data_3D67
#
_model_server_result.job_id            S9uCFJ9r5a8rcAXSYHBV9w 
_model_server_result.datetime_utc      '2024-11-25 09:08:13' 
_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          3d67 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":603}' 
#
_entry.id    3D67 
#
_exptl.entry_id    3D67 
_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    11 
_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            3D67 
_cell.length_a            161.05 
_cell.length_b            161.05 
_cell.length_c            138.99 
_cell.Z_PDB               18 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D67 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        152 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 31 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
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,D,E,F,G,H,I 1 1 
B,J,K,L,M,N,O 2 1 
C,P,Q,R,S,T 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
? 2 D N N 
? 2 E N N 
? 2 F N N 
? 2 G N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 P N N 
? 2 Q N N 
? 2 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 179 A CYS 156 1_555 A SG CYS 192 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 251 A CYS 228 1_555 A SG CYS 275 A CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? 
disulf ? disulf3 A SG CYS 266 A CYS 243 1_555 A SG CYS 280 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.084 ? 
disulf ? disulf4 B SG CYS 179 B CYS 156 1_555 B SG CYS 192 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf5 B SG CYS 251 B CYS 228 1_555 B SG CYS 275 B CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
disulf ? disulf6 B SG CYS 266 B CYS 243 1_555 B SG CYS 280 B CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? 
disulf ? disulf7 C SG CYS 179 C CYS 156 1_555 C SG CYS 192 C CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? 
disulf ? disulf8 C SG CYS 251 C CYS 228 1_555 C SG CYS 275 C CYS 252 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? 
disulf ? disulf9 C SG CYS 266 C CYS 243 1_555 C SG CYS 280 C CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? 
covale ? covale1 A ND2 ASN 45 A ASN 22 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? 
covale ? covale2 A ND2 ASN 74 A ASN 51 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? 
covale ? covale3 A ND2 ASN 86 A ASN 63 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? 
covale ? covale4 A ND2 ASN 109 A ASN 86 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale5 B ND2 ASN 45 B ASN 22 1_555 J C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? 
covale ? covale6 B ND2 ASN 74 B ASN 51 1_555 K C1 NAG . B NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? 
covale ? covale7 B ND2 ASN 86 B ASN 63 1_555 L C1 NAG . B NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale8 B ND2 ASN 109 B ASN 86 1_555 M C1 NAG . B NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? 
covale ? covale9 C ND2 ASN 45 C ASN 22 1_555 P C1 NAG . C NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? 
covale ? covale10 C ND2 ASN 74 C ASN 51 1_555 Q C1 NAG . C NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? 
covale ? covale11 C ND2 ASN 109 C ASN 86 1_555 R C1 NAG . C NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? 
metalc ? metalc1 A ND1 HIS 182 A HIS 159 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.085 ? 
metalc ? metalc2 A OE1 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc3 A OE2 GLU 185 A GLU 162 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
metalc ? metalc4 A ND1 HIS 311 A HIS 288 1_555 H ZN ZN . A ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? 
metalc ? metalc5 H ZN ZN . A ZN 501 1_555 I O13 GEM . A GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.667 ? 
metalc ? metalc6 B ND1 HIS 182 B HIS 159 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? 
metalc ? metalc7 B OE1 GLU 185 B GLU 162 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? 
metalc ? metalc8 B OE2 GLU 185 B GLU 162 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? 
metalc ? metalc9 B ND1 HIS 311 B HIS 288 1_555 N ZN ZN . B ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? 
metalc ? metalc10 N ZN ZN . B ZN 501 1_555 O O13 GEM . B GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? 
metalc ? metalc11 C ND1 HIS 182 C HIS 159 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? 
metalc ? metalc12 C OE1 GLU 185 C GLU 162 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc13 C OE2 GLU 185 C GLU 162 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? 
metalc ? metalc14 C ND1 HIS 311 C HIS 288 1_555 S ZN ZN . C ZN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? 
metalc ? metalc15 S ZN ZN . C ZN 501 1_555 T O13 GEM . C GEM 660 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.143 ? 
#
_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 262 n n 
C1 O1 NAG sing 263 n n 
C1 O5 NAG sing 264 n n 
C1 H1 NAG sing 265 n n 
C2 C3 NAG sing 266 n n 
C2 N2 NAG sing 267 n n 
C2 H2 NAG sing 268 n n 
C3 C4 NAG sing 269 n n 
C3 O3 NAG sing 270 n n 
C3 H3 NAG sing 271 n n 
C4 C5 NAG sing 272 n n 
C4 O4 NAG sing 273 n n 
C4 H4 NAG sing 274 n n 
C5 C6 NAG sing 275 n n 
C5 O5 NAG sing 276 n n 
C5 H5 NAG sing 277 n n 
C6 O6 NAG sing 278 n n 
C6 H61 NAG sing 279 n n 
C6 H62 NAG sing 280 n n 
C7 C8 NAG sing 281 n n 
C7 N2 NAG sing 282 n n 
C7 O7 NAG doub 283 n n 
C8 H81 NAG sing 284 n n 
C8 H82 NAG sing 285 n n 
C8 H83 NAG sing 286 n n 
N2 HN2 NAG sing 287 n n 
O1 HO1 NAG sing 288 n n 
O3 HO3 NAG sing 289 n n 
O4 HO4 NAG sing 290 n n 
O6 HO6 NAG sing 291 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                     3D67 
_atom_sites.fract_transf_matrix[1][1]    0.006209 
_atom_sites.fract_transf_matrix[1][2]    0.003585 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.00717 
_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]    0.007195 
_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
D 2 NAG A 1 601 601 NAG NAG . 
E 2 NAG A 1 602 602 NAG NAG . 
F 2 NAG A 1 603 603 NAG NAG . 
G 2 NAG A 1 604 604 NAG NAG . 
H 3 ZN A 1 501 501 ZN ZN . 
I 4 GEM A 1 660 660 GEM GEM . 
J 2 NAG B 1 601 601 NAG NAG . 
K 2 NAG B 1 602 602 NAG NAG . 
L 2 NAG B 1 603 603 NAG NAG . 
M 2 NAG B 1 604 604 NAG NAG . 
N 3 ZN B 1 501 501 ZN ZN . 
O 4 GEM B 1 660 660 GEM GEM . 
P 2 NAG C 1 601 601 NAG NAG . 
Q 2 NAG C 1 602 602 NAG NAG . 
R 2 NAG C 1 604 604 NAG NAG . 
S 3 ZN C 1 501 501 ZN ZN . 
T 4 GEM C 1 660 660 GEM GEM . 
#
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 . . . L 2 84.865 -21.65 10.837 1 123.25 ? C1 NAG 603 B 1 
HETATM 2 C C2 NAG . . . L 2 85.215 -21.265 12.284 1 123.71 ? C2 NAG 603 B 1 
HETATM 3 C C3 NAG . . . L 2 86.503 -21.994 12.669 1 123.04 ? C3 NAG 603 B 1 
HETATM 4 C C4 NAG . . . L 2 86.195 -23.487 12.632 1 122.83 ? C4 NAG 603 B 1 
HETATM 5 C C5 NAG . . . L 2 85.713 -23.873 11.233 1 122.65 ? C5 NAG 603 B 1 
HETATM 6 C C6 NAG . . . L 2 85.3 -25.34 11.224 1 122.53 ? C6 NAG 603 B 1 
HETATM 7 C C7 NAG . . . L 2 84.686 -19.199 13.503 1 123.96 ? C7 NAG 603 B 1 
HETATM 8 C C8 NAG . . . L 2 85.003 -19.664 14.903 1 123.28 ? C8 NAG 603 B 1 
HETATM 9 N N2 NAG . . . L 2 85.317 -19.825 12.501 1 124.19 ? N2 NAG 603 B 1 
HETATM 10 O O3 NAG . . . L 2 86.965 -21.605 13.945 1 122.58 ? O3 NAG 603 B 1 
HETATM 11 O O4 NAG . . . L 2 87.323 -24.251 13.008 1 122.71 ? O4 NAG 603 B 1 
HETATM 12 O O5 NAG . . . L 2 84.624 -23.058 10.813 1 122.99 ? O5 NAG 603 B 1 
HETATM 13 O O6 NAG . . . L 2 86.438 -26.145 11.484 1 122.41 ? O6 NAG 603 B 1 
HETATM 14 O O7 NAG . . . L 2 83.886 -18.276 13.311 1 123.48 ? O7 NAG 603 B 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           445 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           14 
#