data_7RPV # _model_server_result.job_id RYTqpS9vJ3BYWvUU3JF-6Q _model_server_result.datetime_utc '2024-11-01 16:28:21' _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 7rpv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1002}' # _entry.id 7RPV # _exptl.entry_id 7RPV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 221.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-acetamido-2-deoxy-beta-D-glucopyranose _entity.pdbx_number_of_molecules 24 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.51 _cell.angle_gamma 90 _cell.entry_id 7RPV _cell.length_a 132.666 _cell.length_b 136.307 _cell.length_c 132.673 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7RPV _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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 ? dimeric 2 author_defined_assembly 3 ? dimeric 2 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K,L,M,N,O 1 1 C,D,P,Q,R,S,T,U,V 2 1 E,F,W,X,Y,Z,AA,BA,CA 3 1 G,H,DA,EA,FA,GA,HA,IA,JA,KA 4 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 I N N ? 3 J N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 T N N ? 3 U N N ? 3 W N N ? 3 X N N ? 3 Y N N ? 3 Z N N ? 3 AA N N ? 3 BA N N ? 3 DA N N ? 3 EA N N ? 3 FA N N ? 3 GA N N ? 3 HA N N ? 3 IA 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 326 A CYS 344 1_555 A SG CYS 343 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 A SG CYS 512 A CYS 530 1_555 A SG CYS 524 A CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 B SG CYS 17 E CYS 336 1_555 B SG CYS 42 E CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 B SG CYS 60 E CYS 379 1_555 B SG CYS 113 E CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 B SG CYS 72 E CYS 391 1_555 B SG CYS 206 E CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 B SG CYS 161 E CYS 480 1_555 B SG CYS 169 E CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf8 C SG CYS 115 B CYS 133 1_555 C SG CYS 123 B CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf9 C SG CYS 326 B CYS 344 1_555 C SG CYS 343 B CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf10 D SG CYS 17 F CYS 336 1_555 D SG CYS 42 F CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf11 D SG CYS 60 F CYS 379 1_555 D SG CYS 113 F CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf12 D SG CYS 72 F CYS 391 1_555 D SG CYS 206 F CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 D SG CYS 161 F CYS 480 1_555 D SG CYS 169 F CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf14 E SG CYS 115 C CYS 133 1_555 E SG CYS 123 C CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf15 E SG CYS 326 C CYS 344 1_555 E SG CYS 343 C CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf16 E SG CYS 512 C CYS 530 1_555 E SG CYS 524 C CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf17 F SG CYS 17 G CYS 336 1_555 F SG CYS 42 G CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf18 F SG CYS 60 G CYS 379 1_555 F SG CYS 113 G CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf19 F SG CYS 72 G CYS 391 1_555 F SG CYS 206 G CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf20 F SG CYS 161 G CYS 480 1_555 F SG CYS 169 G CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf21 G SG CYS 115 D CYS 133 1_555 G SG CYS 123 D CYS 141 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf22 G SG CYS 326 D CYS 344 1_555 G SG CYS 343 D CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf23 G SG CYS 512 D CYS 530 1_555 G SG CYS 524 D CYS 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf24 H SG CYS 17 H CYS 336 1_555 H SG CYS 42 H CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf25 H SG CYS 60 H CYS 379 1_555 H SG CYS 113 H CYS 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf26 H SG CYS 72 H CYS 391 1_555 H SG CYS 206 H CYS 525 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf27 H SG CYS 161 H CYS 480 1_555 H SG CYS 169 H CYS 488 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 35 A ASN 53 1_555 I C1 NAG . A NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.483 ? covale ? covale2 A ND2 ASN 72 A ASN 90 1_555 J C1 NAG . A NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale3 A ND2 ASN 85 A ASN 103 1_555 K C1 NAG . A NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.585 ? covale ? covale4 A ND2 ASN 304 A ASN 322 1_555 L C1 NAG . A NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.497 ? covale ? covale5 A ND2 ASN 414 A ASN 432 1_555 M C1 NAG . A NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.474 ? covale ? covale6 A ND2 ASN 528 A ASN 546 1_555 N C1 NAG . A NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.433 ? covale ? covale7 C ND2 ASN 35 B ASN 53 1_555 P C1 NAG . B NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.514 ? covale ? covale8 C ND2 ASN 72 B ASN 90 1_555 Q C1 NAG . B NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale9 C ND2 ASN 85 B ASN 103 1_555 R C1 NAG . B NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? covale ? covale10 C ND2 ASN 304 B ASN 322 1_555 S C1 NAG . B NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.408 ? covale ? covale11 C ND2 ASN 414 B ASN 432 1_555 T C1 NAG . B NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.49 ? covale ? covale12 C ND2 ASN 528 B ASN 546 1_555 U C1 NAG . B NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale13 E ND2 ASN 35 C ASN 53 1_555 W C1 NAG . C NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale14 E ND2 ASN 72 C ASN 90 1_555 X C1 NAG . C NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.471 ? covale ? covale15 E ND2 ASN 85 C ASN 103 1_555 Y C1 NAG . C NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale16 E ND2 ASN 304 C ASN 322 1_555 Z C1 NAG . C NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale17 E ND2 ASN 414 C ASN 432 1_555 AA C1 NAG . C NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale18 E ND2 ASN 528 C ASN 546 1_555 BA C1 NAG . C NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale19 G ND2 ASN 35 D ASN 53 1_555 DA C1 NAG . D NAG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale20 G ND2 ASN 72 D ASN 90 1_555 EA C1 NAG . D NAG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale21 G ND2 ASN 85 D ASN 103 1_555 FA C1 NAG . D NAG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.581 ? covale ? covale22 G ND2 ASN 304 D ASN 322 1_555 GA C1 NAG . D NAG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.416 ? covale ? covale23 G ND2 ASN 414 D ASN 432 1_555 HA C1 NAG . D NAG 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale24 G ND2 ASN 528 D ASN 546 1_555 IA C1 NAG . D NAG 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? metalc ? metalc1 A OH TYR 497 A TYR 515 1_555 O ZN ZN . A ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc2 C OH TYR 497 B TYR 515 1_555 V ZN ZN . B ZN 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.456 ? # _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 237 n n C1 O1 NAG sing 238 n n C1 O5 NAG sing 239 n n C1 H1 NAG sing 240 n n C2 C3 NAG sing 241 n n C2 N2 NAG sing 242 n n C2 H2 NAG sing 243 n n C3 C4 NAG sing 244 n n C3 O3 NAG sing 245 n n C3 H3 NAG sing 246 n n C4 C5 NAG sing 247 n n C4 O4 NAG sing 248 n n C4 H4 NAG sing 249 n n C5 C6 NAG sing 250 n n C5 O5 NAG sing 251 n n C5 H5 NAG sing 252 n n C6 O6 NAG sing 253 n n C6 H61 NAG sing 254 n n C6 H62 NAG sing 255 n n C7 C8 NAG sing 256 n n C7 N2 NAG sing 257 n n C7 O7 NAG doub 258 n n C8 H81 NAG sing 259 n n C8 H82 NAG sing 260 n n C8 H83 NAG sing 261 n n N2 HN2 NAG sing 262 n n O1 HO1 NAG sing 263 n n O3 HO3 NAG sing 264 n n O4 HO4 NAG sing 265 n n O6 HO6 NAG sing 266 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 7RPV _atom_sites.fract_transf_matrix[1][1] 0.007538 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00033 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007336 _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] 0.007545 _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 I 3 NAG A 1 1001 1001 NAG NAG . J 3 NAG A 1 1002 1002 NAG NAG . K 3 NAG A 1 1003 1003 NAG NAG . L 3 NAG A 1 1004 1004 NAG NAG . M 3 NAG A 1 1005 1005 NAG NAG . N 3 NAG A 1 1006 1006 NAG NAG . O 4 ZN A 1 1007 2001 ZN ZN . P 3 NAG B 1 1001 1001 NAG NAG . Q 3 NAG B 1 1002 1002 NAG NAG . R 3 NAG B 1 1003 1003 NAG NAG . S 3 NAG B 1 1004 1004 NAG NAG . T 3 NAG B 1 1005 1005 NAG NAG . U 3 NAG B 1 1006 1006 NAG NAG . V 4 ZN B 1 1007 2001 ZN ZN . W 3 NAG C 1 1001 1001 NAG NAG . X 3 NAG C 1 1002 1002 NAG NAG . Y 3 NAG C 1 1003 1003 NAG NAG . Z 3 NAG C 1 1004 1004 NAG NAG . AA 3 NAG C 1 1005 1005 NAG NAG . BA 3 NAG C 1 1006 1006 NAG NAG . CA 4 ZN C 1 1007 2001 ZN ZN . DA 3 NAG D 1 1001 1001 NAG NAG . EA 3 NAG D 1 1002 1002 NAG NAG . FA 3 NAG D 1 1003 1003 NAG NAG . GA 3 NAG D 1 1004 1004 NAG NAG . HA 3 NAG D 1 1005 1005 NAG NAG . IA 3 NAG D 1 1006 1006 NAG NAG . JA 4 ZN D 1 1007 2001 ZN ZN . KA 5 HOH D 1 1101 3 HOH HOH . KA 5 HOH D 2 1102 1 HOH HOH . KA 5 HOH D 3 1103 2 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 . . . J 3 10.87 5.115 -14.025 1 75.36 ? C1 NAG 1002 A 1 HETATM 2 C C2 NAG . . . J 3 10.961 4.527 -15.431 1 79.18 ? C2 NAG 1002 A 1 HETATM 3 C C3 NAG . . . J 3 11.133 3.014 -15.416 1 83.69 ? C3 NAG 1002 A 1 HETATM 4 C C4 NAG . . . J 3 11.658 2.544 -14.07 1 88.1 ? C4 NAG 1002 A 1 HETATM 5 C C5 NAG . . . J 3 10.681 2.913 -12.959 1 86.09 ? C5 NAG 1002 A 1 HETATM 6 C C6 NAG . . . J 3 11.317 2.733 -11.584 1 90.98 ? C6 NAG 1002 A 1 HETATM 7 C C7 NAG . . . J 3 9.813 5.831 -17.12 1 80.63 ? C7 NAG 1002 A 1 HETATM 8 C C8 NAG . . . J 3 10.062 5.361 -18.522 1 81.62 ? C8 NAG 1002 A 1 HETATM 9 N N2 NAG . . . J 3 9.778 4.882 -16.19 1 77.05 ? N2 NAG 1002 A 1 HETATM 10 O O3 NAG . . . J 3 12.055 2.635 -16.443 1 83.74 ? O3 NAG 1002 A 1 HETATM 11 O O4 NAG . . . J 3 11.852 1.125 -14.099 1 90.94 ? O4 NAG 1002 A 1 HETATM 12 O O5 NAG . . . J 3 10.205 4.26 -13.082 1 80.57 ? O5 NAG 1002 A 1 HETATM 13 O O6 NAG . . . J 3 11.222 1.361 -11.188 1 97.29 ? O6 NAG 1002 A 1 HETATM 14 O O7 NAG . . . J 3 9.651 7.01 -16.852 1 81.99 ? O7 NAG 1002 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 51 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 21 _model_server_stats.element_count 14 #