data_4DVL # _model_server_result.job_id xsixuhF2qMg-TLAylwDa0g _model_server_result.datetime_utc '2024-10-26 06:33:10' _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 4dvl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":1110}' # _entry.id 4DVL # _exptl.entry_id 4DVL _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 5 _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 4DVL _cell.length_a 70.515 _cell.length_b 105.934 _cell.length_c 63.405 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DVL _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,H,I,J,K,L,S 1 1 B,F,G,M,N,O,P,Q,R,T 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 ? 7 H N N ? 7 I N N ? 7 M N N ? 7 N N N ? 7 O N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide 4 oligosaccharide 5 oligosaccharide 6 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 2 4 3 MAN BMA C1 O1 . O3 HO3 . sing 4 ? 2 5 3 BMA BMA C1 O1 . O6 HO6 . sing 5 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 6 ? 3 3 2 MAN NAG C1 O1 . O4 HO4 . sing 7 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 8 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 9 ? 4 4 3 MAN BMA C1 O1 . O3 HO3 . sing 10 ? 5 2 1 NAG NAG C1 O1 . O4 HO4 . sing 11 ? 5 3 2 BMA NAG C1 O1 . O4 HO4 . sing 12 ? 5 4 3 MAN BMA C1 O1 . O3 HO3 . sing 13 ? 5 5 4 BMA MAN C1 O1 . O2 HO2 . sing 14 ? 5 6 3 MAN BMA C1 O1 . O6 HO6 . sing 15 ? 6 2 1 NAG 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 2 n C NAG 1 C 1 NAG A 1101 NAG 2 n C NAG 2 C 2 NAG A 1102 NAG 2 n C BMA 3 C 3 BMA A 1103 MAN 2 n C MAN 4 C 4 MAN A 1105 MAN 2 n C BMA 5 C 5 BMA A 1104 MAN 3 n D NAG 1 D 1 NAG A 1501 NAG 3 n D NAG 2 D 2 NAG A 1502 NAG 3 n D MAN 3 D 3 MAN A 1503 MAN 4 n E NAG 1 E 1 NAG A 1601 NAG 4 n E NAG 2 E 2 NAG A 1602 NAG 4 n E BMA 3 E 3 BMA A 1603 MAN 4 n E MAN 4 E 4 MAN A 1604 MAN 5 n F NAG 1 F 1 NAG B 1101 NAG 5 n F NAG 2 F 2 NAG B 1102 NAG 5 n F BMA 3 F 3 BMA B 1103 MAN 5 n F MAN 4 F 4 MAN B 1105 MAN 5 n F BMA 5 F 5 BMA B 1106 MAN 5 n F MAN 6 F 6 MAN B 1104 MAN 6 n G NAG 1 G 1 NAG B 1201 NAG 6 n G NAG 2 G 2 NAG B 1202 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 40 A CYS 40 1_555 A SG CYS 84 A CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 A SG CYS 70 A CYS 70 1_555 A SG CYS 71 A CYS 71 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.026 ? disulf ? disulf3 A SG CYS 112 A CYS 112 1_555 A SG CYS 157 A CYS 157 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 116 A CYS 116 1_555 A SG CYS 140 A CYS 140 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 116 A CYS 116 1_555 A SG CYS 140 A CYS 140 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.695 ? disulf ? disulf6 B SG CYS 40 B CYS 40 1_555 B SG CYS 84 B CYS 84 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf7 B SG CYS 70 B CYS 70 1_555 B SG CYS 71 B CYS 71 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 112 B CYS 112 1_555 B SG CYS 157 B CYS 157 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.03 ? disulf ? disulf9 B SG CYS 116 B CYS 116 1_555 B SG CYS 140 B CYS 140 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 B SG CYS 116 B CYS 116 1_555 B SG CYS 140 B CYS 140 1_555 ? B ? ? B ? ? ? ? ? ? ? 2.689 ? covale ? covale1 A ND2 ASN 4 A ASN 4 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale2 A ND2 ASN 13 A ASN 13 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.431 ? covale ? covale3 A ND2 ASN 28 A ASN 28 1_555 H C1 NAG . A NAG 1106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.421 ? covale ? covale4 A ND2 ASN 97 A ASN 97 1_555 I C1 NAG . A NAG 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 102 A ASN 102 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.478 ? covale ? covale6 B ND2 ASN 4 B ASN 4 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale7 B ND2 ASN 13 B ASN 13 1_555 O C1 NAG . B NAG 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale8 B ND2 ASN 28 B ASN 28 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? covale ? covale9 B ND2 ASN 97 B ASN 97 1_555 M C1 NAG . B NAG 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale10 B ND2 ASN 102 B ASN 102 1_555 N C1 NAG . B NAG 1110 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.465 ? covale ? covale11 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? covale ? covale12 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? covale ? covale13 C O3 BMA . C BMA 3 1_555 C C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale14 C O6 BMA . C BMA 3 1_555 C C1 BMA . C BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale15 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.484 ? covale ? covale16 D O4 NAG . D NAG 2 1_555 D C1 MAN . D MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.479 ? covale ? covale17 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale18 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.394 ? covale ? covale19 E O3 BMA . E BMA 3 1_555 E C1 MAN . E MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.422 ? covale ? covale20 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale21 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? covale ? covale22 F O3 BMA . F BMA 3 1_555 F C1 MAN . F MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 ? covale ? covale23 F O6 BMA . F BMA 3 1_555 F C1 MAN . F MAN 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale24 F O2 MAN . F MAN 4 1_555 F C1 BMA . F BMA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale25 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? # _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 318 n n C1 O1 NAG sing 319 n n C1 O5 NAG sing 320 n n C1 H1 NAG sing 321 n n C2 C3 NAG sing 322 n n C2 N2 NAG sing 323 n n C2 H2 NAG sing 324 n n C3 C4 NAG sing 325 n n C3 O3 NAG sing 326 n n C3 H3 NAG sing 327 n n C4 C5 NAG sing 328 n n C4 O4 NAG sing 329 n n C4 H4 NAG sing 330 n n C5 C6 NAG sing 331 n n C5 O5 NAG sing 332 n n C5 H5 NAG sing 333 n n C6 O6 NAG sing 334 n n C6 H61 NAG sing 335 n n C6 H62 NAG sing 336 n n C7 C8 NAG sing 337 n n C7 N2 NAG sing 338 n n C7 O7 NAG doub 339 n n C8 H81 NAG sing 340 n n C8 H82 NAG sing 341 n n C8 H83 NAG sing 342 n n N2 HN2 NAG sing 343 n n O1 HO1 NAG sing 344 n n O3 HO3 NAG sing 345 n n O4 HO4 NAG sing 346 n n O6 HO6 NAG sing 347 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 4DVL _atom_sites.fract_transf_matrix[1][1] 0.014181 _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] 0.00944 _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] 0.015772 _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 H 7 NAG A 1 1106 1201 NAG NAG . I 7 NAG A 1 1107 1401 NAG NAG . J 8 SO4 A 1 1115 3 SO4 SO4 . K 8 SO4 A 1 1116 4 SO4 SO4 . L 9 JKM A 1 1117 1 JKM LIG . M 7 NAG B 1 1109 1401 NAG NAG . N 7 NAG B 1 1110 1501 NAG NAG . O 7 NAG B 1 1111 1601 NAG NAG . P 8 SO4 B 1 1112 1 SO4 SO4 . Q 8 SO4 B 1 1113 2 SO4 SO4 . R 9 JKM B 1 1114 1 JKM LIG . S 10 HOH A 1 1201 2 HOH HOH . S 10 HOH A 2 1202 5 HOH HOH . S 10 HOH A 3 1203 6 HOH HOH . S 10 HOH A 4 1204 7 HOH HOH . S 10 HOH A 5 1205 10 HOH HOH . S 10 HOH A 6 1206 14 HOH HOH . S 10 HOH A 7 1207 15 HOH HOH . S 10 HOH A 8 1208 21 HOH HOH . S 10 HOH A 9 1209 22 HOH HOH . S 10 HOH A 10 1210 24 HOH HOH . S 10 HOH A 11 1211 29 HOH HOH . S 10 HOH A 12 1212 31 HOH HOH . S 10 HOH A 13 1213 34 HOH HOH . S 10 HOH A 14 1214 36 HOH HOH . S 10 HOH A 15 1215 40 HOH HOH . S 10 HOH A 16 1216 42 HOH HOH . S 10 HOH A 17 1217 46 HOH HOH . S 10 HOH A 18 1218 47 HOH HOH . S 10 HOH A 19 1219 53 HOH HOH . S 10 HOH A 20 1220 56 HOH HOH . S 10 HOH A 21 1221 58 HOH HOH . S 10 HOH A 22 1222 62 HOH HOH . S 10 HOH A 23 1223 65 HOH HOH . T 10 HOH B 1 1201 1 HOH HOH . T 10 HOH B 2 1202 18 HOH HOH . T 10 HOH B 3 1203 19 HOH HOH . T 10 HOH B 4 1204 25 HOH HOH . T 10 HOH B 5 1205 28 HOH HOH . T 10 HOH B 6 1206 35 HOH HOH . T 10 HOH B 7 1207 45 HOH HOH . T 10 HOH B 8 1208 60 HOH HOH . T 10 HOH B 9 1209 63 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 . . . N 7 6.059 -7.794 18.283 1 77.99 ? C1 NAG 1110 B 1 HETATM 2 C C2 NAG . . . N 7 6.201 -6.552 19.212 1 79.64 ? C2 NAG 1110 B 1 HETATM 3 C C3 NAG . . . N 7 5.135 -6.46 20.356 1 81.11 ? C3 NAG 1110 B 1 HETATM 4 C C4 NAG . . . N 7 3.757 -7.185 20.163 1 81.72 ? C4 NAG 1110 B 1 HETATM 5 C C5 NAG . . . N 7 3.618 -8.046 18.841 0.81 80.96 ? C5 NAG 1110 B 1 HETATM 6 C C6 NAG . . . N 7 2.316 -7.762 18.067 1 82.18 ? C6 NAG 1110 B 1 HETATM 7 C C7 NAG . . . N 7 8.438 -5.578 19.182 0.87 81.91 ? C7 NAG 1110 B 1 HETATM 8 C C8 NAG . . . N 7 9.709 -5.575 19.978 0.96 82.7 ? C8 NAG 1110 B 1 HETATM 9 N N2 NAG . . . N 7 7.535 -6.369 19.762 0.94 80.5 ? N2 NAG 1110 B 1 HETATM 10 O O3 NAG . . . N 7 4.974 -5.072 20.721 0.82 83.14 ? O3 NAG 1110 B 1 HETATM 11 O O4 NAG . . . N 7 3.5 -7.998 21.347 0.44 84.09 ? O4 NAG 1110 B 1 HETATM 12 O O5 NAG . . . N 7 4.669 -7.855 17.836 1 79.34 ? O5 NAG 1110 B 1 HETATM 13 O O6 NAG . . . N 7 2.34 -6.415 17.546 0.93 84.45 ? O6 NAG 1110 B 1 HETATM 14 O O7 NAG . . . N 7 8.229 -4.945 18.137 0.67 83.78 ? O7 NAG 1110 B 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #