data_4YK4
#
_model_server_result.job_id            xxSGLb6tR-bpU37k92Oq0Q 
_model_server_result.datetime_utc      '2024-12-04 07:24:34' 
_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          4yk4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":303}' 
#
_entry.id    4YK4 
#
_exptl.entry_id    4YK4 
_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    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          105.88 
_cell.angle_gamma         90 
_cell.entry_id            4YK4 
_cell.length_a            235.365 
_cell.length_b            130.154 
_cell.length_c            68.972 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4YK4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? trimeric 3 author_defined_assembly 1 
? trimeric 3 author_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,M,N,O 1 1 
D,E,F,J,K,L,P,Q,R 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 H N N 
? 4 I N N 
? 4 J N N 
? 4 K N N 
? 4 L 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 23 Y CYS 23 1_555 A SG CYS 88 Y CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? 
disulf ? disulf2 A SG CYS 134 Y CYS 134 1_555 A SG CYS 194 Y CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf3 B SG CYS 22 Z CYS 22 1_555 B SG CYS 95 Z CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 B SG CYS 152 Z CYS 152 1_555 B SG CYS 208 Z CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf5 C SG CYS 16 E CYS 59 1_555 C SG CYS 28 E CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? 
disulf ? disulf6 C SG CYS 51 E CYS 94 1_555 C SG CYS 96 E CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf7 D SG CYS 23 B CYS 23 1_555 D SG CYS 88 B CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? 
disulf ? disulf8 D SG CYS 134 B CYS 134 1_555 D SG CYS 194 B CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf9 E SG CYS 22 C CYS 22 1_555 E SG CYS 95 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf10 E SG CYS 152 C CYS 152 1_555 E SG CYS 208 C CYS 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf11 F SG CYS 16 A CYS 59 1_555 F SG CYS 28 A CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? 
disulf ? disulf12 F SG CYS 51 A CYS 94 1_555 F SG CYS 96 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
covale ? covale1 C ND2 ASN 15 E ASN 58 1_555 G C1 NAG . E NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 sing 
covale ? covale2 C ND2 ASN 48 E ASN 91 1_555 H C1 NAG . E NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 sing 
covale ? covale3 C ND2 ASN 86 E ASN 129 1_555 I C1 NAG . E NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.548 sing 
covale ? covale4 F ND2 ASN 15 A ASN 58 1_555 J C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.491 sing 
covale ? covale5 F ND2 ASN 48 A ASN 91 1_555 K C1 NAG . A NAG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.492 sing 
covale ? covale6 F ND2 ASN 86 A ASN 129 1_555 L C1 NAG . A NAG 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.656 sing 
#
_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                     4YK4 
_atom_sites.fract_transf_matrix[1][1]    0.004249 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001209 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.007683 
_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]    0.015074 
_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 E 1 301 269 NAG NAG . 
H 4 NAG E 1 302 270 NAG NAG . 
I 4 NAG E 1 303 271 NAG NAG . 
J 4 NAG A 1 301 272 NAG NAG . 
K 4 NAG A 1 302 273 NAG NAG . 
L 4 NAG A 1 303 274 NAG NAG . 
M 5 HOH Y 1 301 69 HOH HOH . 
M 5 HOH Y 2 302 48 HOH HOH . 
M 5 HOH Y 3 303 1 HOH HOH . 
M 5 HOH Y 4 304 76 HOH HOH . 
M 5 HOH Y 5 305 38 HOH HOH . 
M 5 HOH Y 6 306 40 HOH HOH . 
M 5 HOH Y 7 307 91 HOH HOH . 
M 5 HOH Y 8 308 41 HOH HOH . 
M 5 HOH Y 9 309 126 HOH HOH . 
M 5 HOH Y 10 310 29 HOH HOH . 
M 5 HOH Y 11 311 52 HOH HOH . 
M 5 HOH Y 12 312 94 HOH HOH . 
M 5 HOH Y 13 313 14 HOH HOH . 
M 5 HOH Y 14 314 47 HOH HOH . 
M 5 HOH Y 15 315 39 HOH HOH . 
M 5 HOH Y 16 316 28 HOH HOH . 
M 5 HOH Y 17 317 11 HOH HOH . 
M 5 HOH Y 18 318 62 HOH HOH . 
M 5 HOH Y 19 319 3 HOH HOH . 
M 5 HOH Y 20 320 79 HOH HOH . 
M 5 HOH Y 21 321 51 HOH HOH . 
M 5 HOH Y 22 322 10 HOH HOH . 
M 5 HOH Y 23 323 19 HOH HOH . 
M 5 HOH Y 24 324 7 HOH HOH . 
M 5 HOH Y 25 325 26 HOH HOH . 
M 5 HOH Y 26 326 111 HOH HOH . 
M 5 HOH Y 27 327 82 HOH HOH . 
M 5 HOH Y 28 328 102 HOH HOH . 
M 5 HOH Y 29 329 77 HOH HOH . 
M 5 HOH Y 30 330 97 HOH HOH . 
M 5 HOH Y 31 331 84 HOH HOH . 
M 5 HOH Y 32 332 105 HOH HOH . 
M 5 HOH Y 33 333 90 HOH HOH . 
M 5 HOH Y 34 334 87 HOH HOH . 
M 5 HOH Y 35 335 73 HOH HOH . 
M 5 HOH Y 36 336 121 HOH HOH . 
M 5 HOH Y 37 337 98 HOH HOH . 
N 5 HOH Z 1 301 61 HOH HOH . 
N 5 HOH Z 2 302 93 HOH HOH . 
N 5 HOH Z 3 303 13 HOH HOH . 
N 5 HOH Z 4 304 18 HOH HOH . 
N 5 HOH Z 5 305 4 HOH HOH . 
N 5 HOH Z 6 306 71 HOH HOH . 
N 5 HOH Z 7 307 35 HOH HOH . 
N 5 HOH Z 8 308 22 HOH HOH . 
N 5 HOH Z 9 309 109 HOH HOH . 
N 5 HOH Z 10 310 119 HOH HOH . 
N 5 HOH Z 11 311 15 HOH HOH . 
N 5 HOH Z 12 312 100 HOH HOH . 
N 5 HOH Z 13 313 96 HOH HOH . 
N 5 HOH Z 14 314 23 HOH HOH . 
N 5 HOH Z 15 315 81 HOH HOH . 
N 5 HOH Z 16 316 46 HOH HOH . 
N 5 HOH Z 17 317 115 HOH HOH . 
N 5 HOH Z 18 318 117 HOH HOH . 
N 5 HOH Z 19 319 116 HOH HOH . 
O 5 HOH E 1 401 54 HOH HOH . 
O 5 HOH E 2 402 16 HOH HOH . 
O 5 HOH E 3 403 25 HOH HOH . 
O 5 HOH E 4 404 60 HOH HOH . 
O 5 HOH E 5 405 85 HOH HOH . 
O 5 HOH E 6 406 45 HOH HOH . 
O 5 HOH E 7 407 9 HOH HOH . 
O 5 HOH E 8 408 5 HOH HOH . 
O 5 HOH E 9 409 104 HOH HOH . 
O 5 HOH E 10 410 114 HOH HOH . 
O 5 HOH E 11 411 95 HOH HOH . 
O 5 HOH E 12 412 33 HOH HOH . 
P 5 HOH B 1 301 78 HOH HOH . 
P 5 HOH B 2 302 31 HOH HOH . 
P 5 HOH B 3 303 64 HOH HOH . 
P 5 HOH B 4 304 101 HOH HOH . 
P 5 HOH B 5 305 108 HOH HOH . 
P 5 HOH B 6 306 122 HOH HOH . 
P 5 HOH B 7 307 2 HOH HOH . 
P 5 HOH B 8 308 50 HOH HOH . 
P 5 HOH B 9 309 55 HOH HOH . 
P 5 HOH B 10 310 30 HOH HOH . 
P 5 HOH B 11 311 80 HOH HOH . 
P 5 HOH B 12 312 36 HOH HOH . 
P 5 HOH B 13 313 67 HOH HOH . 
P 5 HOH B 14 314 57 HOH HOH . 
P 5 HOH B 15 315 32 HOH HOH . 
P 5 HOH B 16 316 113 HOH HOH . 
P 5 HOH B 17 317 107 HOH HOH . 
P 5 HOH B 18 318 56 HOH HOH . 
P 5 HOH B 19 319 8 HOH HOH . 
P 5 HOH B 20 320 17 HOH HOH . 
P 5 HOH B 21 321 59 HOH HOH . 
P 5 HOH B 22 322 70 HOH HOH . 
P 5 HOH B 23 323 66 HOH HOH . 
P 5 HOH B 24 324 88 HOH HOH . 
P 5 HOH B 25 325 86 HOH HOH . 
P 5 HOH B 26 326 65 HOH HOH . 
P 5 HOH B 27 327 34 HOH HOH . 
P 5 HOH B 28 328 75 HOH HOH . 
Q 5 HOH C 1 301 21 HOH HOH . 
Q 5 HOH C 2 302 6 HOH HOH . 
Q 5 HOH C 3 303 110 HOH HOH . 
Q 5 HOH C 4 304 112 HOH HOH . 
Q 5 HOH C 5 305 68 HOH HOH . 
Q 5 HOH C 6 306 63 HOH HOH . 
Q 5 HOH C 7 307 12 HOH HOH . 
Q 5 HOH C 8 308 99 HOH HOH . 
Q 5 HOH C 9 309 43 HOH HOH . 
Q 5 HOH C 10 310 124 HOH HOH . 
Q 5 HOH C 11 311 24 HOH HOH . 
Q 5 HOH C 12 312 92 HOH HOH . 
Q 5 HOH C 13 313 106 HOH HOH . 
Q 5 HOH C 14 314 89 HOH HOH . 
Q 5 HOH C 15 315 27 HOH HOH . 
Q 5 HOH C 16 316 53 HOH HOH . 
Q 5 HOH C 17 317 44 HOH HOH . 
Q 5 HOH C 18 318 37 HOH HOH . 
Q 5 HOH C 19 319 123 HOH HOH . 
Q 5 HOH C 20 320 72 HOH HOH . 
Q 5 HOH C 21 321 74 HOH HOH . 
R 5 HOH A 1 401 83 HOH HOH . 
R 5 HOH A 2 402 20 HOH HOH . 
R 5 HOH A 3 403 120 HOH HOH . 
R 5 HOH A 4 404 42 HOH HOH . 
R 5 HOH A 5 405 49 HOH HOH . 
R 5 HOH A 6 406 58 HOH HOH . 
R 5 HOH A 7 407 118 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 . . . L 4 -44.25 15.853 9.562 1 167.34 ? C1 NAG 303 A 1 
HETATM 2 C C2 NAG . . . L 4 -43.943 17.34 9.684 1 167.34 ? C2 NAG 303 A 1 
HETATM 3 C C3 NAG . . . L 4 -42.625 17.567 10.416 1 167.34 ? C3 NAG 303 A 1 
HETATM 4 C C4 NAG . . . L 4 -42.575 16.764 11.711 1 167.34 ? C4 NAG 303 A 1 
HETATM 5 C C5 NAG . . . L 4 -42.963 15.311 11.466 1 167.34 ? C5 NAG 303 A 1 
HETATM 6 C C6 NAG . . . L 4 -42.985 14.524 12.771 1 167.34 ? C6 NAG 303 A 1 
HETATM 7 C C7 NAG . . . L 4 -44.603 19.03 8.073 1 167.34 ? C7 NAG 303 A 1 
HETATM 8 C C8 NAG . . . L 4 -44.503 20.161 9.053 1 167.34 ? C8 NAG 303 A 1 
HETATM 9 N N2 NAG . . . L 4 -43.89 17.946 8.368 1 167.34 ? N2 NAG 303 A 1 
HETATM 10 O O3 NAG . . . L 4 -42.479 18.961 10.714 1 167.34 ? O3 NAG 303 A 1 
HETATM 11 O O4 NAG . . . L 4 -41.253 16.819 12.257 1 167.34 ? O4 NAG 303 A 1 
HETATM 12 O O5 NAG . . . L 4 -44.252 15.26 10.858 1 167.34 ? O5 NAG 303 A 1 
HETATM 13 O O6 NAG . . . L 4 -41.742 14.703 13.458 1 167.34 ? O6 NAG 303 A 1 
HETATM 14 O O7 NAG . . . L 4 -45.292 19.099 7.069 1 167.34 ? O7 NAG 303 A 1 
#
_model_server_stats.io_time_ms              26 
_model_server_stats.parse_time_ms           33 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           294 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#