data_4DEP
#
_model_server_result.job_id            vi6LVlW5I5FN6Y3XStJgIw 
_model_server_result.datetime_utc      '2024-12-26 23:43:58' 
_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          4dep 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":401}' 
#
_entry.id    4DEP 
#
_exptl.entry_id    4DEP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          4 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-beta-D-glucopyranose 
_entity.pdbx_number_of_molecules    14 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          90.35 
_cell.angle_gamma         90 
_cell.entry_id            4DEP 
_cell.length_a            105.99 
_cell.length_b            65.9 
_cell.length_c            163.4 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4DEP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        4 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1 21 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
PISA trimeric 3 author_and_software_defined_assembly 1 
PISA trimeric 3 author_and_software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,G,H,I,J,K,L,M,U 1 1 
D,E,F,N,O,P,Q,R,S,T,V,W 2 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 G N N 
? 4 H N N 
? 4 I N N 
? 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 
? 4 S N N 
? 4 T 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 B SG CYS 29 B CYS 27 1_555 B SG CYS 81 B CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? 
disulf ? disulf2 B SG CYS 106 B CYS 104 1_555 B SG CYS 149 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? 
disulf ? disulf3 B SG CYS 127 B CYS 125 1_555 B SG CYS 181 B CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf4 B SG CYS 233 B CYS 231 1_555 B SG CYS 297 B CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? 
disulf ? disulf5 C SG CYS 6 C CYS 4 1_555 C SG CYS 104 C CYS 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? 
disulf ? disulf6 C SG CYS 29 C CYS 27 1_555 C SG CYS 96 C CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? 
disulf ? disulf7 C SG CYS 119 C CYS 117 1_555 C SG CYS 163 C CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? 
disulf ? disulf8 C SG CYS 142 C CYS 140 1_555 C SG CYS 194 C CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
disulf ? disulf9 C SG CYS 248 C CYS 246 1_555 C SG CYS 314 C CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf10 E SG CYS 8 E CYS 6 1_555 E SG CYS 89 E CYS 87 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
disulf ? disulf11 E SG CYS 29 E CYS 27 1_555 E SG CYS 81 E CYS 79 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? 
disulf ? disulf12 E SG CYS 106 E CYS 104 1_555 E SG CYS 149 E CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
disulf ? disulf13 E SG CYS 127 E CYS 125 1_555 E SG CYS 181 E CYS 179 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? 
disulf ? disulf14 E SG CYS 233 E CYS 231 1_555 E SG CYS 297 E CYS 295 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? 
disulf ? disulf15 F SG CYS 29 F CYS 27 1_555 F SG CYS 96 F CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? 
disulf ? disulf16 F SG CYS 119 F CYS 117 1_555 F SG CYS 163 F CYS 161 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
disulf ? disulf17 F SG CYS 142 F CYS 140 1_555 F SG CYS 194 F CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
disulf ? disulf18 F SG CYS 248 F CYS 246 1_555 F SG CYS 314 F CYS 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? 
covale ? covale1 B ND2 ASN 178 B ASN 176 1_555 G C1 NAG . B NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? 
covale ? covale2 B ND2 ASN 218 B ASN 216 1_555 H C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? 
covale ? covale3 B ND2 ASN 234 B ASN 232 1_555 I C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.627 ? 
covale ? covale4 C ND2 ASN 39 C ASN 37 1_555 K C1 NAG . C NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? 
covale ? covale5 C ND2 ASN 93 C ASN 91 1_555 L C1 NAG . C NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale6 C ND2 ASN 100 C ASN 98 1_555 J C1 NAG . C NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? 
covale ? covale7 C ND2 ASN 191 C ASN 189 1_555 M C1 NAG . C NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? 
covale ? covale8 E ND2 ASN 178 E ASN 176 1_555 N C1 NAG . E NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.512 ? 
covale ? covale9 E ND2 ASN 218 E ASN 216 1_555 O C1 NAG . E NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? 
covale ? covale10 E ND2 ASN 234 E ASN 232 1_555 P C1 NAG . E NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale11 E ND2 ASN 248 E ASN 246 1_555 Q C1 NAG . E NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale12 F ND2 ASN 93 F ASN 91 1_555 S C1 NAG . F NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
covale ? covale13 F ND2 ASN 100 F ASN 98 1_555 T C1 NAG . F NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.565 ? 
covale ? covale14 F ND2 ASN 191 F ASN 189 1_555 R C1 NAG . F NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? 
#
_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                     4DEP 
_atom_sites.fract_transf_matrix[1][1]    0.009435 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000058 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015175 
_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]    0.00612 
_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 4 NAG B 1 401 350 NAG NAG . 
H 4 NAG B 1 402 351 NAG NAG . 
I 4 NAG B 1 403 403 NAG NAG . 
J 4 NAG C 1 401 401 NAG NAG . 
K 4 NAG C 1 402 351 NAG NAG . 
L 4 NAG C 1 403 352 NAG NAG . 
M 4 NAG C 1 404 353 NAG NAG . 
N 4 NAG E 1 401 401 NAG NAG . 
O 4 NAG E 1 402 351 NAG NAG . 
P 4 NAG E 1 403 352 NAG NAG . 
Q 4 NAG E 1 404 353 NAG NAG . 
R 4 NAG F 1 401 351 NAG NAG . 
S 4 NAG F 1 402 352 NAG NAG . 
T 4 NAG F 1 403 403 NAG NAG . 
U 5 HOH C 1 501 1 HOH HOH . 
V 5 HOH E 1 501 2 HOH HOH . 
V 5 HOH E 2 502 3 HOH HOH . 
V 5 HOH E 3 503 4 HOH HOH . 
V 5 HOH E 4 504 5 HOH HOH . 
W 5 HOH F 1 501 6 HOH HOH . 
W 5 HOH F 2 502 7 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 . . . G 4 94.29 59.849 58.667 1 66.42 ? C1 NAG 401 B 1 
HETATM 2 C C2 NAG . . . G 4 95.236 59.28 59.737 1 72.17 ? C2 NAG 401 B 1 
HETATM 3 C C3 NAG . . . G 4 94.697 59.435 61.168 1 78.2 ? C3 NAG 401 B 1 
HETATM 4 C C4 NAG . . . G 4 94.119 60.82 61.434 1 78.21 ? C4 NAG 401 B 1 
HETATM 5 C C5 NAG . . . G 4 93.226 61.292 60.287 1 74.21 ? C5 NAG 401 B 1 
HETATM 6 C C6 NAG . . . G 4 92.782 62.739 60.517 1 72.58 ? C6 NAG 401 B 1 
HETATM 7 C C7 NAG . . . G 4 96.761 57.484 59.112 1 61.9 ? C7 NAG 401 B 1 
HETATM 8 C C8 NAG . . . G 4 97.146 56.103 59.561 1 61.24 ? C8 NAG 401 B 1 
HETATM 9 N N2 NAG . . . G 4 95.54 57.882 59.464 1 67.9 ? N2 NAG 401 B 1 
HETATM 10 O O3 NAG . . . G 4 95.707 59.206 62.129 1 69.04 ? O3 NAG 401 B 1 
HETATM 11 O O4 NAG . . . G 4 93.382 60.776 62.64 1 73.22 ? O4 NAG 401 B 1 
HETATM 12 O O5 NAG . . . G 4 93.879 61.164 59.027 1 73.23 ? O5 NAG 401 B 1 
HETATM 13 O O6 NAG . . . G 4 93.632 63.649 59.849 1 76.53 ? O6 NAG 401 B 1 
HETATM 14 O O7 NAG . . . G 4 97.532 58.196 58.459 1 56.03 ? O7 NAG 401 B 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           253 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           14 
#