data_4AP6 # _model_server_result.job_id 2GmJuPyEa2bZvKt63oM62g _model_server_result.datetime_utc '2024-11-23 19:08:51' _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 4ap6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1430}' # _entry.id 4AP6 # _exptl.entry_id 4AP6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 589.342 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" _entity.pdbx_number_of_molecules 4 _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 4AP6 _cell.length_a 153.01 _cell.length_b 153.01 _cell.length_c 185.68 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4AP6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 32 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,S 1 1 B,H,I,J,K,L,T 2 1 C,M,N,O,P 3 1 D,Q,R 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 ? 2 E N N ? 2 H N N ? 2 M N N ? 2 Q 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 154 A CYS 161 1_555 A SG CYS 185 A CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf2 A SG CYS 405 A CYS 412 1_555 A SG CYS 412 A CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf3 B SG CYS 154 B CYS 161 1_555 B SG CYS 185 B CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? disulf ? disulf4 B SG CYS 405 B CYS 412 1_555 B SG CYS 412 B CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 C SG CYS 154 C CYS 161 1_555 C SG CYS 185 C CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf6 C SG CYS 405 C CYS 412 1_555 C SG CYS 412 C CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf7 D SG CYS 154 D CYS 161 1_555 D SG CYS 185 D CYS 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf8 D SG CYS 405 D CYS 412 1_555 D SG CYS 412 D CYS 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? covale ? covale1 A ND2 ASN 202 A ASN 209 1_555 F C1 NAG . A NAG 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 B ND2 ASN 182 B ASN 189 1_555 I C1 NAG . B NAG 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.455 ? covale ? covale3 B ND2 ASN 202 B ASN 209 1_555 J C1 NAG . B NAG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale4 B ND2 ASN 252 B ASN 259 1_555 K C1 NAG . B NAG 1433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale5 C ND2 ASN 182 C ASN 189 1_555 N C1 NAG . C NAG 1431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale6 C ND2 ASN 202 C ASN 209 1_555 O C1 NAG . C NAG 1432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? # _chem_comp.formula 'C16 H25 N5 O15 P2' _chem_comp.formula_weight 589.342 _chem_comp.id GFB _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE" _chem_comp.type non-polymer _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 P O1P GFB sing 83 n n O1P HO1P GFB sing 84 n n O3P P GFB doub 85 n n P O5' GFB sing 86 n n P O2P GFB sing 87 n n O2P P1 GFB sing 88 n n O5' C5' GFB sing 89 n n O1 P1 GFB sing 90 n n O1X P1 GFB doub 91 n n P1 O2X GFB sing 92 n n C4' C5' GFB sing 93 n n C5' "H5'A" GFB sing 94 n n C5' H5' GFB sing 95 n n H4' C4' GFB sing 96 n n C3' C4' GFB sing 97 n n C4' O4' GFB sing 98 n n O4' C1' GFB sing 99 n n O3' C3' GFB sing 100 n n C3' C2' GFB sing 101 n n C3' H3' GFB sing 102 n n C2' C1' GFB sing 103 n n H1' C1' GFB sing 104 n n C1' N9 GFB sing 105 n n HO3' O3' GFB sing 106 n n O2' C2' GFB sing 107 n n C2' H2' GFB sing 108 n n O2' HO2' GFB sing 109 n n N9 C4 GFB sing 110 n y N9 C8 GFB sing 111 n y H8 C8 GFB sing 112 n n C8 N7 GFB doub 113 n y N3 C4 GFB sing 114 n n C4 C5 GFB doub 115 n y C5 N7 GFB sing 116 n y C5 C6 GFB sing 117 n n N1 C6 GFB sing 118 n n C6 O6 GFB doub 119 n n C2 N1 GFB sing 120 n n N1 HN1 GFB sing 121 n n N3 C2 GFB doub 122 n n N2 C2 GFB sing 123 n n HN2 N2 GFB sing 124 n n N2 HN2A GFB sing 125 n n C2A C1 GFB sing 126 n n C1 O5 GFB sing 127 n n C1 H1 GFB sing 128 n n C1 O1 GFB sing 129 n n C3 C2A GFB sing 130 n n O2 C2A GFB sing 131 n n H2A C2A GFB sing 132 n n C5A O5 GFB sing 133 n n O3 C3 GFB sing 134 n n C3 H3 GFB sing 135 n n C3 C4A GFB sing 136 n n HO2 O2 GFB sing 137 n n H4A C4A GFB sing 138 n n O4 C4A GFB sing 139 n n C4A C5A GFB sing 140 n n HO3 O3 GFB sing 141 n n C5A H5A GFB sing 142 n n C5A C6A GFB sing 143 n n O4 HO4 GFB sing 144 n n H6A C6A GFB sing 145 n n H6AA C6A GFB sing 146 n n C6A H6AB GFB sing 147 n n O2X HO2X GFB sing 148 n n # _atom_sites.entry_id 4AP6 _atom_sites.fract_transf_matrix[1][1] 0.006536 _atom_sites.fract_transf_matrix[1][2] 0.003773 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007547 _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] 0.005386 _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 2 GFB A 1 1430 1430 GFB GFB . F 3 NAG A 1 1431 1431 NAG NAG . G 4 CL A 1 1432 1432 CL CL . H 2 GFB B 1 1430 1430 GFB GFB . I 3 NAG B 1 1431 1431 NAG NAG . J 3 NAG B 1 1432 1432 NAG NAG . K 3 NAG B 1 1433 1433 NAG NAG . L 4 CL B 1 1434 1434 CL CL . M 2 GFB C 1 1430 1430 GFB GFB . N 3 NAG C 1 1431 1431 NAG NAG . O 3 NAG C 1 1432 1432 NAG NAG . P 4 CL C 1 1433 1433 CL CL . Q 2 GFB D 1 1430 1430 GFB GFB . R 4 CL D 1 1431 1431 CL CL . S 5 HOH A 1 2001 2001 HOH HOH . S 5 HOH A 2 2002 2002 HOH HOH . S 5 HOH A 3 2003 2003 HOH HOH . S 5 HOH A 4 2004 2004 HOH HOH . S 5 HOH A 5 2005 2005 HOH HOH . S 5 HOH A 6 2006 2006 HOH HOH . T 5 HOH B 1 2001 2001 HOH HOH . T 5 HOH B 2 2002 2002 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 O O1P GFB . . . E 2 18.171 -11.651 14.227 1 75.51 ? O1P GFB 1430 A 1 HETATM 2 P P GFB . . . E 2 17.659 -10.672 15.249 1 68.42 ? P GFB 1430 A 1 HETATM 3 O O3P GFB . . . E 2 17.985 -9.219 15 1 87.25 ? O3P GFB 1430 A 1 HETATM 4 O O2P GFB . . . E 2 16.054 -10.906 15.332 1 56.26 ? O2P GFB 1430 A 1 HETATM 5 O O5' GFB . . . E 2 18.139 -11.123 16.692 1 73.54 ? O5' GFB 1430 A 1 HETATM 6 P P1 GFB . . . E 2 15.016 -10.768 16.551 1 89.22 ? P1 GFB 1430 A 1 HETATM 7 C C5' GFB . . . E 2 19.254 -12.003 16.756 1 74.29 ? C5' GFB 1430 A 1 HETATM 8 C C4' GFB . . . E 2 20.482 -11.106 16.86 1 73.15 ? C4' GFB 1430 A 1 HETATM 9 O O4' GFB . . . E 2 21.562 -11.868 17.382 1 71.41 ? O4' GFB 1430 A 1 HETATM 10 C C3' GFB . . . E 2 20.937 -10.554 15.506 1 77.78 ? C3' GFB 1430 A 1 HETATM 11 C C1' GFB . . . E 2 22.537 -12.089 16.382 1 70.15 ? C1' GFB 1430 A 1 HETATM 12 O O3' GFB . . . E 2 20.651 -9.15 15.338 1 85.33 ? O3' GFB 1430 A 1 HETATM 13 C C2' GFB . . . E 2 22.431 -10.883 15.473 1 71.5 ? C2' GFB 1430 A 1 HETATM 14 O O2' GFB . . . E 2 23.224 -9.806 15.996 1 65.92 ? O2' GFB 1430 A 1 HETATM 15 N N9 GFB . . . E 2 22.177 -13.261 15.52 1 84.67 ? N9 GFB 1430 A 1 HETATM 16 C C8 GFB . . . E 2 21.009 -13.924 15.412 1 75.83 ? C8 GFB 1430 A 1 HETATM 17 C C4 GFB . . . E 2 23.091 -13.881 14.763 1 81.36 ? C4 GFB 1430 A 1 HETATM 18 N N7 GFB . . . E 2 21.176 -14.952 14.546 1 72.98 ? N7 GFB 1430 A 1 HETATM 19 C C5 GFB . . . E 2 22.459 -14.944 14.13 1 76.47 ? C5 GFB 1430 A 1 HETATM 20 C C6 GFB . . . E 2 23.231 -15.724 13.266 1 76.62 ? C6 GFB 1430 A 1 HETATM 21 O O6 GFB . . . E 2 22.683 -16.694 12.682 1 76.52 ? O6 GFB 1430 A 1 HETATM 22 N N1 GFB . . . E 2 24.532 -15.422 13.079 1 77.4 ? N1 GFB 1430 A 1 HETATM 23 C C2 GFB . . . E 2 25.104 -14.375 13.718 1 80.08 ? C2 GFB 1430 A 1 HETATM 24 N N2 GFB . . . E 2 26.401 -14.031 13.563 1 80.91 ? N2 GFB 1430 A 1 HETATM 25 N N3 GFB . . . E 2 24.397 -13.617 14.557 1 82.31 ? N3 GFB 1430 A 1 HETATM 26 C C1 GFB . . . E 2 14.868 -8.976 18.517 1 173.97 ? C1 GFB 1430 A 1 HETATM 27 C C2A GFB . . . E 2 16.082 -8.564 19.373 1 173.94 ? C2A GFB 1430 A 1 HETATM 28 O O1 GFB . . . E 2 15.376 -9.372 17.252 1 172.45 ? O1 GFB 1430 A 1 HETATM 29 O O5 GFB . . . E 2 14.241 -10.161 19.015 1 175.47 ? O5 GFB 1430 A 1 HETATM 30 C C3 GFB . . . E 2 15.759 -8.451 20.862 1 173.45 ? C3 GFB 1430 A 1 HETATM 31 O O2 GFB . . . E 2 16.564 -7.301 18.924 1 174.33 ? O2 GFB 1430 A 1 HETATM 32 C C4A GFB . . . E 2 15.008 -9.7 21.327 1 174.38 ? C4A GFB 1430 A 1 HETATM 33 O O3 GFB . . . E 2 16.985 -8.264 21.615 1 172.18 ? O3 GFB 1430 A 1 HETATM 34 C C5A GFB . . . E 2 13.85 -10.102 20.402 1 174.94 ? C5A GFB 1430 A 1 HETATM 35 O O4 GFB . . . E 2 15.935 -10.792 21.385 1 174.25 ? O4 GFB 1430 A 1 HETATM 36 C C6A GFB . . . E 2 13.318 -11.478 20.79 1 174.12 ? C6A GFB 1430 A 1 HETATM 37 O O1X GFB . . . E 2 13.634 -10.785 15.938 1 92.03 ? O1X GFB 1430 A 1 HETATM 38 O O2X GFB . . . E 2 15.318 -11.84 17.555 1 90.2 ? O2X GFB 1430 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 63 _model_server_stats.query_time_ms 834 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 38 #