data_3TV8 # _model_server_result.job_id 2N3x6RHIHlC606wYpoCXmg _model_server_result.datetime_utc '2024-11-21 22:57:51' _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 3tv8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":801}' # _entry.id 3TV8 # _exptl.entry_id 3TV8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 163.172 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol _entity.pdbx_number_of_molecules 2 _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 120 _cell.entry_id 3TV8 _cell.length_a 90.465 _cell.length_b 90.465 _cell.length_c 216.544 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TV8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 J N N ? 7 P N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 3 4 3 MAN BMA C1 O1 . O3 HO3 . 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 692 NAG 2 n C NAG 2 C 2 NAG A 693 NAG 2 n C BMA 3 C 3 BMA A 694 BMA 3 n D NAG 1 D 1 NAG B 692 NAG 3 n D NAG 2 D 2 NAG B 693 NAG 3 n D BMA 3 D 3 BMA B 694 BMA 3 n D MAN 4 D 4 MAN B 695 MAN # 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 21 A CYS 52 1_555 A SG CYS 63 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 25 A CYS 56 1_555 A SG CYS 32 A CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf3 A SG CYS 111 A CYS 142 1_555 A SG CYS 141 A CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf4 A SG CYS 171 A CYS 202 1_555 A SG CYS 192 A CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 347 A CYS 378 1_555 A SG CYS 351 A CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf6 B SG CYS 21 B CYS 52 1_555 B SG CYS 63 B CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf7 B SG CYS 25 B CYS 56 1_555 B SG CYS 32 B CYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf8 B SG CYS 111 B CYS 142 1_555 B SG CYS 141 B CYS 172 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf9 B SG CYS 171 B CYS 202 1_555 B SG CYS 192 B CYS 223 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf10 B SG CYS 347 B CYS 378 1_555 B SG CYS 351 B CYS 382 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 A ND2 ASN 108 A ASN 139 1_555 E C1 NAG . A NAG 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale2 A ND2 ASN 161 A ASN 192 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale3 A ND2 ASN 184 A ASN 215 1_555 F C1 NAG . A NAG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.458 ? covale ? covale4 B ND2 ASN 108 B ASN 139 1_555 K C1 NAG . B NAG 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale5 B ND2 ASN 161 B ASN 192 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale6 B ND2 ASN 184 B ASN 215 1_555 L C1 NAG . B NAG 715 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale7 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 C O4 NAG . C NAG 2 1_555 C C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.447 ? covale ? covale10 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale11 D O3 BMA . D BMA 3 1_555 D C1 MAN . D MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _chem_comp.formula 'C6 H13 N O4' _chem_comp.formula_weight 163.172 _chem_comp.id DGJ _chem_comp.mon_nstd_flag . _chem_comp.name (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 1-deoxygalactonojirimycin # 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 N5 C1 DGJ sing 172 n n C2 C1 DGJ sing 173 n n C1 H1 DGJ sing 174 n n C1 H1A DGJ sing 175 n n C3 C2 DGJ sing 176 n n C2 O2 DGJ sing 177 n n C2 H2 DGJ sing 178 n n O2 HO2 DGJ sing 179 n n C4 C3 DGJ sing 180 n n O3 C3 DGJ sing 181 n n C3 H3 DGJ sing 182 n n O3 HO3 DGJ sing 183 n n O4 C4 DGJ sing 184 n n C4 C5 DGJ sing 185 n n C4 H4 DGJ sing 186 n n O4 HO4 DGJ sing 187 n n C6 C5 DGJ sing 188 n n C5 N5 DGJ sing 189 n n C5 H5 DGJ sing 190 n n N5 HN5 DGJ sing 191 n n C6 O6 DGJ sing 192 n n C6 H6 DGJ sing 193 n n C6 H6A DGJ sing 194 n n O6 HO6 DGJ sing 195 n n # _atom_sites.entry_id 3TV8 _atom_sites.fract_transf_matrix[1][1] 0.011054 _atom_sites.fract_transf_matrix[1][2] 0.006382 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012764 _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] 0.004618 _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 E 4 NAG A 1 639 639 NAG NAG . F 4 NAG A 1 715 715 NAG NAG . G 5 SO4 A 1 8 8 SO4 SO4 . H 6 2PE A 1 9 9 2PE 2PE . I 6 2PE A 1 11 11 2PE 2PE . J 7 DGJ A 1 801 801 DGJ DGJ . K 4 NAG B 1 639 639 NAG NAG . L 4 NAG B 1 715 715 NAG NAG . M 5 SO4 B 1 6 6 SO4 SO4 . N 5 SO4 B 1 7 7 SO4 SO4 . O 6 2PE B 1 12 12 2PE 2PE . P 7 DGJ B 1 802 802 DGJ DGJ . Q 8 HOH A 1 3 3 HOH HOH . Q 8 HOH A 2 5 5 HOH HOH . Q 8 HOH A 3 6 6 HOH HOH . Q 8 HOH A 4 7 7 HOH HOH . Q 8 HOH A 5 20 20 HOH HOH . Q 8 HOH A 6 25 25 HOH HOH . Q 8 HOH A 7 26 26 HOH HOH . Q 8 HOH A 8 31 31 HOH HOH . Q 8 HOH A 9 436 32 HOH HOH . Q 8 HOH A 10 437 49 HOH HOH . Q 8 HOH A 11 438 58 HOH HOH . Q 8 HOH A 12 439 62 HOH HOH . Q 8 HOH A 13 440 63 HOH HOH . Q 8 HOH A 14 441 64 HOH HOH . Q 8 HOH A 15 442 79 HOH HOH . Q 8 HOH A 16 443 80 HOH HOH . Q 8 HOH A 17 444 81 HOH HOH . Q 8 HOH A 18 445 82 HOH HOH . Q 8 HOH A 19 446 86 HOH HOH . Q 8 HOH A 20 447 88 HOH HOH . Q 8 HOH A 21 448 94 HOH HOH . Q 8 HOH A 22 449 101 HOH HOH . Q 8 HOH A 23 450 108 HOH HOH . Q 8 HOH A 24 451 109 HOH HOH . Q 8 HOH A 25 452 110 HOH HOH . Q 8 HOH A 26 453 113 HOH HOH . Q 8 HOH A 27 454 116 HOH HOH . Q 8 HOH A 28 455 117 HOH HOH . Q 8 HOH A 29 456 119 HOH HOH . Q 8 HOH A 30 457 122 HOH HOH . Q 8 HOH A 31 458 124 HOH HOH . Q 8 HOH A 32 459 125 HOH HOH . Q 8 HOH A 33 460 126 HOH HOH . Q 8 HOH A 34 461 127 HOH HOH . Q 8 HOH A 35 462 128 HOH HOH . Q 8 HOH A 36 463 130 HOH HOH . R 8 HOH B 1 2 2 HOH HOH . R 8 HOH B 2 15 15 HOH HOH . R 8 HOH B 3 19 19 HOH HOH . R 8 HOH B 4 29 29 HOH HOH . R 8 HOH B 5 436 12 HOH HOH . R 8 HOH B 6 437 40 HOH HOH . R 8 HOH B 7 438 44 HOH HOH . R 8 HOH B 8 439 46 HOH HOH . R 8 HOH B 9 440 47 HOH HOH . R 8 HOH B 10 441 48 HOH HOH . R 8 HOH B 11 442 53 HOH HOH . R 8 HOH B 12 443 55 HOH HOH . R 8 HOH B 13 444 69 HOH HOH . R 8 HOH B 14 445 72 HOH HOH . R 8 HOH B 15 446 74 HOH HOH . R 8 HOH B 16 447 75 HOH HOH . R 8 HOH B 17 448 77 HOH HOH . R 8 HOH B 18 449 78 HOH HOH . R 8 HOH B 19 450 95 HOH HOH . R 8 HOH B 20 451 102 HOH HOH . R 8 HOH B 21 452 103 HOH HOH . R 8 HOH B 22 453 104 HOH HOH . R 8 HOH B 23 454 105 HOH HOH . R 8 HOH B 24 455 106 HOH HOH . R 8 HOH B 25 456 115 HOH HOH . R 8 HOH B 26 457 121 HOH HOH . R 8 HOH B 27 458 123 HOH HOH . R 8 HOH B 28 459 129 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 DGJ . . . J 7 -17.801 61.593 105.691 1 38.6 ? C1 DGJ 801 A 1 HETATM 2 C C2 DGJ . . . J 7 -16.914 60.544 106.329 1 33.21 ? C2 DGJ 801 A 1 HETATM 3 O O2 DGJ . . . J 7 -15.861 61.191 107.054 1 38.31 ? O2 DGJ 801 A 1 HETATM 4 C C3 DGJ . . . J 7 -16.389 59.606 105.245 1 31.75 ? C3 DGJ 801 A 1 HETATM 5 O O3 DGJ . . . J 7 -15.48 58.66 105.814 1 28.15 ? O3 DGJ 801 A 1 HETATM 6 C C4 DGJ . . . J 7 -17.553 58.887 104.569 1 33.39 ? C4 DGJ 801 A 1 HETATM 7 O O4 DGJ . . . J 7 -18.223 58.058 105.526 1 22.27 ? O4 DGJ 801 A 1 HETATM 8 C C5 DGJ . . . J 7 -18.525 59.901 103.968 1 37.88 ? C5 DGJ 801 A 1 HETATM 9 N N5 DGJ . . . J 7 -18.844 60.921 104.944 1 40.6 ? N5 DGJ 801 A 1 HETATM 10 C C6 DGJ . . . J 7 -19.815 59.241 103.497 1 43.06 ? C6 DGJ 801 A 1 HETATM 11 O O6 DGJ . . . J 7 -20.671 60.188 102.846 1 40.96 ? O6 DGJ 801 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 37 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 11 #