data_4RUB # _model_server_result.job_id 1iMjRB03MwNtX0A_mA-0aA _model_server_result.datetime_utc '2024-11-23 20:22:38' _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 4rub # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":490}' # _entry.id 4RUB # _exptl.entry_id 4RUB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 356.115 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE _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 4RUB _cell.length_a 204.6 _cell.length_b 204.6 _cell.length_c 117.4 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4RUB _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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,S,T _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 5_555 x-y,-y,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 0 78.266667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 J N N ? 4 M N N ? 4 P N N ? 4 S 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 247 A CYS 247 1_555 G SG CYS 247 D CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf2 A SG CYS 449 A CYS 449 1_555 A SG CYS 459 A CYS 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? disulf ? disulf3 C SG CYS 247 B CYS 247 1_555 E SG CYS 247 C CYS 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.758 ? disulf ? disulf4 C SG CYS 449 B CYS 449 1_555 C SG CYS 459 B CYS 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? disulf ? disulf5 E SG CYS 449 C CYS 449 1_555 E SG CYS 459 C CYS 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf6 G SG CYS 449 D CYS 449 1_555 G SG CYS 459 D CYS 459 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? covale ? covale1 A NZ LYS 201 A LYS 201 1_555 K C FMT . A FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.236 ? covale ? covale2 C NZ LYS 201 B LYS 201 1_555 N C FMT . B FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.269 ? covale ? covale3 E NZ LYS 201 C LYS 201 1_555 Q C FMT . C FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.293 ? covale ? covale4 G NZ LYS 201 D LYS 201 1_555 T C FMT . D FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.28 ? metalc ? metalc1 A OD1 ASP 203 A ASP 203 1_555 I MG MG . A MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc2 A OE1 GLU 204 A GLU 204 1_555 I MG MG . A MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.859 ? metalc ? metalc3 J O2 CAP . A CAP 490 1_555 I MG MG . A MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc4 J O4 CAP . A CAP 490 1_555 I MG MG . A MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc5 J O7 CAP . A CAP 490 1_555 I MG MG . A MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc6 I MG MG . A MG 491 1_555 K O1 FMT . A FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.277 ? metalc ? metalc7 I MG MG . A MG 491 1_555 K O2 FMT . A FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc8 C OD1 ASP 203 B ASP 203 1_555 L MG MG . B MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc9 C OE1 GLU 204 B GLU 204 1_555 L MG MG . B MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc10 M O2 CAP . B CAP 490 1_555 L MG MG . B MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc11 M O4 CAP . B CAP 490 1_555 L MG MG . B MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc12 M O7 CAP . B CAP 490 1_555 L MG MG . B MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc13 L MG MG . B MG 491 1_555 N O1 FMT . B FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.497 ? metalc ? metalc14 L MG MG . B MG 491 1_555 N O2 FMT . B FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc15 E OD1 ASP 203 C ASP 203 1_555 O MG MG . C MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.425 ? metalc ? metalc16 E OE1 GLU 204 C GLU 204 1_555 O MG MG . C MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc17 P O4 CAP . C CAP 490 1_555 O MG MG . C MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc18 P O7 CAP . C CAP 490 1_555 O MG MG . C MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc19 P O2 CAP . C CAP 490 1_555 O MG MG . C MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc20 O MG MG . C MG 491 1_555 Q O1 FMT . C FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.231 ? metalc ? metalc21 O MG MG . C MG 491 1_555 Q O2 FMT . C FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.64 ? metalc ? metalc22 G OD1 ASP 203 D ASP 203 1_555 R MG MG . D MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc23 G OE1 GLU 204 D GLU 204 1_555 R MG MG . D MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.775 ? metalc ? metalc24 S O4 CAP . D CAP 490 1_555 R MG MG . D MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc25 S O7 CAP . D CAP 490 1_555 R MG MG . D MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.675 ? metalc ? metalc26 S O2 CAP . D CAP 490 1_555 R MG MG . D MG 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc27 R MG MG . D MG 491 1_555 T O2 FMT . D FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.498 ? metalc ? metalc28 R MG MG . D MG 491 1_555 T O1 FMT . D FMT 492 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _chem_comp.formula 'C6 H14 O13 P2' _chem_comp.formula_weight 356.115 _chem_comp.id CAP _chem_comp.mon_nstd_flag . _chem_comp.name 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE _chem_comp.type 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 C1 C2 CAP sing 70 n n C1 O1 CAP sing 71 n n C1 H11 CAP sing 72 n n C1 H12 CAP sing 73 n n C2 C3 CAP sing 74 n n C2 C CAP sing 75 n n C2 O2 CAP sing 76 n n C3 C4 CAP sing 77 n n C3 O3 CAP sing 78 n n C3 H3 CAP sing 79 n n C4 C5 CAP sing 80 n n C4 O4 CAP sing 81 n n C4 H4 CAP sing 82 n n C5 O5 CAP sing 83 n n C5 H51 CAP sing 84 n n C5 H52 CAP sing 85 n n C O6 CAP doub 86 n n C O7 CAP sing 87 n n O1 P1 CAP sing 88 n n O2 HO2 CAP sing 89 n n O3 HO3 CAP sing 90 n n O4 HO4 CAP sing 91 n n O5 P2 CAP sing 92 n n O7 HO7 CAP sing 93 n n P1 O1P CAP doub 94 n n P1 O2P CAP sing 95 n n P1 O3P CAP sing 96 n n P2 O4P CAP doub 97 n n P2 O5P CAP sing 98 n n P2 O6P CAP sing 99 n n O2P HOP2 CAP sing 100 n n O3P HOP3 CAP sing 101 n n O5P HOP5 CAP sing 102 n n O6P HOP6 CAP sing 103 n n # _atom_sites.entry_id 4RUB _atom_sites.fract_transf_matrix[1][1] 0.004888 _atom_sites.fract_transf_matrix[1][2] 0.002822 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005644 _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] 0.008518 _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 I 3 MG A 1 491 491 MG MG . J 4 CAP A 1 490 490 CAP CAP . K 5 FMT A 1 492 201 FMT CBX . L 3 MG B 1 491 491 MG MG . M 4 CAP B 1 490 490 CAP CAP . N 5 FMT B 1 492 201 FMT CBX . O 3 MG C 1 491 491 MG MG . P 4 CAP C 1 490 490 CAP CAP . Q 5 FMT C 1 492 201 FMT CBX . R 3 MG D 1 491 491 MG MG . S 4 CAP D 1 490 490 CAP CAP . T 5 FMT D 1 492 201 FMT CBX . # 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 CAP . . . P 4 56.807 -31.037 18.147 1 20.04 ? C1 CAP 490 C 1 HETATM 2 C C2 CAP . . . P 4 58.227 -30.574 18.314 1 20.08 ? C2 CAP 490 C 1 HETATM 3 C C3 CAP . . . P 4 58.781 -31.786 19.098 1 19.94 ? C3 CAP 490 C 1 HETATM 4 C C4 CAP . . . P 4 59.878 -31.491 20.044 1 19.63 ? C4 CAP 490 C 1 HETATM 5 C C5 CAP . . . P 4 60.49 -32.653 19.374 1 18.99 ? C5 CAP 490 C 1 HETATM 6 C C CAP . . . P 4 58.947 -30.178 17.049 1 20.31 ? C CAP 490 C 1 HETATM 7 O O1 CAP . . . P 4 55.972 -30.314 17.294 1 19.69 ? O1 CAP 490 C 1 HETATM 8 O O2 CAP . . . P 4 58.246 -29.227 18.54 1 19.8 ? O2 CAP 490 C 1 HETATM 9 O O3 CAP . . . P 4 58.375 -32.449 20.32 1 20.4 ? O3 CAP 490 C 1 HETATM 10 O O4 CAP . . . P 4 60.047 -30.162 19.667 1 19.84 ? O4 CAP 490 C 1 HETATM 11 O O5 CAP . . . P 4 61.183 -33.305 20.317 1 18.64 ? O5 CAP 490 C 1 HETATM 12 O O6 CAP . . . P 4 58.95 -31.03 16.144 1 21.04 ? O6 CAP 490 C 1 HETATM 13 O O7 CAP . . . P 4 59.486 -29.107 16.839 1 20.23 ? O7 CAP 490 C 1 HETATM 14 P P1 CAP . . . P 4 54.693 -31.194 16.952 1 18.75 ? P1 CAP 490 C 1 HETATM 15 P P2 CAP . . . P 4 61.144 -34.221 21.578 1 18.86 ? P2 CAP 490 C 1 HETATM 16 O O1P CAP . . . P 4 53.96 -30.4 15.774 1 18.34 ? O1P CAP 490 C 1 HETATM 17 O O2P CAP . . . P 4 53.99 -31.434 18.193 1 18.9 ? O2P CAP 490 C 1 HETATM 18 O O3P CAP . . . P 4 55.501 -32.358 16.319 1 19.07 ? O3P CAP 490 C 1 HETATM 19 O O4P CAP . . . P 4 59.987 -33.993 22.371 1 18.7 ? O4P CAP 490 C 1 HETATM 20 O O5P CAP . . . P 4 61.562 -35.734 21.119 1 18.96 ? O5P CAP 490 C 1 HETATM 21 O O6P CAP . . . P 4 62.497 -34.017 22.412 1 19.35 ? O6P CAP 490 C 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 21 #