data_2GRX # _model_server_result.job_id whF3X3PS-pO1A0Hyu5BkbA _model_server_result.datetime_utc '2024-11-18 04:25:12' _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 2grx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":980}' # _entry.id 2GRX # _exptl.entry_id 2GRX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 139.047 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-AMINO-VINYL-PHOSPHATE _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 118.86 _cell.angle_gamma 90 _cell.entry_id 2GRX _cell.length_a 234.32 _cell.length_b 91.84 _cell.length_c 138.51 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GRX _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 dimeric 2 author_and_software_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,G,H,I,J,K,L,M,N,O 1 1 B,D,F,P,Q,R,S,T,U,V,W,X,Y 2 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 N N N ? 8 X N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type 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 ? 3 2 1 GCN GCN C1 O1 . O6 HO6 . sing 2 ? 3 3 2 KDO GCN C2 O2 . O6 HO6 . sing 3 ? 3 4 3 KDO KDO C2 O2 . O4 HO4 . sing 4 ? 3 5 3 GMH KDO C1 O1 . O5 HO5 . 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 3 n E GCN 1 E 1 GCN A 920 GCN 3 n E GCN 2 E 2 GCN A 921 GCN 3 n E KDO 3 E 3 KDO A 970 KDO 3 n E KDO 4 E 4 KDO A 971 KDO 3 n E GMH 5 E 5 GMH A 960 GMH 3 n F GCN 1 F 1 GCN B 920 GCN 3 n F GCN 2 F 2 GCN B 921 GCN 3 n F KDO 3 F 3 KDO B 970 KDO 3 n F KDO 4 F 4 KDO B 971 KDO 3 n F GMH 5 F 5 GMH B 960 GMH # 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 318 A CYS 318 1_555 A SG CYS 329 A CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 703 A CYS 703 1_555 A SG CYS 709 A CYS 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 B SG CYS 318 B CYS 318 1_555 B SG CYS 329 B CYS 329 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 703 B CYS 703 1_555 B SG CYS 709 B CYS 709 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 H C1 FTT . A FTT 900 1_555 E N2 GCN . E GCN 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale2 J O3 FTT . A FTT 902 1_555 M C1 DAO . A DAO 930 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 0.894 ? covale ? covale3 J C1 FTT . A FTT 902 1_555 E N2 GCN . E GCN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 G P PO4 . A PO4 950 1_555 E O4 GCN . E GCN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.503 ? covale ? covale5 N P EAP . A EAP 980 1_555 E O4 GMH . E GMH 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.498 ? covale ? covale6 Q C1 FTT . B FTT 900 1_555 F N2 GCN . F GCN 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale7 S O3 FTT . B FTT 902 1_555 V C1 DAO . B DAO 930 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 0.894 ? covale ? covale8 S C1 FTT . B FTT 902 1_555 F N2 GCN . F GCN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale9 T O3 FTT . B FTT 903 1_555 W C1 MYR . B MYR 940 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? covale ? covale10 P P PO4 . B PO4 950 1_555 F O4 GCN . F GCN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.503 ? covale ? covale11 X P EAP . B EAP 980 1_555 F O4 GMH . F GMH 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale12 E O6 GCN . E GCN 1 1_555 E C1 GCN . E GCN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.39 ? covale ? covale13 E O6 GCN . E GCN 2 1_555 E C2 KDO . E KDO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.384 ? covale ? covale14 E O4 KDO . E KDO 3 1_555 E C2 KDO . E KDO 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale15 E O5 KDO . E KDO 3 1_555 E C1 GMH . E GMH 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? covale ? covale16 F O6 GCN . F GCN 1 1_555 F C1 GCN . F GCN 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale17 F O6 GCN . F GCN 2 1_555 F C2 KDO . F KDO 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.385 ? covale ? covale18 F O4 KDO . F KDO 3 1_555 F C2 KDO . F KDO 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.396 ? covale ? covale19 F O5 KDO . F KDO 3 1_555 F C1 GMH . F GMH 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.402 ? # _chem_comp.formula 'C2 H6 N O4 P' _chem_comp.formula_weight 139.047 _chem_comp.id EAP _chem_comp.mon_nstd_flag . _chem_comp.name 2-AMINO-VINYL-PHOSPHATE _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 O1 P EAP doub 128 n n O2 P EAP sing 129 n n O2 HO2 EAP sing 130 n n O3 P EAP sing 131 n n O3 HO3 EAP sing 132 n n O4 P EAP sing 133 n n O4 C1 EAP sing 134 n n C1 C2 EAP doub 135 e n C1 H11 EAP sing 136 n n C2 N3 EAP sing 137 n n C2 H21 EAP sing 138 n n N3 HN31 EAP sing 139 n n N3 HN32 EAP sing 140 n n # _atom_sites.entry_id 2GRX _atom_sites.fract_transf_matrix[1][1] 0.004268 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002352 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010889 _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] 0.008244 _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 G 4 PO4 A 1 950 950 PO4 PO4 . H 5 FTT A 1 900 900 FTT FTT . I 5 FTT A 1 901 901 FTT FTT . J 5 FTT A 1 902 902 FTT FTT . K 5 FTT A 1 903 903 FTT FTT . L 6 DPO A 1 910 910 DPO DPO . M 7 DAO A 1 930 930 DAO DAO . N 8 EAP A 1 980 980 EAP EAP . O 9 FCI A 1 1050 1050 FCI FCI . P 4 PO4 B 1 950 950 PO4 PO4 . Q 5 FTT B 1 900 900 FTT FTT . R 5 FTT B 1 901 901 FTT FTT . S 5 FTT B 1 902 902 FTT FTT . T 5 FTT B 1 903 903 FTT FTT . U 6 DPO B 1 910 910 DPO DPO . V 7 DAO B 1 930 930 DAO DAO . W 10 MYR B 1 940 940 MYR MYR . X 8 EAP B 1 980 980 EAP EAP . Y 9 FCI B 1 1050 1050 FCI FCI . # 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 O2 EAP . . . X 8 42.67 25.831 53.616 1 81.15 ? O2 EAP 980 B 1 HETATM 2 O O3 EAP . . . X 8 41.388 23.734 53.888 1 93.84 ? O3 EAP 980 B 1 HETATM 3 O O4 EAP . . . X 8 43.231 23.867 52.325 1 88.01 ? O4 EAP 980 B 1 HETATM 4 P P EAP . . . X 8 42.111 24.631 52.947 1 87.26 ? P EAP 980 B 1 HETATM 5 C C1 EAP . . . X 8 42.746 22.641 51.748 1 81.38 ? C1 EAP 980 B 1 HETATM 6 C C2 EAP . . . X 8 43.632 22.227 50.587 1 91.52 ? C2 EAP 980 B 1 HETATM 7 N N3 EAP . . . X 8 43.986 20.956 50.72 1 95.42 ? N3 EAP 980 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 7 #