data_4N5J
#
_model_server_result.job_id            t8h1dLB30Fi5Ybmo1wNVJw 
_model_server_result.datetime_utc      '2024-11-28 03:30:37' 
_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          4n5j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":404}' 
#
_entry.id    4N5J 
#
_exptl.entry_id    4N5J 
_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    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            4N5J 
_cell.length_a            154.513 
_cell.length_b            154.513 
_cell.length_c            154.513 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4N5J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        198 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 3' 
#
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 hexameric 6 author_and_software_defined_assembly 1 
PISA hexameric 6 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,E,F,G,H,I 1 1,2,3 
C,D,J,K 2 1,4,5 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_544 -z,x-1/2,-y-1/2 0 0 -1 1 0 0 0 -1 0 0 -77.2565 -77.2565 
3 'crystal symmetry operation' 11_545 y+1/2,-z-1/2,-x 0 1 0 0 0 -1 -1 0 0 77.2565 -77.2565 0 
4 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
5 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 G N N 
#
_pdbx_entity_branch.entity_id    3 
_pdbx_entity_branch.type         oligosaccharide 
#
loop_
_pdbx_entity_branch_link.link_id
_pdbx_entity_branch_link.details
_pdbx_entity_branch_link.entity_id
_pdbx_entity_branch_link.entity_branch_list_num_1
_pdbx_entity_branch_link.entity_branch_list_num_2
_pdbx_entity_branch_link.comp_id_1
_pdbx_entity_branch_link.comp_id_2
_pdbx_entity_branch_link.atom_id_1
_pdbx_entity_branch_link.leaving_atom_id_1
_pdbx_entity_branch_link.atom_stereo_config_1
_pdbx_entity_branch_link.atom_id_2
_pdbx_entity_branch_link.leaving_atom_id_2
_pdbx_entity_branch_link.atom_stereo_config_2
_pdbx_entity_branch_link.value_order
1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 
2 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
3 n E NAG 1 E 1 NAG A 521 NAG 
3 n E NAG 2 E 2 NAG A 522 NAG 
3 n E BMA 3 E 3 BMA A 523 BMA 
#
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 4 A CYS 14 1_555 B SG CYS 137 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf2 A SG CYS 42 A CYS 52 1_555 A SG CYS 268 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 A SG CYS 54 A CYS 64 1_555 A SG CYS 66 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf4 A SG CYS 87 A CYS 97 1_555 A SG CYS 129 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf5 A SG CYS 272 A CYS 281 1_555 A SG CYS 296 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf6 B SG CYS 144 B CYS 144 1_555 B SG CYS 148 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 C SG CYS 4 C CYS 14 1_555 D SG CYS 137 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf8 C SG CYS 42 C CYS 52 1_555 C SG CYS 268 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf9 C SG CYS 54 C CYS 64 1_555 C SG CYS 66 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf10 C SG CYS 87 C CYS 97 1_555 C SG CYS 129 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? 
disulf ? disulf11 C SG CYS 272 C CYS 281 1_555 C SG CYS 296 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf12 D SG CYS 144 D CYS 144 1_555 D SG CYS 148 D CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
covale ? covale1 A ND2 ASN 28 A ASN 38 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? 
covale ? covale2 A ND2 ASN 231 A ASN 240 1_555 F C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale3 B ND2 ASN 82 B ASN 82 1_555 G C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.434 ? 
covale ? covale5 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
#
_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 261 n n 
C1 O1 NAG sing 262 n n 
C1 O5 NAG sing 263 n n 
C1 H1 NAG sing 264 n n 
C2 C3 NAG sing 265 n n 
C2 N2 NAG sing 266 n n 
C2 H2 NAG sing 267 n n 
C3 C4 NAG sing 268 n n 
C3 O3 NAG sing 269 n n 
C3 H3 NAG sing 270 n n 
C4 C5 NAG sing 271 n n 
C4 O4 NAG sing 272 n n 
C4 H4 NAG sing 273 n n 
C5 C6 NAG sing 274 n n 
C5 O5 NAG sing 275 n n 
C5 H5 NAG sing 276 n n 
C6 O6 NAG sing 277 n n 
C6 H61 NAG sing 278 n n 
C6 H62 NAG sing 279 n n 
C7 C8 NAG sing 280 n n 
C7 N2 NAG sing 281 n n 
C7 O7 NAG doub 282 n n 
C8 H81 NAG sing 283 n n 
C8 H82 NAG sing 284 n n 
C8 H83 NAG sing 285 n n 
N2 HN2 NAG sing 286 n n 
O1 HO1 NAG sing 287 n n 
O3 HO3 NAG sing 288 n n 
O4 HO4 NAG sing 289 n n 
O6 HO6 NAG sing 290 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                     4N5J 
_atom_sites.fract_transf_matrix[1][1]    0.006472 
_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]    0.006472 
_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]    0.006472 
_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
F 4 NAG A 1 404 531 NAG NAG . 
G 4 NAG B 1 201 541 NAG NAG . 
H 5 HOH A 1 501 2 HOH HOH . 
H 5 HOH A 2 502 3 HOH HOH . 
H 5 HOH A 3 503 5 HOH HOH . 
H 5 HOH A 4 504 6 HOH HOH . 
H 5 HOH A 5 505 8 HOH HOH . 
H 5 HOH A 6 506 9 HOH HOH . 
H 5 HOH A 7 507 11 HOH HOH . 
H 5 HOH A 8 508 17 HOH HOH . 
H 5 HOH A 9 509 19 HOH HOH . 
H 5 HOH A 10 510 21 HOH HOH . 
H 5 HOH A 11 511 27 HOH HOH . 
H 5 HOH A 12 512 29 HOH HOH . 
H 5 HOH A 13 513 35 HOH HOH . 
H 5 HOH A 14 514 36 HOH HOH . 
H 5 HOH A 15 515 40 HOH HOH . 
H 5 HOH A 16 516 41 HOH HOH . 
H 5 HOH A 17 517 45 HOH HOH . 
H 5 HOH A 18 518 49 HOH HOH . 
H 5 HOH A 19 519 52 HOH HOH . 
H 5 HOH A 20 520 55 HOH HOH . 
H 5 HOH A 21 521 57 HOH HOH . 
H 5 HOH A 22 522 58 HOH HOH . 
H 5 HOH A 23 523 62 HOH HOH . 
H 5 HOH A 24 524 63 HOH HOH . 
H 5 HOH A 25 525 64 HOH HOH . 
H 5 HOH A 26 526 66 HOH HOH . 
H 5 HOH A 27 527 70 HOH HOH . 
H 5 HOH A 28 528 77 HOH HOH . 
H 5 HOH A 29 529 79 HOH HOH . 
H 5 HOH A 30 530 81 HOH HOH . 
I 5 HOH B 1 301 1 HOH HOH . 
I 5 HOH B 2 302 4 HOH HOH . 
I 5 HOH B 3 303 7 HOH HOH . 
I 5 HOH B 4 304 10 HOH HOH . 
I 5 HOH B 5 305 12 HOH HOH . 
I 5 HOH B 6 306 13 HOH HOH . 
I 5 HOH B 7 307 15 HOH HOH . 
I 5 HOH B 8 308 16 HOH HOH . 
I 5 HOH B 9 309 24 HOH HOH . 
I 5 HOH B 10 310 28 HOH HOH . 
I 5 HOH B 11 311 30 HOH HOH . 
I 5 HOH B 12 312 32 HOH HOH . 
I 5 HOH B 13 313 34 HOH HOH . 
I 5 HOH B 14 314 37 HOH HOH . 
I 5 HOH B 15 315 39 HOH HOH . 
I 5 HOH B 16 316 50 HOH HOH . 
I 5 HOH B 17 317 54 HOH HOH . 
I 5 HOH B 18 318 56 HOH HOH . 
I 5 HOH B 19 319 60 HOH HOH . 
I 5 HOH B 20 320 61 HOH HOH . 
I 5 HOH B 21 321 67 HOH HOH . 
I 5 HOH B 22 322 71 HOH HOH . 
I 5 HOH B 23 323 73 HOH HOH . 
I 5 HOH B 24 324 74 HOH HOH . 
I 5 HOH B 25 325 76 HOH HOH . 
I 5 HOH B 26 326 80 HOH HOH . 
J 5 HOH C 1 401 47 HOH HOH . 
J 5 HOH C 2 402 51 HOH HOH . 
K 5 HOH D 1 201 78 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 . . . F 4 66.077 -42.858 -23.447 1 144.34 ? C1 NAG 404 A 1 
HETATM 2 C C2 NAG . . . F 4 66.412 -44.305 -23.816 1 163.22 ? C2 NAG 404 A 1 
HETATM 3 C C3 NAG . . . F 4 67.833 -44.4 -24.372 1 164.08 ? C3 NAG 404 A 1 
HETATM 4 C C4 NAG . . . F 4 68.034 -43.395 -25.5 1 160.59 ? C4 NAG 404 A 1 
HETATM 5 C C5 NAG . . . F 4 67.631 -41.999 -25.036 1 155.17 ? C5 NAG 404 A 1 
HETATM 6 C C6 NAG . . . F 4 67.71 -40.962 -26.131 1 151.2 ? C6 NAG 404 A 1 
HETATM 7 C C7 NAG . . . F 4 66.896 -45.097 -21.522 1 170.91 ? C7 NAG 404 A 1 
HETATM 8 C C8 NAG . . . F 4 66.561 -46.126 -20.484 1 164.66 ? C8 NAG 404 A 1 
HETATM 9 N N2 NAG . . . F 4 66.235 -45.203 -22.682 1 171.38 ? N2 NAG 404 A 1 
HETATM 10 O O3 NAG . . . F 4 68.068 -45.72 -24.852 1 161.43 ? O3 NAG 404 A 1 
HETATM 11 O O4 NAG . . . F 4 69.397 -43.382 -25.906 1 161.11 ? O4 NAG 404 A 1 
HETATM 12 O O5 NAG . . . F 4 66.27 -42.019 -24.582 1 151.14 ? O5 NAG 404 A 1 
HETATM 13 O O6 NAG . . . F 4 67.241 -39.697 -25.682 1 150.82 ? O6 NAG 404 A 1 
HETATM 14 O O7 NAG . . . F 4 67.727 -44.215 -21.316 1 174.29 ? O7 NAG 404 A 1 
#
_model_server_stats.io_time_ms              20 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           298 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#