data_4XX1
#
_model_server_result.job_id            TUVuBEhcUEDD3RQZ2Cq-Nw 
_model_server_result.datetime_utc      '2024-11-13 07:21:23' 
_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          4xx1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"O","auth_seq_id":503}' 
#
_entry.id    4XX1 
#
_exptl.entry_id    4XX1 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    9 
_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         120 
_cell.entry_id            4XX1 
_cell.length_a            166.419 
_cell.length_b            166.419 
_cell.length_c            97.66 
_cell.Z_PDB               9 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XX1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
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 trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
PISA trimeric 3 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,J,K,L 1 1 
D,E,F,M,N,O 2 1 
G,H,I,P,Q,R 3 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
? 4 J N N 
? 4 K N N 
? 4 L N N 
? 4 M N N 
? 4 N N N 
? 4 O N N 
? 4 P N N 
? 4 Q N N 
? 4 R 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 22 L CYS 22 1_555 A SG CYS 87 L CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf2 A SG CYS 135 L CYS 135 1_555 A SG CYS 194 L CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf3 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf4 B SG CYS 153 H CYS 153 1_555 B SG CYS 209 H CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf5 C SG CYS 50 A CYS 50 1_555 C SG CYS 74 A CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf6 C SG CYS 313 A CYS 313 1_555 C SG CYS 356 A CYS 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf7 D SG CYS 22 G CYS 22 1_555 D SG CYS 87 G CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf8 D SG CYS 135 G CYS 135 1_555 D SG CYS 194 G CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf9 E SG CYS 22 E CYS 22 1_555 E SG CYS 96 E CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
disulf ? disulf10 E SG CYS 153 E CYS 153 1_555 E SG CYS 209 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf11 F SG CYS 50 B CYS 50 1_555 F SG CYS 74 B CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf12 F SG CYS 313 B CYS 313 1_555 F SG CYS 356 B CYS 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf13 G SG CYS 22 O CYS 22 1_555 G SG CYS 87 O CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf14 H SG CYS 22 M CYS 22 1_555 H SG CYS 96 M CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf15 I SG CYS 50 J CYS 50 1_555 I SG CYS 74 J CYS 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf16 I SG CYS 313 J CYS 313 1_555 I SG CYS 356 J CYS 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
covale ? covale1 C ND2 ASN 84 A ASN 84 1_555 J C1 NAG . A NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? 
covale ? covale2 C ND2 ASN 272 A ASN 272 1_555 K C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? 
covale ? covale3 C ND2 ASN 384 A ASN 384 1_555 L C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale4 F ND2 ASN 84 B ASN 84 1_555 M C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale5 F ND2 ASN 272 B ASN 272 1_555 N C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? 
covale ? covale6 F ND2 ASN 384 B ASN 384 1_555 O C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? 
covale ? covale7 I ND2 ASN 84 J ASN 84 1_555 P C1 NAG . J NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? 
covale ? covale8 I ND2 ASN 272 J ASN 272 1_555 Q C1 NAG . J NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale9 I ND2 ASN 384 J ASN 384 1_555 R C1 NAG . J NAG 503 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 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                     4XX1 
_atom_sites.fract_transf_matrix[1][1]    0.006009 
_atom_sites.fract_transf_matrix[1][2]    0.003469 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.006939 
_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]    0.01024 
_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
J 4 NAG A 1 501 2 NAG NAG . 
K 4 NAG A 1 502 3 NAG NAG . 
L 4 NAG A 1 503 4 NAG NAG . 
M 4 NAG B 1 501 2 NAG NAG . 
N 4 NAG B 1 502 3 NAG NAG . 
O 4 NAG B 1 503 4 NAG NAG . 
P 4 NAG J 1 501 2 NAG NAG . 
Q 4 NAG J 1 502 3 NAG NAG . 
R 4 NAG J 1 503 4 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 . . . O 4 34.451 7.571 -24.545 1 181.51 ? C1 NAG 503 B 1 
HETATM 2 C C2 NAG . . . O 4 34.024 7.418 -23.083 1 192.49 ? C2 NAG 503 B 1 
HETATM 3 C C3 NAG . . . O 4 35.242 7.498 -22.157 1 193.42 ? C3 NAG 503 B 1 
HETATM 4 C C4 NAG . . . O 4 36.322 6.514 -22.602 1 187.76 ? C4 NAG 503 B 1 
HETATM 5 C C5 NAG . . . O 4 36.638 6.712 -24.084 1 178.25 ? C5 NAG 503 B 1 
HETATM 6 C C6 NAG . . . O 4 37.634 5.712 -24.62 1 173.89 ? C6 NAG 503 B 1 
HETATM 7 C C7 NAG . . . O 4 32.129 8.27 -21.756 1 188.95 ? C7 NAG 503 B 1 
HETATM 8 C C8 NAG . . . O 4 31.198 9.423 -21.52 1 181.47 ? C8 NAG 503 B 1 
HETATM 9 N N2 NAG . . . O 4 33.043 8.435 -22.726 1 192.16 ? N2 NAG 503 B 1 
HETATM 10 O O3 NAG . . . O 4 34.859 7.234 -20.81 1 188.4 ? O3 NAG 503 B 1 
HETATM 11 O O4 NAG . . . O 4 37.506 6.701 -21.838 1 189.41 ? O4 NAG 503 B 1 
HETATM 12 O O5 NAG . . . O 4 35.445 6.567 -24.867 1 175.58 ? O5 NAG 503 B 1 
HETATM 13 O O6 NAG . . . O 4 37.056 4.421 -24.757 1 164.84 ? O6 NAG 503 B 1 
HETATM 14 O O7 NAG . . . O 4 32.058 7.237 -21.09 1 188.51 ? O7 NAG 503 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    25 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#