data_5F4P
#
_model_server_result.job_id            1VanH5RDMhHjjXXyGz6nwA 
_model_server_result.datetime_utc      '2024-10-18 02:27:06' 
_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          5f4p 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":502}' 
#
_entry.id    5F4P 
#
_exptl.entry_id    5F4P 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          2 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    12 
_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            5F4P 
_cell.length_a            67.378 
_cell.length_b            127.517 
_cell.length_c            192.945 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5F4P 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        20 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 2 2 21' 
#
_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,N,O,P,Q,R 
_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
? 2 C N N 
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 H N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P 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 6 D CYS 54 1_555 A SG CYS 26 D CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 71 D CYS 119 1_555 A SG CYS 84 D CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf3 A SG CYS 97 D CYS 218 1_555 A SG CYS 126 D CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf4 A SG CYS 107 D CYS 228 1_555 A SG CYS 118 D CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf5 A SG CYS 175 D CYS 296 1_555 A SG CYS 194 D CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf6 A SG CYS 240 D CYS 378 1_555 A SG CYS 304 D CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf7 A SG CYS 247 D CYS 385 1_555 A SG CYS 277 D CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf8 B SG CYS 6 A CYS 54 1_555 B SG CYS 26 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf9 B SG CYS 71 A CYS 119 1_555 B SG CYS 84 A CYS 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf10 B SG CYS 97 A CYS 218 1_555 B SG CYS 126 A CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf11 B SG CYS 107 A CYS 228 1_555 B SG CYS 118 A CYS 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf12 B SG CYS 175 A CYS 296 1_555 B SG CYS 194 A CYS 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
disulf ? disulf13 B SG CYS 240 A CYS 378 1_555 B SG CYS 304 A CYS 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
disulf ? disulf14 B SG CYS 247 A CYS 385 1_555 B SG CYS 277 A CYS 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? 
#
_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 294 n n 
C1 O1 NAG sing 295 n n 
C1 O5 NAG sing 296 n n 
C1 H1 NAG sing 297 n n 
C2 C3 NAG sing 298 n n 
C2 N2 NAG sing 299 n n 
C2 H2 NAG sing 300 n n 
C3 C4 NAG sing 301 n n 
C3 O3 NAG sing 302 n n 
C3 H3 NAG sing 303 n n 
C4 C5 NAG sing 304 n n 
C4 O4 NAG sing 305 n n 
C4 H4 NAG sing 306 n n 
C5 C6 NAG sing 307 n n 
C5 O5 NAG sing 308 n n 
C5 H5 NAG sing 309 n n 
C6 O6 NAG sing 310 n n 
C6 H61 NAG sing 311 n n 
C6 H62 NAG sing 312 n n 
C7 C8 NAG sing 313 n n 
C7 N2 NAG sing 314 n n 
C7 O7 NAG doub 315 n n 
C8 H81 NAG sing 316 n n 
C8 H82 NAG sing 317 n n 
C8 H83 NAG sing 318 n n 
N2 HN2 NAG sing 319 n n 
O1 HO1 NAG sing 320 n n 
O3 HO3 NAG sing 321 n n 
O4 HO4 NAG sing 322 n n 
O6 HO6 NAG sing 323 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                     5F4P 
_atom_sites.fract_transf_matrix[1][1]    0.014842 
_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]    0.007842 
_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]    0.005183 
_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 2 NAG D 1 501 503 NAG NAG . 
D 2 NAG D 1 502 504 NAG NAG . 
E 2 NAG D 1 503 505 NAG NAG . 
F 2 NAG D 1 504 506 NAG NAG . 
G 2 NAG D 1 505 507 NAG NAG . 
H 2 NAG D 1 506 508 NAG NAG . 
I 3 5VG D 1 507 501 5VG LIG . 
J 3 5VG A 1 501 501 5VG LIG . 
K 2 NAG A 1 502 503 NAG NAG . 
L 2 NAG A 1 503 504 NAG NAG . 
M 2 NAG A 1 504 505 NAG NAG . 
N 2 NAG A 1 505 506 NAG NAG . 
O 2 NAG A 1 506 507 NAG NAG . 
P 2 NAG A 1 507 508 NAG NAG . 
Q 4 HOH D 1 601 6 HOH HOH . 
Q 4 HOH D 2 602 8 HOH HOH . 
Q 4 HOH D 3 603 9 HOH HOH . 
Q 4 HOH D 4 604 12 HOH HOH . 
Q 4 HOH D 5 605 10 HOH HOH . 
Q 4 HOH D 6 606 2 HOH HOH . 
R 4 HOH A 1 601 11 HOH HOH . 
R 4 HOH A 2 602 13 HOH HOH . 
R 4 HOH A 3 603 1 HOH HOH . 
R 4 HOH A 4 604 7 HOH HOH . 
R 4 HOH A 5 605 5 HOH HOH . 
R 4 HOH A 6 606 4 HOH HOH . 
R 4 HOH A 7 607 3 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 . . . D 2 -11.121 -37.315 16.123 1 75.89 ? C1 NAG 502 D 1 
HETATM 2 C C2 NAG . . . D 2 -10.281 -38.408 15.483 1 75.74 ? C2 NAG 502 D 1 
HETATM 3 C C3 NAG . . . D 2 -8.917 -37.855 15.09 1 78.32 ? C3 NAG 502 D 1 
HETATM 4 C C4 NAG . . . D 2 -9.076 -36.609 14.226 1 86.25 ? C4 NAG 502 D 1 
HETATM 5 C C5 NAG . . . D 2 -10.016 -35.602 14.888 1 86.92 ? C5 NAG 502 D 1 
HETATM 6 C C6 NAG . . . D 2 -10.349 -34.43 13.994 1 86 ? C6 NAG 502 D 1 
HETATM 7 C C7 NAG . . . D 2 -10.446 -40.796 16.028 1 77.14 ? C7 NAG 502 D 1 
HETATM 8 C C8 NAG . . . D 2 -10.23 -41.848 17.075 1 68.51 ? C8 NAG 502 D 1 
HETATM 9 N N2 NAG . . . D 2 -10.132 -39.546 16.381 1 78.3 ? N2 NAG 502 D 1 
HETATM 10 O O3 NAG . . . D 2 -8.19 -38.852 14.382 1 80.57 ? O3 NAG 502 D 1 
HETATM 11 O O4 NAG . . . D 2 -7.806 -35.998 14.028 1 93.71 ? O4 NAG 502 D 1 
HETATM 12 O O5 NAG . . . D 2 -11.261 -36.235 15.215 1 78.14 ? O5 NAG 502 D 1 
HETATM 13 O O6 NAG . . . D 2 -10.815 -34.863 12.723 1 77.6 ? O6 NAG 502 D 1 
HETATM 14 O O7 NAG . . . D 2 -10.885 -41.067 14.913 1 66.1 ? O7 NAG 502 D 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           14 
#