data_4V3D # _model_server_result.job_id BeDaa2uVS3Msl1dt3c_FMg _model_server_result.datetime_utc '2024-11-23 22:35:20' _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 4v3d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":205}' # _entry.id 4V3D # _exptl.entry_id 4V3D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 6 _entity.src_method man _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 3 _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 4V3D _cell.length_a 66.13 _cell.length_b 94.67 _cell.length_c 290.7 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4V3D _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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 C,D,G,H,I,M,N 1 1 A,B,E,F,J,K,L 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 ? 6 K N N ? 6 L N N ? 6 N 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 MAN 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 E NAG 1 E 1 NAG B 202 NAG 3 n E NAG 2 E 2 NAG B 201 NAG 4 n F NAG 1 F 1 NAG B 203 NAG 4 n F NAG 2 F 2 NAG B 204 NAG 4 n F MAN 3 F 3 MAN B 207 MAN 3 n G NAG 1 G 1 NAG D 202 NAG 3 n G NAG 2 G 2 NAG D 201 NAG 4 n H NAG 1 H 1 NAG D 206 NAG 4 n H NAG 2 H 2 NAG D 207 NAG 4 n H MAN 3 H 3 MAN D 203 MAN 3 n I NAG 1 I 1 NAG D 205 NAG 3 n I NAG 2 I 2 NAG D 204 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 59 A CYS 526 1_555 A SG CYS 147 A CYS 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf2 A SG CYS 75 A CYS 542 1_555 A SG CYS 86 A CYS 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 129 A CYS 596 1_555 A SG CYS 141 A CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? disulf ? disulf4 A SG CYS 145 A CYS 612 1_555 A SG CYS 243 A CYS 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf5 B SG CYS 94 B CYS 101 1_555 B SG CYS 162 B CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf6 C SG CYS 59 C CYS 526 1_555 C SG CYS 147 C CYS 614 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf7 C SG CYS 75 C CYS 542 1_555 C SG CYS 86 C CYS 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf8 C SG CYS 129 C CYS 596 1_555 C SG CYS 141 C CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf9 C SG CYS 145 C CYS 612 1_555 C SG CYS 243 C CYS 710 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf10 D SG CYS 94 D CYS 101 1_555 D SG CYS 162 D CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? covale ? covale1 B ND2 ASN 23 B ASN 30 1_555 K C1 NAG . B NAG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale2 B ND2 ASN 40 B ASN 47 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 B ND2 ASN 112 B ASN 119 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 B ND2 ASN 148 B ASN 155 1_555 L C1 NAG . B NAG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 D ND2 ASN 23 D ASN 30 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale6 D ND2 ASN 40 D ASN 47 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale7 D ND2 ASN 112 D ASN 119 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale8 D ND2 ASN 148 D ASN 155 1_555 N C1 NAG . D NAG 208 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale10 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale11 F O4 NAG . F NAG 2 1_555 F C1 MAN . F MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale12 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale13 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale14 H O4 NAG . H NAG 2 1_555 H C1 MAN . H MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale15 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? # _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 4V3D _atom_sites.fract_transf_matrix[1][1] 0.015122 _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] 0.010563 _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] 0.00344 _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 J 5 PTY B 1 200 200 PTY PTY . K 6 NAG B 1 205 205 NAG NAG . L 6 NAG B 1 206 206 NAG NAG . M 5 PTY D 1 200 200 PTY PTY . N 6 NAG D 1 208 208 NAG NAG . # 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 . . . K 6 -1.129 -52.858 -43.649 1 42.82 ? C1 NAG 205 B 1 HETATM 2 C C2 NAG . . . K 6 -1.51 -54.119 -42.862 1 43.71 ? C2 NAG 205 B 1 HETATM 3 C C3 NAG . . . K 6 -1.691 -55.206 -43.928 1 49.28 ? C3 NAG 205 B 1 HETATM 4 C C4 NAG . . . K 6 -2.768 -54.81 -44.932 1 52.38 ? C4 NAG 205 B 1 HETATM 5 C C5 NAG . . . K 6 -2.408 -53.477 -45.584 1 47.64 ? C5 NAG 205 B 1 HETATM 6 C C6 NAG . . . K 6 -3.488 -52.949 -46.503 1 46.54 ? C6 NAG 205 B 1 HETATM 7 C C7 NAG . . . K 6 -0.828 -55.138 -40.714 1 44.75 ? C7 NAG 205 B 1 HETATM 8 C C8 NAG . . . K 6 0.339 -55.571 -39.877 1 43.99 ? C8 NAG 205 B 1 HETATM 9 N N2 NAG . . . K 6 -0.519 -54.533 -41.88 1 39.06 ? N2 NAG 205 B 1 HETATM 10 O O3 NAG . . . K 6 -2.045 -56.456 -43.354 1 51.85 ? O3 NAG 205 B 1 HETATM 11 O O4 NAG . . . K 6 -2.919 -55.839 -45.909 1 57.9 ? O4 NAG 205 B 1 HETATM 12 O O5 NAG . . . K 6 -2.171 -52.483 -44.564 1 44.46 ? O5 NAG 205 B 1 HETATM 13 O O6 NAG . . . K 6 -4.634 -52.521 -45.78 1 51.91 ? O6 NAG 205 B 1 HETATM 14 O O7 NAG . . . K 6 -1.994 -55.317 -40.351 1 47.18 ? O7 NAG 205 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #