data_4N5K
#
_model_server_result.job_id            jDJbMK5v7zEK7SelfrFeIQ 
_model_server_result.datetime_utc      '2024-11-24 08:59:51' 
_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          4n5k 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":201}' 
#
_entry.id    4N5K 
#
_exptl.entry_id    4N5K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          5 
_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         90 
_cell.entry_id            4N5K 
_cell.length_a            154.698 
_cell.length_b            154.698 
_cell.length_c            154.698 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4N5K 
_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,K,L 1 1,2,3 
C,D,I,J,M 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 -77.349 -77.349 
3 'crystal symmetry operation' 11_545 y+1/2,-z-1/2,-x 0 1 0 0 0 -1 -1 0 0 77.349 -77.349 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
? 5 G N N 
? 5 H N N 
? 5 J N N 
#
loop_
_pdbx_entity_branch.entity_id
_pdbx_entity_branch.type
3 oligosaccharide 
4 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 
3 ? 4 2 1 SIA GAL C2 O2 . O3 HO3 . 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 
4 n F GAL 1 F 1 GAL X 102 GAL 
4 n F SIA 2 F 2 SIA X 101 SIA 
#
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 134 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf2 A SG CYS 42 A CYS 52 1_555 A SG CYS 268 A CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf3 A SG CYS 54 A CYS 64 1_555 A SG CYS 66 A CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf4 A SG CYS 87 A CYS 97 1_555 A SG CYS 129 A CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 A SG CYS 272 A CYS 281 1_555 A SG CYS 296 A CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf6 B SG CYS 141 B CYS 144 1_555 B SG CYS 145 B CYS 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf7 C SG CYS 4 C CYS 14 1_555 D SG CYS 134 D CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf8 C SG CYS 42 C CYS 52 1_555 C SG CYS 268 C CYS 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf9 C SG CYS 54 C CYS 64 1_555 C SG CYS 66 C CYS 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf10 C SG CYS 87 C CYS 97 1_555 C SG CYS 129 C CYS 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf11 C SG CYS 272 C CYS 281 1_555 C SG CYS 296 C CYS 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf12 D SG CYS 141 D CYS 144 1_555 D SG CYS 145 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 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? 
covale ? covale2 A ND2 ASN 231 A ASN 240 1_555 G C1 NAG . A NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale3 B ND2 ASN 79 B ASN 82 1_555 H C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale4 D ND2 ASN 79 D ASN 82 1_555 J C1 NAG . D NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale5 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? 
covale ? covale6 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale7 F O3 GAL . F GAL 1 1_555 F C2 SIA . F SIA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
#
_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 285 n n 
C1 O1 NAG sing 286 n n 
C1 O5 NAG sing 287 n n 
C1 H1 NAG sing 288 n n 
C2 C3 NAG sing 289 n n 
C2 N2 NAG sing 290 n n 
C2 H2 NAG sing 291 n n 
C3 C4 NAG sing 292 n n 
C3 O3 NAG sing 293 n n 
C3 H3 NAG sing 294 n n 
C4 C5 NAG sing 295 n n 
C4 O4 NAG sing 296 n n 
C4 H4 NAG sing 297 n n 
C5 C6 NAG sing 298 n n 
C5 O5 NAG sing 299 n n 
C5 H5 NAG sing 300 n n 
C6 O6 NAG sing 301 n n 
C6 H61 NAG sing 302 n n 
C6 H62 NAG sing 303 n n 
C7 C8 NAG sing 304 n n 
C7 N2 NAG sing 305 n n 
C7 O7 NAG doub 306 n n 
C8 H81 NAG sing 307 n n 
C8 H82 NAG sing 308 n n 
C8 H83 NAG sing 309 n n 
N2 HN2 NAG sing 310 n n 
O1 HO1 NAG sing 311 n n 
O3 HO3 NAG sing 312 n n 
O4 HO4 NAG sing 313 n n 
O6 HO6 NAG sing 314 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                     4N5K 
_atom_sites.fract_transf_matrix[1][1]    0.006464 
_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]    0.006464 
_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]    0.006464 
_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 5 NAG A 1 404 531 NAG NAG . 
H 5 NAG B 1 201 541 NAG NAG . 
I 6 SIA C 1 401 201 SIA SIA . 
J 5 NAG D 1 201 541 NAG NAG . 
K 7 HOH A 1 501 3 HOH HOH . 
K 7 HOH A 2 502 5 HOH HOH . 
K 7 HOH A 3 503 6 HOH HOH . 
K 7 HOH A 4 504 12 HOH HOH . 
K 7 HOH A 5 505 16 HOH HOH . 
K 7 HOH A 6 506 17 HOH HOH . 
K 7 HOH A 7 507 19 HOH HOH . 
K 7 HOH A 8 508 22 HOH HOH . 
K 7 HOH A 9 509 23 HOH HOH . 
K 7 HOH A 10 510 24 HOH HOH . 
K 7 HOH A 11 511 25 HOH HOH . 
K 7 HOH A 12 512 31 HOH HOH . 
K 7 HOH A 13 513 32 HOH HOH . 
K 7 HOH A 14 514 33 HOH HOH . 
K 7 HOH A 15 515 35 HOH HOH . 
L 7 HOH B 1 301 1 HOH HOH . 
L 7 HOH B 2 302 2 HOH HOH . 
L 7 HOH B 3 303 4 HOH HOH . 
L 7 HOH B 4 304 7 HOH HOH . 
L 7 HOH B 5 305 9 HOH HOH . 
L 7 HOH B 6 306 10 HOH HOH . 
L 7 HOH B 7 307 13 HOH HOH . 
L 7 HOH B 8 308 14 HOH HOH . 
L 7 HOH B 9 309 20 HOH HOH . 
L 7 HOH B 10 310 21 HOH HOH . 
L 7 HOH B 11 311 29 HOH HOH . 
L 7 HOH B 12 312 30 HOH HOH . 
M 7 HOH C 1 501 8 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 . . . J 5 -11.655 -11.511 4.12 1 143.3 ? C1 NAG 201 D 1 
HETATM 2 C C2 NAG . . . J 5 -11.579 -11.008 5.562 1 143.41 ? C2 NAG 201 D 1 
HETATM 3 C C3 NAG . . . J 5 -11.231 -12.167 6.501 1 144.26 ? C3 NAG 201 D 1 
HETATM 4 C C4 NAG . . . J 5 -12.165 -13.347 6.283 1 143.93 ? C4 NAG 201 D 1 
HETATM 5 C C5 NAG . . . J 5 -12.175 -13.737 4.81 1 144.84 ? C5 NAG 201 D 1 
HETATM 6 C C6 NAG . . . J 5 -13.146 -14.852 4.495 1 144.21 ? C6 NAG 201 D 1 
HETATM 7 C C7 NAG . . . J 5 -10.964 -8.664 5.925 1 142.48 ? C7 NAG 201 D 1 
HETATM 8 C C8 NAG . . . J 5 -9.836 -7.687 6.032 1 142.17 ? C8 NAG 201 D 1 
HETATM 9 N N2 NAG . . . J 5 -10.622 -9.94 5.694 1 142.83 ? N2 NAG 201 D 1 
HETATM 10 O O3 NAG . . . J 5 -11.321 -11.721 7.851 1 144.15 ? O3 NAG 201 D 1 
HETATM 11 O O4 NAG . . . J 5 -11.737 -14.458 7.062 1 142.69 ? O4 NAG 201 D 1 
HETATM 12 O O5 NAG . . . J 5 -12.569 -12.604 4.018 1 144.52 ? O5 NAG 201 D 1 
HETATM 13 O O6 NAG . . . J 5 -13.942 -14.55 3.358 1 144.22 ? O6 NAG 201 D 1 
HETATM 14 O O7 NAG . . . J 5 -12.137 -8.325 6.041 1 142.72 ? O7 NAG 201 D 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           358 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#