data_5Y42
#
_model_server_result.job_id            DQIG5ohdfMWNzZNfPG2zlQ 
_model_server_result.datetime_utc      '2024-12-23 19:22:21' 
_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          5y42 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":301}' 
#
_entry.id    5Y42 
#
_exptl.entry_id    5Y42 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    1 
_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            5Y42 
_cell.length_a            171.226 
_cell.length_b            171.226 
_cell.length_c            75.85 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5Y42 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        172 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 64' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 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,B,C,G,H,I,J 1 1 
D,E,F,K,L,M 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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      4 
_struct_asym.id                             G 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 B SG CYS 202 B CYS 249 1_555 C SG CYS 3 C CYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf2 C SG CYS 19 C CYS 19 1_555 C SG CYS 38 C CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf3 C SG CYS 60 C CYS 60 1_555 C SG CYS 77 C CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? 
disulf ? disulf4 C SG CYS 149 C CYS 149 1_555 C SG CYS 164 C CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf5 C SG CYS 190 C CYS 190 1_555 C SG CYS 209 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf6 E SG CYS 202 E CYS 249 1_555 F SG CYS 3 F CYS 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf7 F SG CYS 19 F CYS 19 1_555 F SG CYS 38 F CYS 38 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf8 F SG CYS 60 F CYS 60 1_555 F SG CYS 77 F CYS 77 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
disulf ? disulf9 F SG CYS 149 F CYS 149 1_555 F SG CYS 164 F CYS 164 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? 
disulf ? disulf10 F SG CYS 190 F CYS 190 1_555 F SG CYS 209 F CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                NAG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-beta-D-glucopyranose 
_chem_comp.type              'd-saccharide, beta linking' 
_chem_comp.pdbx_synonyms     N-acetyl-beta-D-glucosamine;2-acetamido-2-deoxy-beta-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;N-ACETYL-D-GLUCOSAMINE 
#
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 C2 NAG sing 237 n n 
C1 O1 NAG sing 238 n n 
C1 O5 NAG sing 239 n n 
C1 H1 NAG sing 240 n n 
C2 C3 NAG sing 241 n n 
C2 N2 NAG sing 242 n n 
C2 H2 NAG sing 243 n n 
C3 C4 NAG sing 244 n n 
C3 O3 NAG sing 245 n n 
C3 H3 NAG sing 246 n n 
C4 C5 NAG sing 247 n n 
C4 O4 NAG sing 248 n n 
C4 H4 NAG sing 249 n n 
C5 C6 NAG sing 250 n n 
C5 O5 NAG sing 251 n n 
C5 H5 NAG sing 252 n n 
C6 O6 NAG sing 253 n n 
C6 H61 NAG sing 254 n n 
C6 H62 NAG sing 255 n n 
C7 C8 NAG sing 256 n n 
C7 N2 NAG sing 257 n n 
C7 O7 NAG doub 258 n n 
C8 H81 NAG sing 259 n n 
C8 H82 NAG sing 260 n n 
C8 H83 NAG sing 261 n n 
N2 HN2 NAG sing 262 n n 
O1 HO1 NAG sing 263 n n 
O3 HO3 NAG sing 264 n n 
O4 HO4 NAG sing 265 n n 
O6 HO6 NAG sing 266 n n 
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.identifier
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
NAG DGlcpNAcb 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
NAG N-acetyl-b-D-glucopyranosamine 'COMMON NAME' GMML 1 
NAG b-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
NAG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     5Y42 
_atom_sites.fract_transf_matrix[1][1]    0.00584 
_atom_sites.fract_transf_matrix[1][2]    0.003372 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006744 
_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]    0.013184 
_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
G 4 NAG C 1 301 1 NAG NAG . 
H 5 HOH A 1 101 80 HOH HOH . 
H 5 HOH A 2 102 107 HOH HOH . 
H 5 HOH A 3 103 129 HOH HOH . 
H 5 HOH A 4 104 10 HOH HOH . 
H 5 HOH A 5 105 138 HOH HOH . 
I 5 HOH B 1 301 106 HOH HOH . 
I 5 HOH B 2 302 15 HOH HOH . 
I 5 HOH B 3 303 82 HOH HOH . 
I 5 HOH B 4 304 54 HOH HOH . 
I 5 HOH B 5 305 125 HOH HOH . 
I 5 HOH B 6 306 30 HOH HOH . 
I 5 HOH B 7 307 151 HOH HOH . 
I 5 HOH B 8 308 20 HOH HOH . 
I 5 HOH B 9 309 153 HOH HOH . 
I 5 HOH B 10 310 111 HOH HOH . 
I 5 HOH B 11 311 40 HOH HOH . 
I 5 HOH B 12 312 35 HOH HOH . 
I 5 HOH B 13 313 105 HOH HOH . 
I 5 HOH B 14 314 102 HOH HOH . 
I 5 HOH B 15 315 31 HOH HOH . 
I 5 HOH B 16 316 137 HOH HOH . 
J 5 HOH C 1 401 5 HOH HOH . 
J 5 HOH C 2 402 114 HOH HOH . 
J 5 HOH C 3 403 121 HOH HOH . 
J 5 HOH C 4 404 87 HOH HOH . 
J 5 HOH C 5 405 69 HOH HOH . 
J 5 HOH C 6 406 110 HOH HOH . 
J 5 HOH C 7 407 21 HOH HOH . 
J 5 HOH C 8 408 74 HOH HOH . 
J 5 HOH C 9 409 109 HOH HOH . 
J 5 HOH C 10 410 70 HOH HOH . 
J 5 HOH C 11 411 61 HOH HOH . 
J 5 HOH C 12 412 18 HOH HOH . 
J 5 HOH C 13 413 53 HOH HOH . 
J 5 HOH C 14 414 7 HOH HOH . 
J 5 HOH C 15 415 2 HOH HOH . 
J 5 HOH C 16 416 24 HOH HOH . 
J 5 HOH C 17 417 19 HOH HOH . 
J 5 HOH C 18 418 76 HOH HOH . 
J 5 HOH C 19 419 41 HOH HOH . 
J 5 HOH C 20 420 94 HOH HOH . 
J 5 HOH C 21 421 88 HOH HOH . 
J 5 HOH C 22 422 113 HOH HOH . 
J 5 HOH C 23 423 116 HOH HOH . 
J 5 HOH C 24 424 152 HOH HOH . 
J 5 HOH C 25 425 156 HOH HOH . 
J 5 HOH C 26 426 130 HOH HOH . 
J 5 HOH C 27 427 64 HOH HOH . 
J 5 HOH C 28 428 91 HOH HOH . 
J 5 HOH C 29 429 162 HOH HOH . 
J 5 HOH C 30 430 132 HOH HOH . 
J 5 HOH C 31 431 99 HOH HOH . 
J 5 HOH C 32 432 160 HOH HOH . 
J 5 HOH C 33 433 166 HOH HOH . 
K 5 HOH D 1 101 46 HOH HOH . 
K 5 HOH D 2 102 148 HOH HOH . 
K 5 HOH D 3 103 167 HOH HOH . 
K 5 HOH D 4 104 147 HOH HOH . 
K 5 HOH D 5 105 84 HOH HOH . 
K 5 HOH D 6 106 135 HOH HOH . 
L 5 HOH E 1 301 124 HOH HOH . 
L 5 HOH E 2 302 112 HOH HOH . 
L 5 HOH E 3 303 6 HOH HOH . 
L 5 HOH E 4 304 55 HOH HOH . 
L 5 HOH E 5 305 168 HOH HOH . 
L 5 HOH E 6 306 144 HOH HOH . 
L 5 HOH E 7 307 49 HOH HOH . 
L 5 HOH E 8 308 122 HOH HOH . 
L 5 HOH E 9 309 77 HOH HOH . 
L 5 HOH E 10 310 139 HOH HOH . 
L 5 HOH E 11 311 38 HOH HOH . 
L 5 HOH E 12 312 85 HOH HOH . 
L 5 HOH E 13 313 98 HOH HOH . 
L 5 HOH E 14 314 92 HOH HOH . 
L 5 HOH E 15 315 95 HOH HOH . 
L 5 HOH E 16 316 59 HOH HOH . 
L 5 HOH E 17 317 42 HOH HOH . 
L 5 HOH E 18 318 1 HOH HOH . 
L 5 HOH E 19 319 149 HOH HOH . 
L 5 HOH E 20 320 90 HOH HOH . 
L 5 HOH E 21 321 32 HOH HOH . 
L 5 HOH E 22 322 164 HOH HOH . 
M 5 HOH F 1 301 45 HOH HOH . 
M 5 HOH F 2 302 39 HOH HOH . 
M 5 HOH F 3 303 104 HOH HOH . 
M 5 HOH F 4 304 141 HOH HOH . 
M 5 HOH F 5 305 127 HOH HOH . 
M 5 HOH F 6 306 37 HOH HOH . 
M 5 HOH F 7 307 8 HOH HOH . 
M 5 HOH F 8 308 33 HOH HOH . 
M 5 HOH F 9 309 28 HOH HOH . 
M 5 HOH F 10 310 14 HOH HOH . 
M 5 HOH F 11 311 52 HOH HOH . 
M 5 HOH F 12 312 36 HOH HOH . 
M 5 HOH F 13 313 72 HOH HOH . 
M 5 HOH F 14 314 29 HOH HOH . 
M 5 HOH F 15 315 79 HOH HOH . 
M 5 HOH F 16 316 67 HOH HOH . 
M 5 HOH F 17 317 89 HOH HOH . 
M 5 HOH F 18 318 115 HOH HOH . 
M 5 HOH F 19 319 11 HOH HOH . 
M 5 HOH F 20 320 159 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 NAG . . . G 4 18.764 79.832 50.346 1 75.81 ? C1 NAG 301 C 1 
HETATM 2 C C2 NAG . . . G 4 20.021 80.564 49.796 1 81.67 ? C2 NAG 301 C 1 
HETATM 3 C C3 NAG . . . G 4 21.238 80.349 50.722 1 83.54 ? C3 NAG 301 C 1 
HETATM 4 C C4 NAG . . . G 4 20.801 80.795 52.134 1 85.35 ? C4 NAG 301 C 1 
HETATM 5 C C5 NAG . . . G 4 19.682 79.822 52.581 1 81.96 ? C5 NAG 301 C 1 
HETATM 6 C C6 NAG . . . G 4 19.378 79.865 54.089 1 73.2 ? C6 NAG 301 C 1 
HETATM 7 C C7 NAG . . . G 4 20.123 80.724 47.302 1 79.8 ? C7 NAG 301 C 1 
HETATM 8 C C8 NAG . . . G 4 20.834 80.136 46.107 1 73.51 ? C8 NAG 301 C 1 
HETATM 9 N N2 NAG . . . G 4 20.419 80.116 48.458 1 85.35 ? N2 NAG 301 C 1 
HETATM 10 O O1 NAG . . . G 4 17.607 80.198 49.598 1 62.57 ? O1 NAG 301 C 1 
HETATM 11 O O3 NAG . . . G 4 22.452 80.963 50.223 1 69.59 ? O3 NAG 301 C 1 
HETATM 12 O O4 NAG . . . G 4 21.906 80.859 53.048 1 78.79 ? O4 NAG 301 C 1 
HETATM 13 O O5 NAG . . . G 4 18.516 80.082 51.753 1 80.53 ? O5 NAG 301 C 1 
HETATM 14 O O6 NAG . . . G 4 20.025 78.755 54.722 1 60.48 ? O6 NAG 301 C 1 
HETATM 15 O O7 NAG . . . G 4 19.374 81.692 47.224 1 75.17 ? O7 NAG 301 C 1 
#
_model_server_stats.io_time_ms              61 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           252 
_model_server_stats.encode_time_ms          8 
_model_server_stats.element_count           15 
#