data_4PIR # _model_server_result.job_id '_DFPN2NUZrGI8MoFOtCM9w' _model_server_result.datetime_utc '2024-11-21 14:27:48' _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 4pir # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":504}' # _entry.id 4PIR # _exptl.entry_id 4PIR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 2 _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 4PIR _cell.length_a 121.542 _cell.length_b 187.087 _cell.length_c 240.554 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4PIR _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 decameric _pdbx_struct_assembly.oligomeric_count 10 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 7 DA N N ? 7 EA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n K NAG 1 K 1 NAG A 9082 NAG 3 n K NAG 2 K 2 NAG A 8082 NAG 4 n L NAG 1 L 1 NAG A 7164 NAG 4 n L NAG 2 L 2 NAG A 6164 NAG 4 n L BMA 3 L 3 BMA A 5164 BMA 3 n M NAG 1 M 1 NAG A 9148 NAG 3 n M NAG 2 M 2 NAG A 8148 NAG 4 n N NAG 1 N 1 NAG B 7164 NAG 4 n N NAG 2 N 2 NAG B 6164 NAG 4 n N BMA 3 N 3 BMA B 5164 BMA 3 n O NAG 1 O 1 NAG B 9082 NAG 3 n O NAG 2 O 2 NAG B 8082 NAG 3 n P NAG 1 P 1 NAG B 9148 NAG 3 n P NAG 2 P 2 NAG B 8148 NAG 4 n Q NAG 1 Q 1 NAG C 7164 NAG 4 n Q NAG 2 Q 2 NAG C 6164 NAG 4 n Q BMA 3 Q 3 BMA C 5164 BMA 3 n R NAG 1 R 1 NAG C 9082 NAG 3 n R NAG 2 R 2 NAG C 8082 NAG 3 n S NAG 1 S 1 NAG C 9148 NAG 3 n S NAG 2 S 2 NAG C 8148 NAG 4 n T NAG 1 T 1 NAG D 7164 NAG 4 n T NAG 2 T 2 NAG D 6164 NAG 4 n T BMA 3 T 3 BMA D 5164 BMA 3 n U NAG 1 U 1 NAG D 9082 NAG 3 n U NAG 2 U 2 NAG D 8082 NAG 3 n V NAG 1 V 1 NAG D 9148 NAG 3 n V NAG 2 V 2 NAG D 8148 NAG 4 n W NAG 1 W 1 NAG E 7164 NAG 4 n W NAG 2 W 2 NAG E 6164 NAG 4 n W BMA 3 W 3 BMA E 5164 BMA 3 n X NAG 1 X 1 NAG E 9148 NAG 3 n X NAG 2 X 2 NAG E 8148 NAG # 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 135 A CYS 135 1_555 A SG CYS 149 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 135 B CYS 135 1_555 B SG CYS 149 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 C SG CYS 135 C CYS 135 1_555 C SG CYS 149 C CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 D SG CYS 135 D CYS 135 1_555 D SG CYS 149 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 E SG CYS 135 E CYS 135 1_555 E SG CYS 149 E CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 F SG CYS 22 F CYS 22 1_555 F SG CYS 100 F CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 G SG CYS 22 G CYS 22 1_555 G SG CYS 100 G CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 H SG CYS 22 H CYS 22 1_555 H SG CYS 100 H CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 I SG CYS 22 I CYS 22 1_555 I SG CYS 100 I CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 A ND2 ASN 82 A ASN 82 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 A ND2 ASN 148 A ASN 148 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 164 A ASN 164 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B ND2 ASN 82 B ASN 82 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B ND2 ASN 148 B ASN 148 1_555 P C1 NAG . P NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 164 B ASN 164 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale7 C ND2 ASN 82 C ASN 82 1_555 R C1 NAG . R NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C ND2 ASN 148 C ASN 148 1_555 S C1 NAG . S NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 C ND2 ASN 164 C ASN 164 1_555 Q C1 NAG . Q NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale10 D ND2 ASN 82 D ASN 82 1_555 U C1 NAG . U NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D ND2 ASN 148 D ASN 148 1_555 V C1 NAG . V NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 D ND2 ASN 164 D ASN 164 1_555 T C1 NAG . T NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 E ND2 ASN 82 E ASN 82 1_555 EA C1 NAG . E NAG 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale14 E ND2 ASN 148 E ASN 148 1_555 X C1 NAG . X NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale15 E ND2 ASN 164 E ASN 164 1_555 W C1 NAG . W NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale16 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale17 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale18 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale19 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale20 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale21 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale22 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale23 P O4 NAG . P NAG 1 1_555 P C1 NAG . P NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale24 Q O4 NAG . Q NAG 1 1_555 Q C1 NAG . Q NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale25 Q O4 NAG . Q NAG 2 1_555 Q C1 BMA . Q BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale26 R O4 NAG . R NAG 1 1_555 R C1 NAG . R NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale27 S O4 NAG . S NAG 1 1_555 S C1 NAG . S NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale28 T O4 NAG . T NAG 1 1_555 T C1 NAG . T NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale29 T O4 NAG . T NAG 2 1_555 T C1 BMA . T BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale30 U O4 NAG . U NAG 1 1_555 U C1 NAG . U NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale31 V O4 NAG . V NAG 1 1_555 V C1 NAG . V NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale32 W O4 NAG . W NAG 1 1_555 W C1 NAG . W NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale33 W O4 NAG . W NAG 2 1_555 W C1 BMA . W BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale34 X O4 NAG . X NAG 1 1_555 X C1 NAG . X NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? # _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 259 n n C1 O1 NAG sing 260 n n C1 O5 NAG sing 261 n n C1 H1 NAG sing 262 n n C2 C3 NAG sing 263 n n C2 N2 NAG sing 264 n n C2 H2 NAG sing 265 n n C3 C4 NAG sing 266 n n C3 O3 NAG sing 267 n n C3 H3 NAG sing 268 n n C4 C5 NAG sing 269 n n C4 O4 NAG sing 270 n n C4 H4 NAG sing 271 n n C5 C6 NAG sing 272 n n C5 O5 NAG sing 273 n n C5 H5 NAG sing 274 n n C6 O6 NAG sing 275 n n C6 H61 NAG sing 276 n n C6 H62 NAG sing 277 n n C7 C8 NAG sing 278 n n C7 N2 NAG sing 279 n n C7 O7 NAG doub 280 n n C8 H81 NAG sing 281 n n C8 H82 NAG sing 282 n n C8 H83 NAG sing 283 n n N2 HN2 NAG sing 284 n n O1 HO1 NAG sing 285 n n O3 HO3 NAG sing 286 n n O4 HO4 NAG sing 287 n n O6 HO6 NAG sing 288 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 4PIR _atom_sites.fract_transf_matrix[1][1] 0.008228 _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] 0.005345 _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] 0.004157 _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 Y 5 CL A 1 508 6 CL CL . Z 5 CL B 1 508 4 CL CL . AA 5 CL C 1 508 5 CL CL . BA 6 SO4 D 1 508 1 SO4 SO4 . CA 5 CL D 1 509 2 CL CL . DA 7 NAG E 1 504 8082 NAG NAG . EA 7 NAG E 1 505 9082 NAG NAG . FA 5 CL E 1 508 3 CL CL . GA 6 SO4 H 1 301 301 SO4 SO4 . HA 6 SO4 H 1 302 301 SO4 SO4 . # 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 . . . DA 7 121.152 157.105 238.051 1 138.09 ? C1 NAG 504 E 1 HETATM 2 C C2 NAG . . . DA 7 120.17 156.854 236.911 1 174.1 ? C2 NAG 504 E 1 HETATM 3 C C3 NAG . . . DA 7 119.742 155.389 236.899 1 190.06 ? C3 NAG 504 E 1 HETATM 4 C C4 NAG . . . DA 7 120.963 154.48 236.866 1 183.42 ? C4 NAG 504 E 1 HETATM 5 C C5 NAG . . . DA 7 121.92 154.838 238.001 1 164.19 ? C5 NAG 504 E 1 HETATM 6 C C6 NAG . . . DA 7 123.214 154.06 237.951 1 173.72 ? C6 NAG 504 E 1 HETATM 7 C C7 NAG . . . DA 7 118.883 158.859 236.322 1 172.57 ? C7 NAG 504 E 1 HETATM 8 C C8 NAG . . . DA 7 117.622 159.635 236.555 1 174.89 ? C8 NAG 504 E 1 HETATM 9 N N2 NAG . . . DA 7 119.01 157.725 237.018 1 187.89 ? N2 NAG 504 E 1 HETATM 10 O O3 NAG . . . DA 7 118.92 155.143 235.764 1 191.6 ? O3 NAG 504 E 1 HETATM 11 O O4 NAG . . . DA 7 120.563 153.121 237.002 1 176.59 ? O4 NAG 504 E 1 HETATM 12 O O5 NAG . . . DA 7 122.27 156.228 237.922 1 136.38 ? O5 NAG 504 E 1 HETATM 13 O O6 NAG . . . DA 7 124.291 154.872 237.503 1 180.4 ? O6 NAG 504 E 1 HETATM 14 O O7 NAG . . . DA 7 119.747 159.242 235.539 1 136.75 ? O7 NAG 504 E 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 61 _model_server_stats.query_time_ms 453 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #