data_2GK1 # _model_server_result.job_id dGYd1qBHxg0_lqxZR0wOxg _model_server_result.datetime_utc '2024-10-15 16:17:07' _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 2gk1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"JA","auth_seq_id":530}' # _entry.id 2GK1 # _exptl.entry_id 2GK1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 219.258 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.48 _cell.angle_gamma 90 _cell.entry_id 2GK1 _cell.length_a 322.246 _cell.length_b 109.796 _cell.length_c 132.764 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GK1 _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 PISA pentameric 5 author_and_software_defined_assembly 1 PISA pentameric 5 author_and_software_defined_assembly 2 PISA pentameric 5 author_and_software_defined_assembly 3 PISA decameric 10 software_defined_assembly 4 PISA decameric 10 software_defined_assembly 5 PISA pentameric 5 software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,U,V,W,FA,GA,NA,OA 1 1 F,G,H,I,J,X,Y,Z,HA,IA,PA,QA 2 1 P,Q,R,S,T,CA,DA,EA,LA,MA 3 1 A,B,C,D,E,F,G,H,I,J,U,V,W,X,Y,Z,FA,GA,HA,IA,NA,OA,PA,QA 4 1 K,L,M,N,O,P,Q,R,S,T,AA,BA,CA,DA,EA,JA,KA,LA,MA 5 1 K,L,M,N,O,AA,BA,JA,KA 6 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 ? 8 FA N N ? 8 GA N N ? 8 HA N N ? 8 IA N N ? 8 JA N N ? 8 KA N N ? 8 LA N N ? 8 MA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 6 oligosaccharide 7 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 ? 6 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 6 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 7 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 6 n U NAG 1 U 1 NAG I 1 NAG 6 n U NAG 2 U 2 NAG I 2 NAG 6 n U BMA 3 U 3 BMA I 3 MAN 6 n V NAG 1 V 1 NAG J 4 NAG 6 n V NAG 2 V 2 NAG J 5 NAG 6 n V BMA 3 V 3 BMA J 6 MAN 6 n W NAG 1 W 1 NAG K 7 NAG 6 n W NAG 2 W 2 NAG K 8 NAG 6 n W BMA 3 W 3 BMA K 9 MAN 7 n X NAG 1 X 1 NAG L 10 NAG 7 n X NAG 2 X 2 NAG L 11 NAG 6 n Y NAG 1 Y 1 NAG M 12 NAG 6 n Y NAG 2 Y 2 NAG M 13 NAG 6 n Y BMA 3 Y 3 BMA M 14 MAN 7 n Z NAG 1 Z 1 NAG N 15 NAG 7 n Z NAG 2 Z 2 NAG N 16 NAG 7 n AA NAG 1 a 1 NAG O 17 NAG 7 n AA NAG 2 a 2 NAG O 18 NAG 7 n BA NAG 1 b 1 NAG P 19 NAG 7 n BA NAG 2 b 2 NAG P 20 NAG 7 n CA NAG 1 c 1 NAG Q 21 NAG 7 n CA NAG 2 c 2 NAG Q 22 NAG 6 n DA NAG 1 d 1 NAG R 23 NAG 6 n DA NAG 2 d 2 NAG R 24 NAG 6 n DA BMA 3 d 3 BMA R 25 MAN 7 n EA NAG 1 e 1 NAG S 26 NAG 7 n EA NAG 2 e 2 NAG S 27 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 36 A CYS 58 1_555 B SG CYS 16 I CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 B SG CYS 189 I CYS 277 1_555 B SG CYS 240 I CYS 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf3 B SG CYS 417 I CYS 505 1_555 B SG CYS 434 I CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf4 C SG CYS 42 B CYS 91 1_555 D SG CYS 16 M CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf5 D SG CYS 188 M CYS 309 1_555 E SG CYS 45 N CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 E SG CYS 219 N CYS 534 1_555 E SG CYS 236 N CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 F SG CYS 36 C CYS 58 1_555 G SG CYS 16 J CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf8 G SG CYS 189 J CYS 277 1_555 G SG CYS 240 J CYS 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf9 G SG CYS 417 J CYS 505 1_555 G SG CYS 434 J CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf10 H SG CYS 42 D CYS 91 1_555 I SG CYS 16 O CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf11 I SG CYS 188 O CYS 309 1_555 J SG CYS 45 P CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.061 ? disulf ? disulf12 J SG CYS 219 P CYS 534 1_555 J SG CYS 236 P CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf13 K SG CYS 36 E CYS 58 1_555 L SG CYS 16 K CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf14 L SG CYS 189 K CYS 277 1_555 L SG CYS 240 K CYS 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf15 L SG CYS 417 K CYS 505 1_555 L SG CYS 434 K CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf16 M SG CYS 42 F CYS 91 1_555 N SG CYS 16 Q CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf17 N SG CYS 188 Q CYS 309 1_555 O SG CYS 45 R CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf18 O SG CYS 219 R CYS 534 1_555 O SG CYS 236 R CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf19 P SG CYS 36 G CYS 58 1_555 Q SG CYS 16 L CYS 104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf20 Q SG CYS 189 L CYS 277 1_555 Q SG CYS 240 L CYS 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf21 Q SG CYS 417 L CYS 505 1_555 Q SG CYS 434 L CYS 522 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf22 R SG CYS 42 H CYS 91 1_555 S SG CYS 16 S CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf23 S SG CYS 188 S CYS 309 1_555 T SG CYS 45 T CYS 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf24 T SG CYS 219 T CYS 534 1_555 T SG CYS 236 T CYS 551 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 B ND2 ASN 27 I ASN 115 1_555 U C1 NAG . U NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.746 ? covale ? covale2 B ND2 ASN 69 I ASN 157 1_555 V C1 NAG . V NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? covale ? covale3 G ND2 ASN 27 J ASN 115 1_555 X C1 NAG . X NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale4 G ND2 ASN 69 J ASN 157 1_555 Y C1 NAG . Y NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.86 ? covale ? covale5 I ND2 ASN 69 O ASN 190 1_555 Z C1 NAG . Z NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale6 L ND2 ASN 69 K ASN 157 1_555 AA C1 NAG . a NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale7 N ND2 ASN 69 Q ASN 190 1_555 BA C1 NAG . b NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.361 ? covale ? covale8 Q ND2 ASN 27 L ASN 115 1_555 CA C1 NAG . c NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.223 ? covale ? covale9 Q ND2 ASN 69 L ASN 157 1_555 DA C1 NAG . d NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.289 ? covale ? covale10 S ND2 ASN 69 S ASN 190 1_555 EA C1 NAG . e NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.255 ? covale ? covale11 U O4 NAG . U NAG 1 1_555 U C1 NAG . U NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale12 U O4 NAG . U NAG 2 1_555 U C1 BMA . U BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale13 V O4 NAG . V NAG 1 1_555 V C1 NAG . V NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 V O4 NAG . V NAG 2 1_555 V C1 BMA . V BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.457 ? covale ? covale15 W O4 NAG . W NAG 1 1_555 W C1 NAG . W NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale16 W O4 NAG . W NAG 2 1_555 W C1 BMA . W BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale17 X O4 NAG . X NAG 1 1_555 X C1 NAG . X NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale18 Y O4 NAG . Y NAG 1 1_555 Y C1 NAG . Y NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale19 Y O4 NAG . Y NAG 2 1_555 Y C1 BMA . Y BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale20 Z O4 NAG . Z NAG 1 1_555 Z C1 NAG . Z NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale21 AA O4 NAG . a NAG 1 1_555 AA C1 NAG . a NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 ? covale ? covale22 BA O4 NAG . b NAG 1 1_555 BA C1 NAG . b NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale23 CA O4 NAG . c NAG 1 1_555 CA C1 NAG . c NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale24 DA O4 NAG . d NAG 1 1_555 DA C1 NAG . d NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale25 DA O4 NAG . d NAG 2 1_555 DA C1 BMA . d BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.46 ? covale ? covale26 EA O4 NAG . e NAG 1 1_555 EA C1 NAG . e NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? # _chem_comp.formula 'C8 H13 N O4 S' _chem_comp.formula_weight 219.258 _chem_comp.id NGT _chem_comp.mon_nstd_flag . _chem_comp.name 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 2GK1 _atom_sites.fract_transf_matrix[1][1] 0.003103 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00008 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009108 _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] 0.007535 _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 FA 8 NGT A 1 21 21 NGT NGT . GA 8 NGT B 1 22 22 NGT NGT . HA 8 NGT C 1 530 23 NGT NGT . IA 8 NGT D 1 24 24 NGT NGT . JA 8 NGT E 1 530 25 NGT NGT . KA 8 NGT F 1 26 26 NGT NGT . LA 8 NGT G 1 533 27 NGT NGT . MA 8 NGT H 1 28 28 NGT NGT . NA 9 HOH A 1 530 1 HOH HOH . NA 9 HOH A 2 531 2 HOH HOH . NA 9 HOH A 3 532 3 HOH HOH . NA 9 HOH A 4 533 4 HOH HOH . NA 9 HOH A 5 534 5 HOH HOH . OA 9 HOH B 1 6 6 HOH HOH . PA 9 HOH C 1 7 7 HOH HOH . PA 9 HOH C 2 8 8 HOH HOH . QA 9 HOH D 1 9 9 HOH HOH . QA 9 HOH D 2 10 10 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 NGT . . . JA 8 -90.055 53.387 62.599 1 50.79 ? C1 NGT 530 E 1 HETATM 2 C C2 NGT . . . JA 8 -90.186 54.953 62.708 1 49.88 ? C2 NGT 530 E 1 HETATM 3 C C3 NGT . . . JA 8 -91.382 55.501 61.829 1 48.6 ? C3 NGT 530 E 1 HETATM 4 C C4 NGT . . . JA 8 -91.535 54.755 60.506 1 47.95 ? C4 NGT 530 E 1 HETATM 5 C C5 NGT . . . JA 8 -91.624 53.257 60.755 1 48.15 ? C5 NGT 530 E 1 HETATM 6 C C6 NGT . . . JA 8 -91.829 52.435 59.494 1 48.02 ? C6 NGT 530 E 1 HETATM 7 C C7 NGT . . . JA 8 -90.905 54.315 64.789 1 52.24 ? C7 NGT 530 E 1 HETATM 8 C C8 NGT . . . JA 8 -91.224 54.346 66.278 1 52.68 ? C8 NGT 530 E 1 HETATM 9 N N2 NGT . . . JA 8 -90.427 55.28 64.102 1 51.33 ? N2 NGT 530 E 1 HETATM 10 S S1 NGT . . . JA 8 -91.142 52.764 63.94 1 53.42 ? S1 NGT 530 E 1 HETATM 11 O O3 NGT . . . JA 8 -91.207 56.902 61.596 1 47.84 ? O3 NGT 530 E 1 HETATM 12 O O4 NGT . . . JA 8 -92.704 55.213 59.85 1 49.16 ? O4 NGT 530 E 1 HETATM 13 O O5 NGT . . . JA 8 -90.406 52.784 61.394 1 49.43 ? O5 NGT 530 E 1 HETATM 14 O O6 NGT . . . JA 8 -92.322 51.133 59.812 1 48.98 ? O6 NGT 530 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 54 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 14 #