data_5BPQ
#
_model_server_result.job_id            0DqhANuMGUIAlidOAC2LFA 
_model_server_result.datetime_utc      '2024-11-05 21:11:09' 
_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          5bpq 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":201}' 
#
_entry.id    5BPQ 
#
_exptl.entry_id    5BPQ 
_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    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               'cysteine-rich domain, UNP residues 42-179' 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90 
_cell.angle_gamma         120 
_cell.entry_id            5BPQ 
_cell.length_a            76.075 
_cell.length_b            76.075 
_cell.length_c            204.47 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5BPQ 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 author_and_software_defined_assembly 2 
PISA monomeric 1 author_and_software_defined_assembly 3 
PISA monomeric 1 author_and_software_defined_assembly 4 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,E,F,J 1 1 
B,G,K 2 1 
C,H,L 3 1 
D,I,M 4 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 E N N 
? 2 G N N 
? 2 H N N 
? 2 I 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 7 A CYS 45 1_555 A SG CYS 68 A CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf2 A SG CYS 15 A CYS 53 1_555 A SG CYS 61 A CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf3 A SG CYS 52 A CYS 90 1_555 A SG CYS 90 A CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? 
disulf ? disulf4 A SG CYS 79 A CYS 117 1_555 A SG CYS 120 A CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 A SG CYS 83 A CYS 121 1_555 A SG CYS 107 A CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf6 B SG CYS 7 B CYS 45 1_555 B SG CYS 68 B CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf7 B SG CYS 15 B CYS 53 1_555 B SG CYS 61 B CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf8 B SG CYS 52 B CYS 90 1_555 B SG CYS 90 B CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf9 B SG CYS 79 B CYS 117 1_555 B SG CYS 120 B CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf10 B SG CYS 83 B CYS 121 1_555 B SG CYS 107 B CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf11 C SG CYS 7 C CYS 45 1_555 C SG CYS 68 C CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf12 C SG CYS 15 C CYS 53 1_555 C SG CYS 61 C CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf13 C SG CYS 52 C CYS 90 1_555 C SG CYS 90 C CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf14 C SG CYS 79 C CYS 117 1_555 C SG CYS 120 C CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? 
disulf ? disulf15 C SG CYS 83 C CYS 121 1_555 C SG CYS 107 C CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf16 D SG CYS 7 D CYS 45 1_555 D SG CYS 68 D CYS 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf17 D SG CYS 15 D CYS 53 1_555 D SG CYS 61 D CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf18 D SG CYS 52 D CYS 90 1_555 D SG CYS 90 D CYS 128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf19 D SG CYS 79 D CYS 117 1_555 D SG CYS 120 D CYS 158 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
disulf ? disulf20 D SG CYS 83 D CYS 121 1_555 D SG CYS 107 D CYS 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
covale ? covale1 A ND2 ASN 106 A ASN 144 1_555 E C1 NAG . A NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? 
covale ? covale2 B ND2 ASN 106 B ASN 144 1_555 G C1 NAG . B NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.451 ? 
covale ? covale3 C ND2 ASN 106 C ASN 144 1_555 H C1 NAG . C NAG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? 
covale ? covale4 D ND2 ASN 106 D ASN 144 1_555 I C1 NAG . D NAG 201 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 237 n n 
C1 O1 NAG sing 238 n n 
C1 O5 NAG sing 239 n n 
C1 H1 NAG sing 240 n n 
C2 C3 NAG sing 241 n n 
C2 N2 NAG sing 242 n n 
C2 H2 NAG sing 243 n n 
C3 C4 NAG sing 244 n n 
C3 O3 NAG sing 245 n n 
C3 H3 NAG sing 246 n n 
C4 C5 NAG sing 247 n n 
C4 O4 NAG sing 248 n n 
C4 H4 NAG sing 249 n n 
C5 C6 NAG sing 250 n n 
C5 O5 NAG sing 251 n n 
C5 H5 NAG sing 252 n n 
C6 O6 NAG sing 253 n n 
C6 H61 NAG sing 254 n n 
C6 H62 NAG sing 255 n n 
C7 C8 NAG sing 256 n n 
C7 N2 NAG sing 257 n n 
C7 O7 NAG doub 258 n n 
C8 H81 NAG sing 259 n n 
C8 H82 NAG sing 260 n n 
C8 H83 NAG sing 261 n n 
N2 HN2 NAG sing 262 n n 
O1 HO1 NAG sing 263 n n 
O3 HO3 NAG sing 264 n n 
O4 HO4 NAG sing 265 n n 
O6 HO6 NAG sing 266 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                     5BPQ 
_atom_sites.fract_transf_matrix[1][1]    0.013145 
_atom_sites.fract_transf_matrix[1][2]    0.007589 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015178 
_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]    0.004891 
_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
E 2 NAG A 1 201 1 NAG NAG . 
F 3 CL A 1 202 1 CL CL . 
G 2 NAG B 1 201 1 NAG NAG . 
H 2 NAG C 1 201 1 NAG NAG . 
I 2 NAG D 1 201 1 NAG NAG . 
J 4 HOH A 1 301 18 HOH HOH . 
J 4 HOH A 2 302 57 HOH HOH . 
J 4 HOH A 3 303 38 HOH HOH . 
J 4 HOH A 4 304 16 HOH HOH . 
J 4 HOH A 5 305 37 HOH HOH . 
J 4 HOH A 6 306 17 HOH HOH . 
J 4 HOH A 7 307 19 HOH HOH . 
J 4 HOH A 8 308 7 HOH HOH . 
J 4 HOH A 9 309 2 HOH HOH . 
J 4 HOH A 10 310 22 HOH HOH . 
J 4 HOH A 11 311 58 HOH HOH . 
J 4 HOH A 12 312 30 HOH HOH . 
J 4 HOH A 13 313 36 HOH HOH . 
J 4 HOH A 14 314 20 HOH HOH . 
J 4 HOH A 15 315 56 HOH HOH . 
J 4 HOH A 16 316 25 HOH HOH . 
J 4 HOH A 17 317 11 HOH HOH . 
J 4 HOH A 18 318 4 HOH HOH . 
J 4 HOH A 19 319 21 HOH HOH . 
J 4 HOH A 20 320 34 HOH HOH . 
J 4 HOH A 21 321 54 HOH HOH . 
J 4 HOH A 22 322 15 HOH HOH . 
J 4 HOH A 23 323 33 HOH HOH . 
J 4 HOH A 24 324 31 HOH HOH . 
J 4 HOH A 25 325 23 HOH HOH . 
K 4 HOH B 1 301 32 HOH HOH . 
K 4 HOH B 2 302 41 HOH HOH . 
K 4 HOH B 3 303 44 HOH HOH . 
K 4 HOH B 4 304 43 HOH HOH . 
K 4 HOH B 5 305 35 HOH HOH . 
K 4 HOH B 6 306 42 HOH HOH . 
K 4 HOH B 7 307 12 HOH HOH . 
K 4 HOH B 8 308 24 HOH HOH . 
K 4 HOH B 9 309 62 HOH HOH . 
L 4 HOH C 1 301 9 HOH HOH . 
L 4 HOH C 2 302 64 HOH HOH . 
L 4 HOH C 3 303 59 HOH HOH . 
L 4 HOH C 4 304 10 HOH HOH . 
L 4 HOH C 5 305 45 HOH HOH . 
L 4 HOH C 6 306 46 HOH HOH . 
L 4 HOH C 7 307 63 HOH HOH . 
L 4 HOH C 8 308 14 HOH HOH . 
L 4 HOH C 9 309 13 HOH HOH . 
M 4 HOH D 1 301 60 HOH HOH . 
M 4 HOH D 2 302 52 HOH HOH . 
M 4 HOH D 3 303 61 HOH HOH . 
M 4 HOH D 4 304 51 HOH HOH . 
M 4 HOH D 5 305 69 HOH HOH . 
M 4 HOH D 6 306 27 HOH HOH . 
M 4 HOH D 7 307 47 HOH HOH . 
M 4 HOH D 8 308 6 HOH HOH . 
M 4 HOH D 9 309 8 HOH HOH . 
M 4 HOH D 10 310 3 HOH HOH . 
M 4 HOH D 11 311 28 HOH HOH . 
M 4 HOH D 12 312 53 HOH HOH . 
M 4 HOH D 13 313 29 HOH HOH . 
M 4 HOH D 14 314 68 HOH HOH . 
M 4 HOH D 15 315 26 HOH HOH . 
M 4 HOH D 16 316 5 HOH HOH . 
M 4 HOH D 17 317 40 HOH HOH . 
M 4 HOH D 18 318 1 HOH HOH . 
M 4 HOH D 19 319 49 HOH HOH . 
M 4 HOH D 20 320 67 HOH HOH . 
M 4 HOH D 21 321 39 HOH HOH . 
M 4 HOH D 22 322 65 HOH HOH . 
M 4 HOH D 23 323 55 HOH HOH . 
M 4 HOH D 24 324 48 HOH HOH . 
M 4 HOH D 25 325 66 HOH HOH . 
M 4 HOH D 26 326 50 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 . . . E 2 66.586 42.717 23.647 1 30.91 ? C1 NAG 201 A 1 
HETATM 2 C C2 NAG . . . E 2 65.693 42.061 24.716 1 30.49 ? C2 NAG 201 A 1 
HETATM 3 C C3 NAG . . . E 2 66.455 41.383 25.865 1 30.35 ? C3 NAG 201 A 1 
HETATM 4 C C4 NAG . . . E 2 67.802 40.796 25.473 1 29.88 ? C4 NAG 201 A 1 
HETATM 5 C C5 NAG . . . E 2 68.545 41.813 24.628 1 29.76 ? C5 NAG 201 A 1 
HETATM 6 C C6 NAG . . . E 2 69.944 41.342 24.249 1 29.53 ? C6 NAG 201 A 1 
HETATM 7 C C7 NAG . . . E 2 63.761 42.723 26.069 1 33.02 ? C7 NAG 201 A 1 
HETATM 8 C C8 NAG . . . E 2 62.981 43.853 26.68 1 31.12 ? C8 NAG 201 A 1 
HETATM 9 N N2 NAG . . . E 2 64.836 43.055 25.347 1 32.22 ? N2 NAG 201 A 1 
HETATM 10 O O3 NAG . . . E 2 65.671 40.35 26.425 1 33.61 ? O3 NAG 201 A 1 
HETATM 11 O O4 NAG . . . E 2 68.538 40.497 26.638 1 32.81 ? O4 NAG 201 A 1 
HETATM 12 O O5 NAG . . . E 2 67.776 41.974 23.464 1 32.29 ? O5 NAG 201 A 1 
HETATM 13 O O6 NAG . . . E 2 69.864 40.113 23.561 1 34.17 ? O6 NAG 201 A 1 
HETATM 14 O O7 NAG . . . E 2 63.393 41.559 26.245 1 37.76 ? O7 NAG 201 A 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           293 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#