data_2V5P # _model_server_result.job_id 3ytamR-HvqKGiQZnnjpg1Q _model_server_result.datetime_utc '2024-11-26 02:06:02' _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 2v5p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":2993}' # _entry.id 2V5P # _exptl.entry_id 2V5P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 4 _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 123.41 _cell.angle_gamma 90 _cell.entry_id 2V5P _cell.length_a 165.979 _cell.length_b 117.312 _cell.length_c 116.668 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2V5P _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 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 PQS dimeric 2 author_and_software_defined_assembly 1 PQS 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 A,D,E,F,G 1 1 B,C,H,I,J 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 ? 4 F N N ? 4 G N N ? 4 H N N ? 4 I N N ? 4 J N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 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 E NAG 1 E 1 NAG A 2993 NAG 3 n E NAG 2 E 2 NAG A 2994 NAG 3 n E BMA 3 E 3 BMA A 2995 BMA # 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 9 A CYS 1516 1_555 A SG CYS 46 A CYS 1553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 52 A CYS 1559 1_555 A SG CYS 59 A CYS 1566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 91 A CYS 1598 1_555 A SG CYS 127 A CYS 1634 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf4 A SG CYS 107 A CYS 1614 1_555 A SG CYS 139 A CYS 1646 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 145 A CYS 1652 1_555 A SG CYS 188 A CYS 1695 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf6 A SG CYS 199 A CYS 1706 1_555 A SG CYS 206 A CYS 1713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 A SG CYS 243 A CYS 1750 1_555 A SG CYS 276 A CYS 1783 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 A SG CYS 259 A CYS 1766 1_555 A SG CYS 288 A CYS 1795 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 A SG CYS 297 A CYS 1804 1_555 A SG CYS 332 A CYS 1839 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 A SG CYS 343 A CYS 1850 1_555 A SG CYS 349 A CYS 1856 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf11 A SG CYS 386 A CYS 1893 1_555 A SG CYS 468 A CYS 1975 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf12 A SG CYS 396 A CYS 1903 1_555 A SG CYS 420 A CYS 1927 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf13 A SG CYS 410 A CYS 1917 1_555 A SG CYS 435 A CYS 1942 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf14 A SG CYS 450 A CYS 1957 1_555 A SG CYS 480 A CYS 1987 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf15 B SG CYS 9 B CYS 1516 1_555 B SG CYS 46 B CYS 1553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf16 B SG CYS 52 B CYS 1559 1_555 B SG CYS 59 B CYS 1566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf17 B SG CYS 91 B CYS 1598 1_555 B SG CYS 127 B CYS 1634 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf18 B SG CYS 107 B CYS 1614 1_555 B SG CYS 139 B CYS 1646 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf19 B SG CYS 145 B CYS 1652 1_555 B SG CYS 188 B CYS 1695 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf20 B SG CYS 199 B CYS 1706 1_555 B SG CYS 206 B CYS 1713 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf21 B SG CYS 243 B CYS 1750 1_555 B SG CYS 276 B CYS 1783 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf22 B SG CYS 259 B CYS 1766 1_555 B SG CYS 288 B CYS 1795 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf23 B SG CYS 297 B CYS 1804 1_555 B SG CYS 332 B CYS 1839 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf24 B SG CYS 343 B CYS 1850 1_555 B SG CYS 349 B CYS 1856 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf25 B SG CYS 386 B CYS 1893 1_555 B SG CYS 468 B CYS 1975 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf26 B SG CYS 396 B CYS 1903 1_555 B SG CYS 420 B CYS 1927 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf27 B SG CYS 410 B CYS 1917 1_555 B SG CYS 435 B CYS 1942 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf28 B SG CYS 450 B CYS 1957 1_555 B SG CYS 480 B CYS 1987 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf29 C SG CYS 9 C CYS 9 1_555 C SG CYS 47 C CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf30 C SG CYS 21 C CYS 21 1_555 C SG CYS 60 C CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf31 C SG CYS 46 C CYS 46 1_555 C SG CYS 51 C CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf32 D SG CYS 9 D CYS 9 1_555 D SG CYS 47 D CYS 47 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf33 D SG CYS 21 D CYS 21 1_555 D SG CYS 60 D CYS 60 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf34 D SG CYS 46 D CYS 46 1_555 D SG CYS 51 D CYS 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 149 A ASN 1656 1_555 F C1 NAG . A NAG 2991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale2 A ND2 ASN 250 A ASN 1757 1_555 G C1 NAG . A NAG 2992 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 309 A ASN 1816 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 B ND2 ASN 149 B ASN 1656 1_555 H C1 NAG . B NAG 2991 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale5 B ND2 ASN 250 B ASN 1757 1_555 I C1 NAG . B NAG 2992 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 B ND2 ASN 309 B ASN 1816 1_555 J C1 NAG . B NAG 2993 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale7 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale8 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? # _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 2V5P _atom_sites.fract_transf_matrix[1][1] 0.006025 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003974 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008524 _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] 0.010268 _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 F 4 NAG A 1 2991 2991 NAG NAG . G 4 NAG A 1 2992 2992 NAG NAG . H 4 NAG B 1 2991 2991 NAG NAG . I 4 NAG B 1 2992 2992 NAG NAG . J 4 NAG B 1 2993 2993 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 . . . J 4 72.744 -36.372 20.609 1 63.27 ? C1 NAG 2993 B 1 HETATM 2 C C2 NAG . . . J 4 73.191 -35.804 19.254 1 63.44 ? C2 NAG 2993 B 1 HETATM 3 C C3 NAG . . . J 4 73.389 -36.944 18.251 1 63.49 ? C3 NAG 2993 B 1 HETATM 4 C C4 NAG . . . J 4 74.287 -38.046 18.811 1 63.4 ? C4 NAG 2993 B 1 HETATM 5 C C5 NAG . . . J 4 73.782 -38.509 20.18 1 63.34 ? C5 NAG 2993 B 1 HETATM 6 C C6 NAG . . . J 4 74.719 -39.533 20.818 1 63.38 ? C6 NAG 2993 B 1 HETATM 7 C C7 NAG . . . J 4 72.429 -33.735 18.131 1 63.38 ? C7 NAG 2993 B 1 HETATM 8 C C8 NAG . . . J 4 72.43 -32.489 18.97 1 63.31 ? C8 NAG 2993 B 1 HETATM 9 N N2 NAG . . . J 4 72.174 -34.889 18.753 1 63.49 ? N2 NAG 2993 B 1 HETATM 10 O O3 NAG . . . J 4 73.964 -36.434 17.068 1 63.61 ? O3 NAG 2993 B 1 HETATM 11 O O4 NAG . . . J 4 74.306 -39.131 17.909 1 63.33 ? O4 NAG 2993 B 1 HETATM 12 O O5 NAG . . . J 4 73.603 -37.41 21.059 1 63.26 ? O5 NAG 2993 B 1 HETATM 13 O O6 NAG . . . J 4 74.382 -40.826 20.365 1 63.46 ? O6 NAG 2993 B 1 HETATM 14 O O7 NAG . . . J 4 72.639 -33.66 16.921 1 63.31 ? O7 NAG 2993 B 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 466 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 14 #