data_3D0I
#
_model_server_result.job_id            Sxz3AeCoK3gr-rk1ocGB2w 
_model_server_result.datetime_utc      '2024-11-21 10:27:25' 
_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          3d0i 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":616}' 
#
_entry.id    3D0I 
#
_exptl.entry_id    3D0I 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              221.208 
_entity.id                          3 
_entity.src_method                  man 
_entity.type                        non-polymer 
_entity.pdbx_description            2-acetamido-2-deoxy-alpha-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          95.5 
_cell.angle_gamma         90 
_cell.entry_id            3D0I 
_cell.length_a            80.424 
_cell.length_b            119.824 
_cell.length_c            109.772 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3D0I 
_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
? tetrameric 4 author_defined_assembly 1 
PISA dimeric 2 software_defined_assembly 2 
PISA dimeric 2 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,D,E,F,G,H,I,J,K,L,M,N,O,P 1 1 
A,C,E,F,G,N 2 1 
B,D,H,I,J,K,L,M,O,P 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
? 3 E N N 
? 3 H N N 
? 3 I N N 
? 3 J N N 
? 3 K 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 115 A CYS 133 1_555 A SG CYS 123 A CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf2 A SG CYS 326 A CYS 344 1_555 A SG CYS 343 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? 
disulf ? disulf3 A SG CYS 512 A CYS 530 1_555 A SG CYS 524 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? 
disulf ? disulf4 B SG CYS 115 B CYS 133 1_555 B SG CYS 123 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf5 B SG CYS 326 B CYS 344 1_555 B SG CYS 343 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? 
disulf ? disulf6 B SG CYS 512 B CYS 530 1_555 B SG CYS 524 B CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? 
disulf ? disulf7 C SG CYS 43 E CYS 366 1_555 C SG CYS 96 E CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? 
disulf ? disulf8 C SG CYS 144 E CYS 467 1_555 C SG CYS 151 E CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? 
disulf ? disulf9 D SG CYS 43 F CYS 366 1_555 D SG CYS 96 F CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? 
disulf ? disulf10 D SG CYS 144 F CYS 467 1_555 D SG CYS 151 F CYS 474 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
#
_chem_comp.formula           'C8 H15 N O6' 
_chem_comp.formula_weight    221.208 
_chem_comp.id                NDG 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-acetamido-2-deoxy-alpha-D-glucopyranose 
_chem_comp.type              'd-saccharide, alpha linking' 
_chem_comp.pdbx_synonyms     N-acetyl-alpha-D-glucosamine;2-acetamido-2-deoxy-alpha-D-glucose;2-acetamido-2-deoxy-D-glucose;2-acetamido-2-deoxy-glucose;2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE 
#
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 NDG sing 267 n n 
C1 O5 NDG sing 268 n n 
C1 O1 NDG sing 269 n n 
C1 H1 NDG sing 270 n n 
C2 C3 NDG sing 271 n n 
C2 N2 NDG sing 272 n n 
C2 H2 NDG sing 273 n n 
C3 C4 NDG sing 274 n n 
C3 O3 NDG sing 275 n n 
C3 H3 NDG sing 276 n n 
C4 C5 NDG sing 277 n n 
C4 O4 NDG sing 278 n n 
C4 H4 NDG sing 279 n n 
C5 C6 NDG sing 280 n n 
C5 O5 NDG sing 281 n n 
C5 H5 NDG sing 282 n n 
C6 O6 NDG sing 283 n n 
C6 H61 NDG sing 284 n n 
C6 H62 NDG sing 285 n n 
C7 C8 NDG sing 286 n n 
C7 O7 NDG doub 287 n n 
C7 N2 NDG sing 288 n n 
C8 H81 NDG sing 289 n n 
C8 H82 NDG sing 290 n n 
C8 H83 NDG sing 291 n n 
O3 HO3 NDG sing 292 n n 
O4 HO4 NDG sing 293 n n 
O6 HO6 NDG sing 294 n n 
N2 HN2 NDG sing 295 n n 
O1 HO1 NDG sing 296 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
NDG DGlcpNAca 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1 
NDG N-acetyl-a-D-glucopyranosamine 'COMMON NAME' GMML 1 
NDG a-D-GlcpNAc 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1 
NDG GlcNAc 'SNFG CARBOHYDRATE SYMBOL' GMML 1 
#
_atom_sites.entry_id                     3D0I 
_atom_sites.fract_transf_matrix[1][1]    0.012434 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001197 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008346 
_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]    0.009152 
_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 3 NDG A 1 616 616 NDG NDG . 
F 4 ZN A 1 901 901 ZN ZN . 
G 5 CL A 1 902 902 CL CL . 
H 3 NDG B 1 616 616 NDG NDG . 
I 3 NDG B 1 617 617 NDG NDG . 
J 3 NDG B 1 618 618 NDG NDG . 
K 3 NDG B 1 619 619 NDG NDG . 
L 4 ZN B 1 901 901 ZN ZN . 
M 5 CL B 1 902 902 CL CL . 
N 6 NAG E 1 91 91 NAG NAG . 
O 7 HOH B 1 903 903 HOH HOH . 
O 7 HOH B 2 904 904 HOH HOH . 
O 7 HOH B 3 905 905 HOH HOH . 
O 7 HOH B 4 906 906 HOH HOH . 
O 7 HOH B 5 907 907 HOH HOH . 
O 7 HOH B 6 908 908 HOH HOH . 
O 7 HOH B 7 909 909 HOH HOH . 
O 7 HOH B 8 910 910 HOH HOH . 
O 7 HOH B 9 911 911 HOH HOH . 
O 7 HOH B 10 912 912 HOH HOH . 
O 7 HOH B 11 913 913 HOH HOH . 
O 7 HOH B 12 914 914 HOH HOH . 
O 7 HOH B 13 915 915 HOH HOH . 
O 7 HOH B 14 916 916 HOH HOH . 
O 7 HOH B 15 917 917 HOH HOH . 
O 7 HOH B 16 918 918 HOH HOH . 
O 7 HOH B 17 919 919 HOH HOH . 
O 7 HOH B 18 920 920 HOH HOH . 
O 7 HOH B 19 921 921 HOH HOH . 
O 7 HOH B 20 922 922 HOH HOH . 
O 7 HOH B 21 923 923 HOH HOH . 
P 7 HOH F 1 1 1 HOH HOH . 
P 7 HOH F 2 11 11 HOH HOH . 
P 7 HOH F 3 12 12 HOH HOH . 
P 7 HOH F 4 24 24 HOH HOH . 
P 7 HOH F 5 25 25 HOH HOH . 
P 7 HOH F 6 26 26 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 NDG . . . E 3 31.785 -16.697 101.147 1 113.68 ? C1 NDG 616 A 1 
HETATM 2 C C2 NDG . . . E 3 30.518 -16.044 100.576 1 113.18 ? C2 NDG 616 A 1 
HETATM 3 C C3 NDG . . . E 3 30.398 -14.585 101.033 1 113.48 ? C3 NDG 616 A 1 
HETATM 4 C C4 NDG . . . E 3 30.647 -14.438 102.542 1 113.57 ? C4 NDG 616 A 1 
HETATM 5 C C5 NDG . . . E 3 31.901 -15.208 102.987 1 113.94 ? C5 NDG 616 A 1 
HETATM 6 C C6 NDG . . . E 3 32.11 -15.208 104.5 1 114.65 ? C6 NDG 616 A 1 
HETATM 7 C C7 NDG . . . E 3 31.399 -16.744 98.388 1 110.7 ? C7 NDG 616 A 1 
HETATM 8 C C8 NDG . . . E 3 32.205 -15.849 97.475 1 110.39 ? C8 NDG 616 A 1 
HETATM 9 O O5 NDG . . . E 3 31.837 -16.562 102.557 1 113.85 ? O5 NDG 616 A 1 
HETATM 10 O O3 NDG . . . E 3 29.115 -14.086 100.711 1 113.7 ? O3 NDG 616 A 1 
HETATM 11 O O4 NDG . . . E 3 30.813 -13.066 102.838 1 113.31 ? O4 NDG 616 A 1 
HETATM 12 O O6 NDG . . . E 3 32.441 -16.534 104.953 1 114.99 ? O6 NDG 616 A 1 
HETATM 13 O O7 NDG . . . E 3 31.604 -17.961 98.432 1 109.96 ? O7 NDG 616 A 1 
HETATM 14 N N2 NDG . . . E 3 30.468 -16.134 99.125 1 111.66 ? N2 NDG 616 A 1 
HETATM 15 O O1 NDG . . . E 3 32.935 -16.101 100.612 1 113.88 ? O1 NDG 616 A 1 
#
_model_server_stats.io_time_ms              29 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    13 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           15 
#