data_6YJP
#
_model_server_result.job_id            7-ShjKid8nkQmKsfyufMag 
_model_server_result.datetime_utc      '2024-11-16 13:57:45' 
_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          6yjp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":301}' 
#
_entry.id    6YJP 
#
_exptl.entry_id    6YJP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          97.58 
_cell.angle_gamma         90 
_cell.entry_id            6YJP 
_cell.length_a            166.044 
_cell.length_b            86.462 
_cell.length_c            111.299 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6YJP 
_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
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? monomeric 1 author_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,F,H 1 1 
D,I 2 1 
B,G 2 2 
E,J 3 1 
#
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' 1_556 x,y,z+1 1 0 0 0 1 0 0 0 1 -14.681494 0 110.32643 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 G N N 
? 3 H N N 
? 3 I N N 
? 3 J 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 27 C CYS 48 1_555 A SG CYS 101 C CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf2 A SG CYS 142 C CYS 163 1_555 A SG CYS 207 C CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
disulf ? disulf3 B SG CYS 27 D CYS 48 1_555 B SG CYS 101 D CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf4 B SG CYS 142 D CYS 163 1_555 B SG CYS 207 D CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? 
disulf ? disulf5 C SG CYS 24 A CYS 39 1_555 C SG CYS 93 A CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? 
disulf ? disulf6 D SG CYS 24 B CYS 39 1_555 D SG CYS 93 B CYS 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf7 E SG CYS 27 E CYS 48 1_555 E SG CYS 101 E CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf8 E SG CYS 142 E CYS 163 1_555 E SG CYS 207 E CYS 228 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.002 ? 
covale ? covale1 A ND2 ASN 187 C ASN 208 1_555 F C1 NAG . C NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? 
covale ? covale2 B ND2 ASN 187 D ASN 208 1_555 G C1 NAG . D NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? 
covale ? covale3 C ND2 ASN 27 A ASN 42 1_555 H C1 NAG . A NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale4 D ND2 ASN 27 B ASN 42 1_555 I C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? 
covale ? covale5 E ND2 ASN 22 E ASN 43 1_555 J C1 NAG . E NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
#
_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 235 n n 
C1 O1 NAG sing 236 n n 
C1 O5 NAG sing 237 n n 
C1 H1 NAG sing 238 n n 
C2 C3 NAG sing 239 n n 
C2 N2 NAG sing 240 n n 
C2 H2 NAG sing 241 n n 
C3 C4 NAG sing 242 n n 
C3 O3 NAG sing 243 n n 
C3 H3 NAG sing 244 n n 
C4 C5 NAG sing 245 n n 
C4 O4 NAG sing 246 n n 
C4 H4 NAG sing 247 n n 
C5 C6 NAG sing 248 n n 
C5 O5 NAG sing 249 n n 
C5 H5 NAG sing 250 n n 
C6 O6 NAG sing 251 n n 
C6 H61 NAG sing 252 n n 
C6 H62 NAG sing 253 n n 
C7 C8 NAG sing 254 n n 
C7 N2 NAG sing 255 n n 
C7 O7 NAG doub 256 n n 
C8 H81 NAG sing 257 n n 
C8 H82 NAG sing 258 n n 
C8 H83 NAG sing 259 n n 
N2 HN2 NAG sing 260 n n 
O1 HO1 NAG sing 261 n n 
O3 HO3 NAG sing 262 n n 
O4 HO4 NAG sing 263 n n 
O6 HO6 NAG sing 264 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                     6YJP 
_atom_sites.fract_transf_matrix[1][1]    0.006022 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000801 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.011566 
_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]    0.009064 
_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 3 NAG C 1 301 304 NAG NAG . 
G 3 NAG D 1 301 304 NAG NAG . 
H 3 NAG A 1 201 201 NAG NAG . 
I 3 NAG B 1 201 201 NAG NAG . 
J 3 NAG E 1 301 301 NAG NAG . 
#
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 3 24.639 -2.782 -3.554 1 136.63 ? C1 NAG 301 C 1 
HETATM 2 C C2 NAG . . . F 3 23.126 -2.964 -3.653 1 134.52 ? C2 NAG 301 C 1 
HETATM 3 C C3 NAG . . . F 3 22.768 -4.364 -3.163 1 138.08 ? C3 NAG 301 C 1 
HETATM 4 C C4 NAG . . . F 3 23.385 -5.318 -4.165 1 151.19 ? C4 NAG 301 C 1 
HETATM 5 C C5 NAG . . . F 3 24.908 -5.175 -4.115 1 159.03 ? C5 NAG 301 C 1 
HETATM 6 C C6 NAG . . . F 3 25.53 -6.038 -5.211 1 176.94 ? C6 NAG 301 C 1 
HETATM 7 C C7 NAG . . . F 3 21.186 -1.574 -3.259 1 144.76 ? C7 NAG 301 C 1 
HETATM 8 C C8 NAG . . . F 3 20.223 -1.488 -2.111 1 150.38 ? C8 NAG 301 C 1 
HETATM 9 N N2 NAG . . . F 3 22.427 -1.918 -2.939 1 137.13 ? N2 NAG 301 C 1 
HETATM 10 O O3 NAG . . . F 3 21.356 -4.594 -3.115 1 135.19 ? O3 NAG 301 C 1 
HETATM 11 O O4 NAG . . . F 3 22.924 -6.647 -3.908 1 158.3 ? O4 NAG 301 C 1 
HETATM 12 O O5 NAG . . . F 3 25.305 -3.801 -4.32 1 151.91 ? O5 NAG 301 C 1 
HETATM 13 O O6 NAG . . . F 3 26.872 -6.406 -4.872 1 204.67 ? O6 NAG 301 C 1 
HETATM 14 O O7 NAG . . . F 3 20.852 -1.366 -4.415 1 147.31 ? O7 NAG 301 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           636 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           14 
#