data_5HCH # _model_server_result.job_id NeM0cR219_E2AMfAz-hniQ _model_server_result.datetime_utc '2025-01-02 17:26:22' _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 5hch # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":101}' # _entry.id 5HCH # _exptl.entry_id 5HCH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 256.19 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol _entity.pdbx_number_of_molecules 1 _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 5HCH _cell.length_a 60.451 _cell.length_b 60.451 _cell.length_c 204.828 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HCH _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 62 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # 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,F,G,H,I,J 1 1 A,B,C,D,E,F,G,H,I,J 1 2 A,B,C,D,E,F,G,H,I,J 1 3 A,B,C,D,E,F,G,H,I,J 1 4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 4_585 -x,-y+3,z -1 0 0 0 -1 0 0 0 1 -90.6765 157.056305 0 3 'crystal symmetry operation' 9_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 68.276 4 'crystal symmetry operation' 12_585 x,x-y+3,-z+1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -90.6765 157.056305 68.276 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 B O3' DT 6 B DT 6 1_555 B P 61H 7 B 61H 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? covale ? covale2 B O3' 61H 7 B 61H 7 1_555 B P DT 8 B DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale3 C P DG 1 E DG 14 1_555 G O8 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? covale ? covale4 C P DG 1 E DG 14 1_555 G O06 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? covale ? covale5 C P DG 1 E DG 14 1_555 G O07 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.481 ? covale ? covale6 C O5' DG 1 E DG 14 1_555 G P01 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale7 C O3' DA 6 E DA 19 1_555 C P 61H 7 E 61H 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.607 ? covale ? covale8 C O3' 61H 7 E 61H 20 1_555 C P DA 8 E DA 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.608 ? metalc ? metalc1 A O ASN 21 A ASN 21 1_555 E CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc2 A OE1 GLU 95 A GLU 95 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? metalc ? metalc3 A OE2 GLU 95 A GLU 95 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? metalc ? metalc4 A OD1 ASP 99 A ASP 99 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc5 A OD1 ASP 101 A ASP 101 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.519 ? metalc ? metalc6 A OD2 ASP 101 A ASP 101 1_555 E CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? metalc ? metalc7 A OD1 ASN 103 A ASN 103 1_555 E CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? metalc ? metalc8 A OD1 ASP 104 A ASP 104 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.906 ? metalc ? metalc9 A OD2 ASP 104 A ASP 104 1_555 D CA CA . A CA 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc10 A OD1 ASP 104 A ASP 104 1_555 E CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc11 A O GLY 114 A GLY 114 1_555 E CA CA . A CA 202 12_585 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc12 A OXT GLY 114 A GLY 114 1_555 E CA CA . A CA 202 12_585 ? ? ? ? ? ? ? ? ? ? ? ? 2.881 ? metalc ? metalc13 D CA CA . A CA 201 1_555 G O5 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc14 D CA CA . A CA 201 1_555 G O4 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc15 E CA CA . A CA 202 1_555 G O4 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.475 ? metalc ? metalc16 E CA CA . A CA 202 1_555 G O02 61J . E 61J 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? hydrog WATSON-CRICK hydrog1 B N3 DC 1 B DC 1 1_555 C N1 DG 13 E DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N4 DC 1 B DC 1 1_555 C O6 DG 13 E DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O2 DC 1 B DC 1 1_555 C N2 DG 13 E DG 26 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N1 DG 2 B DG 2 1_555 C N3 DC 12 E DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B N2 DG 2 B DG 2 1_555 C O2 DC 12 E DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B O6 DG 2 B DG 2 1_555 C N4 DC 12 E DC 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N3 DC 3 B DC 3 1_555 C N1 DG 11 E DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N4 DC 3 B DC 3 1_555 C O6 DG 11 E DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B O2 DC 3 B DC 3 1_555 C N2 DG 11 E DG 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B N1 DA 4 B DA 4 1_555 C N3 DT 10 E DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N6 DA 4 B DA 4 1_555 C O4 DT 10 E DT 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N3 DT 5 B DT 5 1_555 C N1 DA 9 E DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O4 DT 5 B DT 5 1_555 C N6 DA 9 E DA 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DT 8 B DT 8 1_555 C N1 DA 6 E DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B O4 DT 8 B DT 8 1_555 C N6 DA 6 E DA 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DA-DT PAIR' hydrog16 B N1 DA 9 B DA 9 1_555 C N3 DT 5 E DT 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 10 B DT 10 1_555 C N1 DA 4 E DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 10 B DT 10 1_555 C N6 DA 4 E DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog19 B O2 DC 11 B DC 11 1_555 C N1 DG 3 E DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B N1 DG 12 B DG 12 1_555 C N3 DC 2 E DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N2 DG 12 B DG 12 1_555 C O2 DC 2 E DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B O6 DG 12 B DG 12 1_555 C N4 DC 2 E DC 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B N3 DC 13 B DC 13 1_555 C N1 DG 1 E DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N4 DC 13 B DC 13 1_555 C O6 DG 1 E DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B O2 DC 13 B DC 13 1_555 C N2 DG 1 E DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C8 H17 O7 P' _chem_comp.formula_weight 256.19 _chem_comp.id 61J _chem_comp.mon_nstd_flag . _chem_comp.name (6S)-2,6-anhydro-1-deoxy-6-(2-{[(S)-hydroxy(oxido)-lambda~5~-phosphanyl]oxy}ethyl)-D-galactitol _chem_comp.type d-saccharide _chem_comp.pdbx_synonyms ? # 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 O5 C5 61J sing 48 n n O07 P01 61J sing 49 n n C5 C6 61J sing 50 n n C5 C4 61J sing 51 n n O06 P01 61J doub 52 n n C6 O6 61J sing 53 n n C6 C7 61J sing 54 n n O4 C4 61J sing 55 n n P01 O8 61J sing 56 n n C8 O8 61J sing 57 n n C8 C7 61J sing 58 n n O6 C2 61J sing 59 n n C4 C3 61J sing 60 n n O02 C3 61J sing 61 n n C3 C2 61J sing 62 n n C2 C1 61J sing 63 n n C2 H1 61J sing 64 n n C3 H31 61J sing 65 n n C4 H4 61J sing 66 n n C5 H5 61J sing 67 n n C6 H6 61J sing 68 n n C1 H6A 61J sing 69 n n C1 H7A 61J sing 70 n n C1 H8 61J sing 71 n n O02 H9 61J sing 72 n n O4 HO4 61J sing 73 n n O5 HO5 61J sing 74 n n C7 H7 61J sing 75 n n C7 H13 61J sing 76 n n C8 H81 61J sing 77 n n C8 H82 61J sing 78 n n O07 H17 61J sing 79 n n P01 H16 61J sing 80 n n # _atom_sites.entry_id 5HCH _atom_sites.fract_transf_matrix[1][1] 0.016542 _atom_sites.fract_transf_matrix[1][2] 0.009551 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019101 _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] 0.004882 _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 D 4 CA A 1 201 116 CA CA . E 4 CA A 1 202 117 CA CA . F 5 NA B 1 101 1 NA NA . G 6 61J E 1 101 14 61J LIG . H 7 HOH A 1 301 13 HOH HOH . H 7 HOH A 2 302 18 HOH HOH . H 7 HOH A 3 303 35 HOH HOH . H 7 HOH A 4 304 22 HOH HOH . H 7 HOH A 5 305 38 HOH HOH . H 7 HOH A 6 306 7 HOH HOH . H 7 HOH A 7 307 8 HOH HOH . H 7 HOH A 8 308 32 HOH HOH . H 7 HOH A 9 309 1 HOH HOH . H 7 HOH A 10 310 10 HOH HOH . H 7 HOH A 11 311 6 HOH HOH . H 7 HOH A 12 312 3 HOH HOH . H 7 HOH A 13 313 5 HOH HOH . H 7 HOH A 14 314 19 HOH HOH . H 7 HOH A 15 315 12 HOH HOH . H 7 HOH A 16 316 34 HOH HOH . H 7 HOH A 17 317 36 HOH HOH . H 7 HOH A 18 318 29 HOH HOH . H 7 HOH A 19 319 11 HOH HOH . H 7 HOH A 20 320 33 HOH HOH . I 7 HOH B 1 201 31 HOH HOH . I 7 HOH B 2 202 2 HOH HOH . I 7 HOH B 3 203 21 HOH HOH . I 7 HOH B 4 204 1 HOH HOH . J 7 HOH E 1 201 23 HOH HOH . J 7 HOH E 2 202 37 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 C2 61J . . . G 6 -23.052 73.095 47.253 1 87.08 ? C2 61J 101 E 1 HETATM 2 C C3 61J . . . G 6 -24.558 73.082 47.076 1 83.28 ? C3 61J 101 E 1 HETATM 3 C C4 61J . . . G 6 -25.037 71.982 46.151 1 81.77 ? C4 61J 101 E 1 HETATM 4 C C5 61J . . . G 6 -24.158 71.828 44.928 1 81.25 ? C5 61J 101 E 1 HETATM 5 C C6 61J . . . G 6 -22.706 71.693 45.33 1 85 ? C6 61J 101 E 1 HETATM 6 O O6 61J . . . G 6 -22.345 72.842 46.058 1 86.38 ? O6 61J 101 E 1 HETATM 7 C C1 61J . . . G 6 -22.65 74.474 47.717 1 88.73 ? C1 61J 101 E 1 HETATM 8 O O02 61J . . . G 6 -24.998 74.331 46.588 1 81.5 ? O02 61J 101 E 1 HETATM 9 O O4 61J . . . G 6 -26.337 72.325 45.729 1 78.67 ? O4 61J 101 E 1 HETATM 10 O O5 61J . . . G 6 -24.55 70.689 44.2 1 80.4 ? O5 61J 101 E 1 HETATM 11 C C7 61J . . . G 6 -22.469 70.431 46.141 1 86.19 ? C7 61J 101 E 1 HETATM 12 C C8 61J . . . G 6 -21.138 69.816 45.746 1 89.41 ? C8 61J 101 E 1 HETATM 13 O O8 61J . . . G 6 -20.809 68.848 45.858 1 91.54 ? O8 61J 101 E 1 HETATM 14 P P01 61J . . . G 6 -20.312 67.378 45.738 1 111.77 ? P01 61J 101 E 1 HETATM 15 O O06 61J . . . G 6 -18.887 67.471 45.312 1 115.49 ? O06 61J 101 E 1 HETATM 16 O O07 61J . . . G 6 -21.303 66.864 44.691 1 109.68 ? O07 61J 101 E 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 16 #