11 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              237.273 
_entity.id                          5 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose 
_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            4D11 
_cell.length_a            116.771 
_cell.length_b            120.898 
_cell.length_c            249.607 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4D11 
_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 tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,I,K,L,M,N,O,P,Q 1 1 
D,E,H,J,T,U,V,W,X,Y 2 1 
C,G,R,S 3 1 
F,Z,AA 4 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
? 5 M N N 
? 5 P N N 
? 5 V N N 
? 5 X 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 126 A CYS 126 1_555 A SG CYS 354 A CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
disulf ? disulf2 A SG CYS 345 A CYS 345 1_555 A SG CYS 423 A CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf3 A SG CYS 456 A CYS 456 1_555 A SG CYS 473 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? 
disulf ? disulf4 A SG CYS 496 A CYS 496 1_555 A SG CYS 513 A CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
disulf ? disulf5 A SG CYS 539 A CYS 539 1_555 A SG CYS 555 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf6 B SG CYS 126 B CYS 126 1_555 B SG CYS 354 B CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf7 B SG CYS 345 B CYS 345 1_555 B SG CYS 423 B CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf8 B SG CYS 456 B CYS 456 1_555 B SG CYS 473 B CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
disulf ? disulf9 B SG CYS 496 B CYS 496 1_555 B SG CYS 513 B CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
disulf ? disulf10 B SG CYS 539 B CYS 539 1_555 B SG CYS 555 B CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
disulf ? disulf11 C SG CYS 126 C CYS 126 1_555 C SG CYS 354 C CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
disulf ? disulf12 C SG CYS 345 C CYS 345 1_555 C SG CYS 423 C CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf13 C SG CYS 456 C CYS 456 1_555 C SG CYS 473 C CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? 
disulf ? disulf14 C SG CYS 496 C CYS 496 1_555 C SG CYS 513 C CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? 
disulf ? disulf15 D SG CYS 126 D CYS 126 1_555 D SG CYS 354 D CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf16 D SG CYS 345 D CYS 345 1_555 D SG CYS 423 D CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf17 D SG CYS 456 D CYS 456 1_555 D SG CYS 473 D CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
disulf ? disulf18 D SG CYS 496 D CYS 496 1_555 D SG CYS 513 D CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? 
disulf ? disulf19 D SG CYS 539 D CYS 539 1_555 D SG CYS 555 D CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
disulf ? disulf20 E SG CYS 126 E CYS 126 1_555 E SG CYS 354 E CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? 
disulf ? disulf21 E SG CYS 345 E CYS 345 1_555 E SG CYS 423 E CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf22 E SG CYS 456 E CYS 456 1_555 E SG CYS 473 E CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? 
disulf ? disulf23 E SG CYS 496 E CYS 496 1_555 E SG CYS 513 E CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? 
disulf ? disulf24 E SG CYS 539 E CYS 539 1_555 E SG CYS 555 E CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? 
disulf ? disulf25 F SG CYS 126 F CYS 126 1_555 F SG CYS 354 F CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc1 A OD2 ASP 224 A ASP 224 1_555 L MN MN . A MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? 
metalc ? metalc2 A NE2 HIS 226 A HIS 226 1_555 L MN MN . A MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc3 A NE2 HIS 359 A HIS 359 1_555 L MN MN . A MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? 
metalc ? metalc4 L MN MN . A MN 1570 1_555 N O3B UDP . A UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? 
metalc ? metalc5 L MN MN . A MN 1570 1_555 N O2A UDP . A UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? 
metalc ? metalc6 B OD2 ASP 224 B ASP 224 1_555 O MN MN . B MN 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? 
metalc ? metalc7 B NE2 HIS 226 B HIS 226 1_555 O MN MN . B MN 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
metalc ? metalc8 B NE2 HIS 359 B HIS 359 1_555 O MN MN . B MN 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? 
metalc ? metalc9 O MN MN . B MN 1571 1_555 Q O3B UDP . B UDP 1573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? 
metalc ? metalc10 C OD2 ASP 224 C ASP 224 1_555 R MN MN . C MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.746 ? 
metalc ? metalc11 C NE2 HIS 226 C HIS 226 1_555 R MN MN . C MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? 
metalc ? metalc12 C NE2 HIS 359 C HIS 359 1_555 R MN MN . C MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? 
metalc ? metalc13 R MN MN . C MN 1570 1_555 S O2A UDP . C UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
metalc ? metalc14 R MN MN . C MN 1570 1_555 S O3B UDP . C UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? 
metalc ? metalc15 D OD2 ASP 224 D ASP 224 1_555 T MN MN . D MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? 
metalc ? metalc16 D NE2 HIS 226 D HIS 226 1_555 T MN MN . D MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? 
metalc ? metalc17 D NE2 HIS 359 D HIS 359 1_555 T MN MN . D MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc18 T MN MN . D MN 1570 1_555 U O3B UDP . D UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? 
metalc ? metalc19 T MN MN . D MN 1570 1_555 U O2A UDP . D UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? 
metalc ? metalc20 E OD2 ASP 224 E ASP 224 1_555 W MN MN . E MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? 
metalc ? metalc21 E NE2 HIS 226 E HIS 226 1_555 W MN MN . E MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? 
metalc ? metalc22 E NE2 HIS 359 E HIS 359 1_555 W MN MN . E MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? 
metalc ? metalc23 W MN MN . E MN 1570 1_555 Y O2A UDP . E UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? 
metalc ? metalc24 W MN MN . E MN 1570 1_555 Y O3B UDP . E UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? 
metalc ? metalc25 F OD2 ASP 224 F ASP 224 1_555 Z MN MN . F MN 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? 
metalc ? metalc26 F NE2 HIS 226 F HIS 226 1_555 Z MN MN . F MN 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? 
metalc ? metalc27 F NE2 HIS 359 F HIS 359 1_555 Z MN MN . F MN 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? 
metalc ? metalc28 Z MN MN . F MN 1363 1_555 AA O2A UDP . F UDP 1364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? 
metalc ? metalc29 Z MN MN . F MN 1363 1_555 AA O3B UDP . F UDP 1364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? 
#
_chem_comp.formula           'C8 H15 N O5 S' 
_chem_comp.formula_weight    237.273 
_chem_comp.id                BBK 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-5-thio-alpha-D-galactopyranose 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     2-(acetylamino)-2-deoxy-5-thio-alpha-D-galactopyranose;2-acetamido-2-deoxy-5-thio-alpha-D-galactose;2-acetamido-2-deoxy-5-thio-D-galactose;2-acetamido-2-deoxy-5-thio-galactose 
#
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
S5 C1 BBK sing 70 n n 
C2 C1 BBK sing 71 n n 
C1 O1 BBK sing 72 n n 
C1 H1 BBK sing 73 n n 
O1 HO1 BBK sing 74 n n 
C2 C3 BBK sing 75 n n 
C2 N2 BBK sing 76 n n 
C2 H2 BBK sing 77 n n 
N2 C7 BBK sing 78 n n 
N2 HN2 BBK sing 79 n n 
C4 C3 BBK sing 80 n n 
C3 O3 BBK sing 81 n n 
C3 H3 BBK sing 82 n n 
O3 HO3 BBK sing 83 n n 
O4 C4 BBK sing 84 n n 
C4 C5 BBK sing 85 n n 
C4 H4 BBK sing 86 n n 
O4 HO4 BBK sing 87 n n 
C6 C5 BBK sing 88 n n 
C5 S5 BBK sing 89 n n 
C5 H5 BBK sing 90 n n 
C6 O6 BBK sing 91 n n 
C6 H6 BBK sing 92 n n 
C6 H6A BBK sing 93 n n 
O6 HO6 BBK sing 94 n n 
O7 C7 BBK doub 95 n n 
C7 C8 BBK sing 96 n n 
C8 H8 BBK sing 97 n n 
C8 H8A BBK sing 98 n n 
C8 H8B BBK sing 99 n n 
#
_atom_sites.entry_id                     4D11 
_atom_sites.fract_transf_matrix[1][1]    0.008564 
_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]    0.008271 
_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]    0.004006 
_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
L 4 MN A 1 1570 1570 MN MN . 
M 5 BBK A 1 1571 1571 BBK BBK . 
N 6 UDP A 1 1572 1572 UDP UDP . 
O 4 MN B 1 1571 1571 MN MN . 
P 5 BBK B 1 1572 1572 BBK BBK . 
Q 6 UDP B 1 1573 1573 UDP UDP . 
R 4 MN C 1 1570 1570 MN MN . 
S 6 UDP C 1 1571 1571 UDP UDP . 
T 4 MN D 1 1570 1570 MN MN . 
U 6 UDP D 1 1571 1571 UDP UDP . 
V 5 BBK D 1 1572 1572 BBK BBK . 
W 4 MN E 1 1570 1570 MN MN . 
X 5 BBK E 1 1571 1571 BBK BBK . 
Y 6 UDP E 1 1572 1572 UDP UDP . 
Z 4 MN F 1 1363 1363 MN MN . 
AA 6 UDP F 1 1364 1364 UDP UDP . 
#
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 BBK . . . M 5 139.134 28.636 18.966 1 78.98 ? C1 BBK 1571 A 1 
HETATM 2 O O1 BBK . . . M 5 138.971 29.115 17.635 1 82.79 ? O1 BBK 1571 A 1 
HETATM 3 C C2 BBK . . . M 5 139.282 27.126 18.788 1 77.29 ? C2 BBK 1571 A 1 
HETATM 4 N N2 BBK . . . M 5 139.994 26.902 17.558 1 75.87 ? N2 BBK 1571 A 1 
HETATM 5 C C3 BBK . . . M 5 137.942 26.448 18.636 1 76.56 ? C3 BBK 1571 A 1 
HETATM 6 O O3 BBK . . . M 5 138.114 25.034 18.483 1 79.83 ? O3 BBK 1571 A 1 
HETATM 7 C C4 BBK . . . M 5 137.016 26.847 19.799 1 72.57 ? C4 BBK 1571 A 1 
HETATM 8 O O4 BBK . . . M 5 137.527 26.402 21.07 1 65.99 ? O4 BBK 1571 A 1 
HETATM 9 C C5 BBK . . . M 5 136.792 28.376 19.727 1 66.88 ? C5 BBK 1571 A 1 
HETATM 10 S S5 BBK . . . M 5 138.04 29.087 19.781 1 77.82 ? S5 BBK 1571 A 1 
HETATM 11 C C6 BBK . . . M 5 135.933 28.94 20.86 1 61.78 ? C6 BBK 1571 A 1 
HETATM 12 O O6 BBK . . . M 5 134.788 29.502 20.272 1 52.55 ? O6 BBK 1571 A 1 
HETATM 13 C C7 BBK . . . M 5 140.762 25.837 17.378 1 81.88 ? C7 BBK 1571 A 1 
HETATM 14 O O7 BBK . . . M 5 140.874 25.015 18.266 1 88.96 ? O7 BBK 1571 A 1 
HETATM 15 C C8 BBK . . . M 5 141.476 25.706 16.048 1 78.44 ? C8 BBK 1571 A 1 
#
_model_server_stats.io_time_ms              49 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    41 
_model_server_stats.query_time_ms           271 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           15 
#