data_3D5O
#
_model_server_result.job_id            GPUR9HjZ1q5R52M6NF-nzQ 
_model_server_result.datetime_utc      '2024-12-01 00:16:34' 
_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          3d5o 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"V","auth_seq_id":208}' 
#
_entry.id    3D5O 
#
_exptl.entry_id    3D5O 
_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    5 
_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            3D5O 
_cell.length_a            64.197 
_cell.length_b            143.477 
_cell.length_c            161.588 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D5O 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_pdbx_struct_assembly.details               author_and_software_defined_assembly 
_pdbx_struct_assembly.id                    1 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
F,AA,BA,HA 1 1 
D,S,T,U,V,FA 1 2 
A,B,C,E,G,H,I,J,K,L,M,N,O,P,Q,R,W,X,Y,Z,CA,DA,EA,GA 1 3 
#
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 'crystal symmetry operation' 1_455 x-1,y,z 1 0 0 0 1 0 0 0 1 -64.197 0 0 
2 'crystal symmetry operation' 3_554 -x,y+1/2,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 71.7385 -80.794 
3 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 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 N N N 
? 4 R N N 
? 4 V N N 
? 4 Z 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 36 A CYS 36 1_555 A SG CYS 95 A CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? 
disulf ? disulf2 B SG CYS 36 B CYS 36 1_555 B SG CYS 95 B CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf3 C SG CYS 36 C CYS 36 1_555 C SG CYS 95 C CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf4 D SG CYS 36 D CYS 36 1_555 D SG CYS 95 D CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? 
disulf ? disulf5 E SG CYS 36 E CYS 36 1_555 E SG CYS 95 E CYS 95 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf6 F SG CYS 26 F CYS 26 1_555 F SG CYS 68 F CYS 68 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf7 F SG CYS 107 F CYS 107 1_555 F SG CYS 151 F CYS 151 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
covale ? covale1 A ND2 ASN 32 A ASN 32 1_555 J C1 NAG . A NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? 
covale ? covale2 B ND2 ASN 32 B ASN 32 1_555 N C1 NAG . B NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale3 C ND2 ASN 32 C ASN 32 1_555 R C1 NAG . C NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? 
covale ? covale4 D ND2 ASN 32 D ASN 32 1_555 V C1 NAG . D NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? 
covale ? covale5 E ND2 ASN 32 E ASN 32 1_555 Z C1 NAG . E NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
#
_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 250 n n 
C1 O1 NAG sing 251 n n 
C1 O5 NAG sing 252 n n 
C1 H1 NAG sing 253 n n 
C2 C3 NAG sing 254 n n 
C2 N2 NAG sing 255 n n 
C2 H2 NAG sing 256 n n 
C3 C4 NAG sing 257 n n 
C3 O3 NAG sing 258 n n 
C3 H3 NAG sing 259 n n 
C4 C5 NAG sing 260 n n 
C4 O4 NAG sing 261 n n 
C4 H4 NAG sing 262 n n 
C5 C6 NAG sing 263 n n 
C5 O5 NAG sing 264 n n 
C5 H5 NAG sing 265 n n 
C6 O6 NAG sing 266 n n 
C6 H61 NAG sing 267 n n 
C6 H62 NAG sing 268 n n 
C7 C8 NAG sing 269 n n 
C7 N2 NAG sing 270 n n 
C7 O7 NAG doub 271 n n 
C8 H81 NAG sing 272 n n 
C8 H82 NAG sing 273 n n 
C8 H83 NAG sing 274 n n 
N2 HN2 NAG sing 275 n n 
O1 HO1 NAG sing 276 n n 
O3 HO3 NAG sing 277 n n 
O4 HO4 NAG sing 278 n n 
O6 HO6 NAG sing 279 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                     3D5O 
_atom_sites.fract_transf_matrix[1][1]    0.015577 
_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]    0.00697 
_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]    0.006189 
_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 3 SO4 A 1 205 1 SO4 SO4 . 
H 3 SO4 A 1 206 2 SO4 SO4 . 
I 3 SO4 A 1 207 3 SO4 SO4 . 
J 4 NAG A 1 208 1 NAG NAG . 
K 3 SO4 B 1 205 4 SO4 SO4 . 
L 3 SO4 B 1 206 5 SO4 SO4 . 
M 3 SO4 B 1 207 6 SO4 SO4 . 
N 4 NAG B 1 208 2 NAG NAG . 
O 3 SO4 C 1 205 7 SO4 SO4 . 
P 3 SO4 C 1 206 8 SO4 SO4 . 
Q 3 SO4 C 1 207 9 SO4 SO4 . 
R 4 NAG C 1 208 3 NAG NAG . 
S 3 SO4 D 1 205 10 SO4 SO4 . 
T 3 SO4 D 1 206 11 SO4 SO4 . 
U 3 SO4 D 1 207 12 SO4 SO4 . 
V 4 NAG D 1 208 4 NAG NAG . 
W 3 SO4 E 1 205 13 SO4 SO4 . 
X 3 SO4 E 1 206 14 SO4 SO4 . 
Y 3 SO4 E 1 207 15 SO4 SO4 . 
Z 4 NAG E 1 208 5 NAG NAG . 
AA 3 SO4 F 1 178 16 SO4 SO4 . 
BA 5 GOL F 1 179 1 GOL GOL . 
CA 6 HOH A 1 209 6 HOH HOH . 
CA 6 HOH A 2 210 13 HOH HOH . 
CA 6 HOH A 3 211 35 HOH HOH . 
DA 6 HOH B 1 209 7 HOH HOH . 
DA 6 HOH B 2 210 8 HOH HOH . 
DA 6 HOH B 3 211 10 HOH HOH . 
DA 6 HOH B 4 212 15 HOH HOH . 
DA 6 HOH B 5 213 16 HOH HOH . 
DA 6 HOH B 6 214 17 HOH HOH . 
DA 6 HOH B 7 215 20 HOH HOH . 
DA 6 HOH B 8 216 21 HOH HOH . 
DA 6 HOH B 9 217 22 HOH HOH . 
DA 6 HOH B 10 218 24 HOH HOH . 
DA 6 HOH B 11 219 27 HOH HOH . 
DA 6 HOH B 12 220 28 HOH HOH . 
DA 6 HOH B 13 221 36 HOH HOH . 
EA 6 HOH C 1 209 9 HOH HOH . 
EA 6 HOH C 2 210 11 HOH HOH . 
EA 6 HOH C 3 211 19 HOH HOH . 
EA 6 HOH C 4 212 23 HOH HOH . 
EA 6 HOH C 5 213 25 HOH HOH . 
EA 6 HOH C 6 214 32 HOH HOH . 
FA 6 HOH D 1 209 30 HOH HOH . 
FA 6 HOH D 2 210 31 HOH HOH . 
FA 6 HOH D 3 211 33 HOH HOH . 
GA 6 HOH E 1 209 12 HOH HOH . 
HA 6 HOH F 1 180 14 HOH HOH . 
HA 6 HOH F 2 181 18 HOH HOH . 
HA 6 HOH F 3 182 26 HOH HOH . 
HA 6 HOH F 4 183 29 HOH HOH . 
HA 6 HOH F 5 184 34 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 . . . V 4 6.867 -39.904 -25.702 1 70.33 ? C1 NAG 208 D 1 
HETATM 2 C C2 NAG . . . V 4 6.15 -40.644 -24.556 1 78.62 ? C2 NAG 208 D 1 
HETATM 3 C C3 NAG . . . V 4 6.844 -40.417 -23.19 1 72.39 ? C3 NAG 208 D 1 
HETATM 4 C C4 NAG . . . V 4 8.347 -40.674 -23.322 1 72.66 ? C4 NAG 208 D 1 
HETATM 5 C C5 NAG . . . V 4 8.893 -39.771 -24.423 1 77.87 ? C5 NAG 208 D 1 
HETATM 6 C C6 NAG . . . V 4 10.403 -39.873 -24.581 1 66.59 ? C6 NAG 208 D 1 
HETATM 7 C C7 NAG . . . V 4 4.363 -38.975 -24.376 1 84.47 ? C7 NAG 208 D 1 
HETATM 8 C C8 NAG . . . V 4 2.944 -38.726 -23.875 1 73.58 ? C8 NAG 208 D 1 
HETATM 9 N N2 NAG . . . V 4 4.742 -40.252 -24.503 1 91.62 ? N2 NAG 208 D 1 
HETATM 10 O O3 NAG . . . V 4 6.302 -41.305 -22.22 1 79.78 ? O3 NAG 208 D 1 
HETATM 11 O O4 NAG . . . V 4 9.007 -40.411 -22.092 1 84.81 ? O4 NAG 208 D 1 
HETATM 12 O O5 NAG . . . V 4 8.285 -40.143 -25.682 1 79.45 ? O5 NAG 208 D 1 
HETATM 13 O O6 NAG . . . V 4 10.914 -38.842 -25.419 1 56.64 ? O6 NAG 208 D 1 
HETATM 14 O O7 NAG . . . V 4 5.092 -38.016 -24.648 1 74.77 ? O7 NAG 208 D 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    12 
_model_server_stats.query_time_ms           354 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           14 
#