data_5YLU
#
_model_server_result.job_id            gVsSvv3gbf3gXLtiKljVQg 
_model_server_result.datetime_utc      '2024-11-04 22:33:13' 
_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          5ylu 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":302}' 
#
_entry.id    5YLU 
#
_exptl.entry_id    5YLU 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          7 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_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         120 
_cell.entry_id            5YLU 
_cell.length_a            104.82 
_cell.length_b            104.82 
_cell.length_c            367.08 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YLU 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    'P 31 2"' 
_symmetry.space_group_name_H-M     'P 31 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
#
_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
? 7 H N N 
? 7 I N N 
? 7 J 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 B SG CYS 130 B CYS 131 1_555 B SG CYS 151 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.94 ? 
disulf ? disulf2 B SG CYS 161 B CYS 162 1_555 B SG CYS 177 B CYS 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf3 B SG CYS 200 B CYS 201 1_555 B SG CYS 261 B CYS 262 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? 
covale ? covale1 A NH1 ARG 214 A ARG 213 1_555 A ND2 ASN 251 A ASN 250 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.172 ? 
covale ? covale2 A C SER 385 A SER 384 1_555 A N BFD 386 A BFD 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? 
covale ? covale3 A C BFD 386 A BFD 385 1_555 A N LYS 387 A LYS 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? 
covale ? covale4 B ND2 ASN 98 B ASN 99 1_555 H C1 NAG . B NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale5 B ND2 ASN 129 B ASN 130 1_555 I C1 NAG . B NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? 
covale ? covale6 B ND2 ASN 160 B ASN 161 1_555 J C1 NAG . B NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
metalc ? metalc1 A OD2 BFD 386 A BFD 385 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.763 ? 
metalc ? metalc2 A O THR 388 A THR 387 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? 
metalc ? metalc3 A OD1 ASP 727 A ASP 726 1_555 F MG MG . A MG 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? 
#
_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 391 n n 
C1 O1 NAG sing 392 n n 
C1 O5 NAG sing 393 n n 
C1 H1 NAG sing 394 n n 
C2 C3 NAG sing 395 n n 
C2 N2 NAG sing 396 n n 
C2 H2 NAG sing 397 n n 
C3 C4 NAG sing 398 n n 
C3 O3 NAG sing 399 n n 
C3 H3 NAG sing 400 n n 
C4 C5 NAG sing 401 n n 
C4 O4 NAG sing 402 n n 
C4 H4 NAG sing 403 n n 
C5 C6 NAG sing 404 n n 
C5 O5 NAG sing 405 n n 
C5 H5 NAG sing 406 n n 
C6 O6 NAG sing 407 n n 
C6 H61 NAG sing 408 n n 
C6 H62 NAG sing 409 n n 
C7 C8 NAG sing 410 n n 
C7 N2 NAG sing 411 n n 
C7 O7 NAG doub 412 n n 
C8 H81 NAG sing 413 n n 
C8 H82 NAG sing 414 n n 
C8 H83 NAG sing 415 n n 
N2 HN2 NAG sing 416 n n 
O1 HO1 NAG sing 417 n n 
O3 HO3 NAG sing 418 n n 
O4 HO4 NAG sing 419 n n 
O6 HO6 NAG sing 420 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                     5YLU 
_atom_sites.fract_transf_matrix[1][1]    0.00954 
_atom_sites.fract_transf_matrix[1][2]    0.005508 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011016 
_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]    0.002724 
_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 3 HKT A 1 1101 1101 HKT HKT . 
D 4 PCW A 1 1102 1102 PCW PCW . 
E 4 PCW A 1 1103 1103 PCW PCW . 
F 5 MG A 1 1104 1104 MG MG . 
G 6 CE1 A 1 1105 1105 CE1 CE1 . 
H 7 NAG B 1 301 301 NAG NAG . 
I 7 NAG B 1 302 302 NAG NAG . 
J 7 NAG B 1 303 303 NAG NAG . 
K 6 CE1 B 1 304 304 CE1 CE1 . 
L 8 HOH A 1 1201 1201 HOH HOH . 
L 8 HOH A 2 1202 1202 HOH HOH . 
L 8 HOH A 3 1203 1203 HOH HOH . 
L 8 HOH A 4 1204 1204 HOH HOH . 
L 8 HOH A 5 1205 1205 HOH HOH . 
L 8 HOH A 6 1206 1206 HOH HOH . 
L 8 HOH A 7 1207 1207 HOH HOH . 
L 8 HOH A 8 1208 1208 HOH HOH . 
L 8 HOH A 9 1209 1209 HOH HOH . 
L 8 HOH A 10 1210 1210 HOH HOH . 
L 8 HOH A 11 1211 1211 HOH HOH . 
L 8 HOH A 12 1212 1212 HOH HOH . 
L 8 HOH A 13 1213 1213 HOH HOH . 
L 8 HOH A 14 1214 1214 HOH HOH . 
L 8 HOH A 15 1215 1215 HOH HOH . 
L 8 HOH A 16 1216 1216 HOH HOH . 
L 8 HOH A 17 1217 1217 HOH HOH . 
L 8 HOH A 18 1218 1218 HOH HOH . 
L 8 HOH A 19 1219 1219 HOH HOH . 
L 8 HOH A 20 1220 1220 HOH HOH . 
L 8 HOH A 21 1221 1221 HOH HOH . 
L 8 HOH A 22 1222 1222 HOH HOH . 
L 8 HOH A 23 1223 1223 HOH HOH . 
L 8 HOH A 24 1224 1224 HOH HOH . 
L 8 HOH A 25 1225 1225 HOH HOH . 
L 8 HOH A 26 1226 1226 HOH HOH . 
L 8 HOH A 27 1227 1227 HOH HOH . 
L 8 HOH A 28 1228 1228 HOH HOH . 
L 8 HOH A 29 1229 1229 HOH HOH . 
L 8 HOH A 30 1230 1230 HOH HOH . 
M 8 HOH B 1 401 401 HOH HOH . 
M 8 HOH B 2 402 402 HOH HOH . 
M 8 HOH B 3 403 403 HOH HOH . 
M 8 HOH B 4 404 404 HOH HOH . 
M 8 HOH B 5 405 405 HOH HOH . 
M 8 HOH B 6 406 406 HOH HOH . 
M 8 HOH B 7 407 407 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 . . . I 7 51.539 5.9 -56.848 1 101.26 ? C1 NAG 302 B 1 
HETATM 2 C C2 NAG . . . I 7 50.678 5.633 -58.178 1 101.93 ? C2 NAG 302 B 1 
HETATM 3 C C3 NAG . . . I 7 51.575 5.324 -59.374 1 108.24 ? C3 NAG 302 B 1 
HETATM 4 C C4 NAG . . . I 7 52.759 6.278 -59.444 1 103.81 ? C4 NAG 302 B 1 
HETATM 5 C C5 NAG . . . I 7 53.492 6.329 -58.098 1 103.93 ? C5 NAG 302 B 1 
HETATM 6 C C6 NAG . . . I 7 54.833 7.068 -58.067 1 98.91 ? C6 NAG 302 B 1 
HETATM 7 C C7 NAG . . . I 7 48.351 4.781 -57.979 1 96.44 ? C7 NAG 302 B 1 
HETATM 8 C C8 NAG . . . I 7 47.938 6.211 -57.932 1 90.2 ? C8 NAG 302 B 1 
HETATM 9 N N2 NAG . . . I 7 49.665 4.574 -58.048 1 100.1 ? N2 NAG 302 B 1 
HETATM 10 O O3 NAG . . . I 7 50.722 5.549 -60.494 1 111.88 ? O3 NAG 302 B 1 
HETATM 11 O O4 NAG . . . I 7 53.628 5.755 -60.436 1 97.97 ? O4 NAG 302 B 1 
HETATM 12 O O5 NAG . . . I 7 52.608 6.896 -57.12 1 99.12 ? O5 NAG 302 B 1 
HETATM 13 O O6 NAG . . . I 7 55.579 7.025 -59.281 1 90.11 ? O6 NAG 302 B 1 
HETATM 14 O O7 NAG . . . I 7 47.551 3.862 -57.971 1 92.57 ? O7 NAG 302 B 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           18 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#