data_4N5K
#
_model_server_result.job_id            SoInUWGUNP77A4llDXwYGA 
_model_server_result.datetime_utc      '2024-11-24 08:40:57' 
_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":"I","auth_seq_id":401}' 
#
_entry.id    4N5K 
#
_exptl.entry_id    4N5K 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              309.27 
_entity.id                          6 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            'N-acetyl-alpha-neuraminic acid' 
_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         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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      6 
_struct_asym.id                             I 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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           'C11 H19 N O9' 
_chem_comp.formula_weight    309.27 
_chem_comp.id                SIA 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'N-acetyl-alpha-neuraminic acid' 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     'N-acetylneuraminic acid;sialic acid;alpha-sialic acid;O-SIALIC ACID' 
#
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 SIA sing 368 n n 
C1 O1A SIA doub 369 n n 
C1 O1B SIA sing 370 n n 
C2 C3 SIA sing 371 n n 
C2 O2 SIA sing 372 n n 
C2 O6 SIA sing 373 n n 
C3 C4 SIA sing 374 n n 
C3 H32 SIA sing 375 n n 
C3 H31 SIA sing 376 n n 
C4 C5 SIA sing 377 n n 
C4 O4 SIA sing 378 n n 
C4 H4 SIA sing 379 n n 
C5 C6 SIA sing 380 n n 
C5 N5 SIA sing 381 n n 
C5 H5 SIA sing 382 n n 
C6 C7 SIA sing 383 n n 
C6 O6 SIA sing 384 n n 
C6 H6 SIA sing 385 n n 
C7 C8 SIA sing 386 n n 
C7 O7 SIA sing 387 n n 
C7 H7 SIA sing 388 n n 
C8 C9 SIA sing 389 n n 
C8 O8 SIA sing 390 n n 
C8 H8 SIA sing 391 n n 
C9 O9 SIA sing 392 n n 
C9 H92 SIA sing 393 n n 
C9 H91 SIA sing 394 n n 
C10 C11 SIA sing 395 n n 
C10 N5 SIA sing 396 n n 
C10 O10 SIA doub 397 n n 
C11 H111 SIA sing 398 n n 
C11 H113 SIA sing 399 n n 
C11 H112 SIA sing 400 n n 
N5 HN5 SIA sing 401 n n 
O1B HO1B SIA sing 402 n n 
O2 HO2 SIA sing 403 n n 
O4 HO4 SIA sing 404 n n 
O7 HO7 SIA sing 405 n n 
O8 HO8 SIA sing 406 n n 
O9 HO9 SIA sing 407 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
SIA DNeup5Aca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
SIA 'N-acetyl-a-D-neuraminic acid' 'COMMON NAME' GMML 1 
SIA a-D-Neup5Ac 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
SIA Neu5Ac '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 SIA . . . I 6 16.385 -8.364 30.134 1 131.4 ? C1 SIA 401 C 1 
HETATM 2 C C2 SIA . . . I 6 17.331 -7.21 29.913 1 128.49 ? C2 SIA 401 C 1 
HETATM 3 C C3 SIA . . . I 6 18.674 -7.519 30.564 1 126.77 ? C3 SIA 401 C 1 
HETATM 4 C C4 SIA . . . I 6 19.775 -7.615 29.516 1 124.42 ? C4 SIA 401 C 1 
HETATM 5 C C5 SIA . . . I 6 19.841 -6.341 28.686 1 122.62 ? C5 SIA 401 C 1 
HETATM 6 C C6 SIA . . . I 6 18.462 -6.025 28.105 1 124.32 ? C6 SIA 401 C 1 
HETATM 7 C C7 SIA . . . I 6 17.991 -4.595 28.407 1 122.46 ? C7 SIA 401 C 1 
HETATM 8 C C8 SIA . . . I 6 16.573 -4.337 27.899 1 119.67 ? C8 SIA 401 C 1 
HETATM 9 C C9 SIA . . . I 6 16.573 -3.355 26.735 1 115.9 ? C9 SIA 401 C 1 
HETATM 10 C C10 SIA . . . I 6 21.287 -5.525 26.864 1 115.86 ? C10 SIA 401 C 1 
HETATM 11 C C11 SIA . . . I 6 22.289 -5.933 25.825 1 115.12 ? C11 SIA 401 C 1 
HETATM 12 N N5 SIA . . . I 6 20.818 -6.514 27.625 1 119.24 ? N5 SIA 401 C 1 
HETATM 13 O O1A SIA . . . I 6 15.914 -8.947 29.134 1 132.11 ? O1A SIA 401 C 1 
HETATM 14 O O1B SIA . . . I 6 16.106 -8.698 31.307 1 132.65 ? O1B SIA 401 C 1 
HETATM 15 O O4 SIA . . . I 6 21.033 -7.853 30.159 1 124.07 ? O4 SIA 401 C 1 
HETATM 16 O O6 SIA . . . I 6 17.492 -7.009 28.505 1 126.98 ? O6 SIA 401 C 1 
HETATM 17 O O7 SIA . . . I 6 18.063 -4.29 29.807 1 122.65 ? O7 SIA 401 C 1 
HETATM 18 O O8 SIA . . . I 6 15.983 -5.569 27.474 1 119.86 ? O8 SIA 401 C 1 
HETATM 19 O O9 SIA . . . I 6 15.242 -2.891 26.493 1 113.23 ? O9 SIA 401 C 1 
HETATM 20 O O10 SIA . . . I 6 20.94 -4.364 26.993 1 113.72 ? O10 SIA 401 C 1 
#
_model_server_stats.io_time_ms              28 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           332 
_model_server_stats.encode_time_ms          17 
_model_server_stats.element_count           20 
#