data_4HO8 # _model_server_result.job_id ot_EKumDMba2eBb3U0oPXA _model_server_result.datetime_utc '2024-11-08 16:12:08' _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 4ho8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":300}' # _entry.id 4HO8 # _exptl.entry_id 4HO8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 566.302 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _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 90.13 _cell.angle_gamma 90 _cell.entry_id 4HO8 _cell.length_a 71.016 _cell.length_b 91.25 _cell.length_c 91.233 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4HO8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 PISA tetrameric 4 software_defined_assembly 5 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,H,I,AA 1 1 B,J,K,L,M,N,O,BA 2 1 C,P,Q,R,S,T,U,CA 3 1 D,V,W,X,Y,Z,DA 4 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA 5 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 J N N ? 2 P N N ? 2 V N N # _chem_comp.formula 'C15 H24 N2 O17 P2' _chem_comp.formula_weight 566.302 _chem_comp.id UPG _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" # 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 N1 C2 UPG sing 394 n n N1 C6 UPG sing 395 n n N1 C1C UPG sing 396 n n C2 N3 UPG sing 397 n n C2 O2 UPG doub 398 n n N3 C4 UPG sing 399 n n N3 HN3 UPG sing 400 n n C4 C5 UPG sing 401 n n C4 O4 UPG doub 402 n n C5 C6 UPG doub 403 n n C5 H5 UPG sing 404 n n C6 H6 UPG sing 405 n n C1C C2C UPG sing 406 n n C1C O4C UPG sing 407 n n C1C H1C UPG sing 408 n n C2C O2C UPG sing 409 n n C2C C3C UPG sing 410 n n C2C H2C UPG sing 411 n n O2C HO2C UPG sing 412 n n C3C C4C UPG sing 413 n n C3C O3C UPG sing 414 n n C3C H3C UPG sing 415 n n C4C O4C UPG sing 416 n n C4C C5C UPG sing 417 n n C4C H4C UPG sing 418 n n O3C HO3C UPG sing 419 n n C5C O5C UPG sing 420 n n C5C H5C1 UPG sing 421 n n C5C H5C2 UPG sing 422 n n O5C PA UPG sing 423 n n PA O1A UPG doub 424 n n PA O2A UPG sing 425 n n PA O3A UPG sing 426 n n O2A HOA2 UPG sing 427 n n O3A PB UPG sing 428 n n PB O1B UPG doub 429 n n PB O2B UPG sing 430 n n PB O3B UPG sing 431 n n O2B HOB2 UPG sing 432 n n O3B C1' UPG sing 433 n n C1' C2' UPG sing 434 n n C1' O5' UPG sing 435 n n C1' H1' UPG sing 436 n n C2' C3' UPG sing 437 n n C2' O2' UPG sing 438 n n C2' H2' UPG sing 439 n n C3' C4' UPG sing 440 n n C3' O3' UPG sing 441 n n C3' H3' UPG sing 442 n n C4' C5' UPG sing 443 n n C4' O4' UPG sing 444 n n C4' H4' UPG sing 445 n n C5' C6' UPG sing 446 n n C5' O5' UPG sing 447 n n C5' H5' UPG sing 448 n n C6' O6' UPG sing 449 n n C6' "H6'1" UPG sing 450 n n C6' "H6'2" UPG sing 451 n n O2' HO2' UPG sing 452 n n O3' HO3' UPG sing 453 n n O4' HO4' UPG sing 454 n n O6' HO6' UPG sing 455 n n # _atom_sites.entry_id 4HO8 _atom_sites.fract_transf_matrix[1][1] 0.014081 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000033 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010959 _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] 0.010961 _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 UPG A 1 300 300 UPG UPG . F 3 THM A 1 301 301 THM THM . G 4 SO4 A 1 302 302 SO4 SO4 . H 4 SO4 A 1 303 303 SO4 SO4 . I 4 SO4 A 1 304 304 SO4 SO4 . J 2 UPG B 1 300 300 UPG UPG . K 3 THM B 1 301 301 THM THM . L 4 SO4 B 1 302 302 SO4 SO4 . M 4 SO4 B 1 303 303 SO4 SO4 . N 4 SO4 B 1 304 304 SO4 SO4 . O 4 SO4 B 1 305 305 SO4 SO4 . P 2 UPG C 1 300 300 UPG UPG . Q 3 THM C 1 301 301 THM THM . R 4 SO4 C 1 302 302 SO4 SO4 . S 4 SO4 C 1 303 303 SO4 SO4 . T 4 SO4 C 1 304 304 SO4 SO4 . U 4 SO4 C 1 305 305 SO4 SO4 . V 2 UPG D 1 300 300 UPG UPG . W 3 THM D 1 301 301 THM THM . X 4 SO4 D 1 302 302 SO4 SO4 . Y 4 SO4 D 1 303 303 SO4 SO4 . Z 4 SO4 D 1 304 304 SO4 SO4 . AA 5 HOH A 1 401 4 HOH HOH . AA 5 HOH A 2 402 8 HOH HOH . AA 5 HOH A 3 403 13 HOH HOH . AA 5 HOH A 4 404 18 HOH HOH . AA 5 HOH A 5 405 21 HOH HOH . AA 5 HOH A 6 406 22 HOH HOH . AA 5 HOH A 7 407 23 HOH HOH . AA 5 HOH A 8 408 24 HOH HOH . AA 5 HOH A 9 409 26 HOH HOH . AA 5 HOH A 10 410 31 HOH HOH . AA 5 HOH A 11 411 40 HOH HOH . AA 5 HOH A 12 412 43 HOH HOH . AA 5 HOH A 13 413 45 HOH HOH . AA 5 HOH A 14 414 46 HOH HOH . AA 5 HOH A 15 415 51 HOH HOH . AA 5 HOH A 16 416 56 HOH HOH . AA 5 HOH A 17 417 61 HOH HOH . AA 5 HOH A 18 418 63 HOH HOH . AA 5 HOH A 19 419 65 HOH HOH . AA 5 HOH A 20 420 71 HOH HOH . AA 5 HOH A 21 421 75 HOH HOH . AA 5 HOH A 22 422 76 HOH HOH . AA 5 HOH A 23 423 78 HOH HOH . AA 5 HOH A 24 424 81 HOH HOH . AA 5 HOH A 25 425 86 HOH HOH . AA 5 HOH A 26 426 87 HOH HOH . AA 5 HOH A 27 427 93 HOH HOH . AA 5 HOH A 28 428 94 HOH HOH . AA 5 HOH A 29 429 103 HOH HOH . AA 5 HOH A 30 430 104 HOH HOH . AA 5 HOH A 31 431 107 HOH HOH . AA 5 HOH A 32 432 111 HOH HOH . AA 5 HOH A 33 433 119 HOH HOH . AA 5 HOH A 34 434 124 HOH HOH . AA 5 HOH A 35 435 127 HOH HOH . AA 5 HOH A 36 436 128 HOH HOH . AA 5 HOH A 37 437 130 HOH HOH . AA 5 HOH A 38 438 131 HOH HOH . AA 5 HOH A 39 439 132 HOH HOH . AA 5 HOH A 40 440 134 HOH HOH . AA 5 HOH A 41 441 139 HOH HOH . AA 5 HOH A 42 442 143 HOH HOH . AA 5 HOH A 43 443 153 HOH HOH . AA 5 HOH A 44 444 116 HOH HOH . BA 5 HOH B 1 401 2 HOH HOH . BA 5 HOH B 2 402 3 HOH HOH . BA 5 HOH B 3 403 5 HOH HOH . BA 5 HOH B 4 404 10 HOH HOH . BA 5 HOH B 5 405 14 HOH HOH . BA 5 HOH B 6 406 17 HOH HOH . BA 5 HOH B 7 407 20 HOH HOH . BA 5 HOH B 8 408 28 HOH HOH . BA 5 HOH B 9 409 33 HOH HOH . BA 5 HOH B 10 410 34 HOH HOH . BA 5 HOH B 11 411 38 HOH HOH . BA 5 HOH B 12 412 42 HOH HOH . BA 5 HOH B 13 413 44 HOH HOH . BA 5 HOH B 14 414 50 HOH HOH . BA 5 HOH B 15 415 58 HOH HOH . BA 5 HOH B 16 416 60 HOH HOH . BA 5 HOH B 17 417 62 HOH HOH . BA 5 HOH B 18 418 66 HOH HOH . BA 5 HOH B 19 419 69 HOH HOH . BA 5 HOH B 20 420 73 HOH HOH . BA 5 HOH B 21 421 77 HOH HOH . BA 5 HOH B 22 422 82 HOH HOH . BA 5 HOH B 23 423 84 HOH HOH . BA 5 HOH B 24 424 88 HOH HOH . BA 5 HOH B 25 425 92 HOH HOH . BA 5 HOH B 26 426 96 HOH HOH . BA 5 HOH B 27 427 99 HOH HOH . BA 5 HOH B 28 428 101 HOH HOH . BA 5 HOH B 29 429 102 HOH HOH . BA 5 HOH B 30 430 105 HOH HOH . BA 5 HOH B 31 431 110 HOH HOH . BA 5 HOH B 32 432 112 HOH HOH . BA 5 HOH B 33 433 114 HOH HOH . BA 5 HOH B 34 434 120 HOH HOH . BA 5 HOH B 35 435 135 HOH HOH . BA 5 HOH B 36 436 138 HOH HOH . BA 5 HOH B 37 437 140 HOH HOH . BA 5 HOH B 38 438 142 HOH HOH . BA 5 HOH B 39 439 144 HOH HOH . BA 5 HOH B 40 440 147 HOH HOH . CA 5 HOH C 1 401 1 HOH HOH . CA 5 HOH C 2 402 7 HOH HOH . CA 5 HOH C 3 403 12 HOH HOH . CA 5 HOH C 4 404 27 HOH HOH . CA 5 HOH C 5 405 29 HOH HOH . CA 5 HOH C 6 406 30 HOH HOH . CA 5 HOH C 7 407 35 HOH HOH . CA 5 HOH C 8 408 41 HOH HOH . CA 5 HOH C 9 409 47 HOH HOH . CA 5 HOH C 10 410 52 HOH HOH . CA 5 HOH C 11 411 53 HOH HOH . CA 5 HOH C 12 412 54 HOH HOH . CA 5 HOH C 13 413 57 HOH HOH . CA 5 HOH C 14 414 59 HOH HOH . CA 5 HOH C 15 415 67 HOH HOH . CA 5 HOH C 16 416 68 HOH HOH . CA 5 HOH C 17 417 70 HOH HOH . CA 5 HOH C 18 418 72 HOH HOH . CA 5 HOH C 19 419 80 HOH HOH . CA 5 HOH C 20 420 90 HOH HOH . CA 5 HOH C 21 421 95 HOH HOH . CA 5 HOH C 22 422 106 HOH HOH . CA 5 HOH C 23 423 109 HOH HOH . CA 5 HOH C 24 424 115 HOH HOH . CA 5 HOH C 25 425 117 HOH HOH . CA 5 HOH C 26 426 118 HOH HOH . CA 5 HOH C 27 427 121 HOH HOH . CA 5 HOH C 28 428 123 HOH HOH . CA 5 HOH C 29 429 129 HOH HOH . CA 5 HOH C 30 430 136 HOH HOH . CA 5 HOH C 31 431 137 HOH HOH . CA 5 HOH C 32 432 148 HOH HOH . CA 5 HOH C 33 433 150 HOH HOH . CA 5 HOH C 34 434 151 HOH HOH . CA 5 HOH C 35 435 154 HOH HOH . CA 5 HOH C 36 436 155 HOH HOH . DA 5 HOH D 1 401 6 HOH HOH . DA 5 HOH D 2 402 9 HOH HOH . DA 5 HOH D 3 403 11 HOH HOH . DA 5 HOH D 4 404 15 HOH HOH . DA 5 HOH D 5 405 16 HOH HOH . DA 5 HOH D 6 406 19 HOH HOH . DA 5 HOH D 7 407 25 HOH HOH . DA 5 HOH D 8 408 32 HOH HOH . DA 5 HOH D 9 409 36 HOH HOH . DA 5 HOH D 10 410 37 HOH HOH . DA 5 HOH D 11 411 39 HOH HOH . DA 5 HOH D 12 412 48 HOH HOH . DA 5 HOH D 13 413 49 HOH HOH . DA 5 HOH D 14 414 55 HOH HOH . DA 5 HOH D 15 415 64 HOH HOH . DA 5 HOH D 16 416 74 HOH HOH . DA 5 HOH D 17 417 79 HOH HOH . DA 5 HOH D 18 418 83 HOH HOH . DA 5 HOH D 19 419 85 HOH HOH . DA 5 HOH D 20 420 89 HOH HOH . DA 5 HOH D 21 421 91 HOH HOH . DA 5 HOH D 22 422 97 HOH HOH . DA 5 HOH D 23 423 98 HOH HOH . DA 5 HOH D 24 424 100 HOH HOH . DA 5 HOH D 25 425 108 HOH HOH . DA 5 HOH D 26 426 113 HOH HOH . DA 5 HOH D 27 427 122 HOH HOH . DA 5 HOH D 28 428 125 HOH HOH . DA 5 HOH D 29 429 126 HOH HOH . DA 5 HOH D 30 430 133 HOH HOH . DA 5 HOH D 31 431 141 HOH HOH . DA 5 HOH D 32 432 145 HOH HOH . DA 5 HOH D 33 433 146 HOH HOH . DA 5 HOH D 34 434 149 HOH HOH . DA 5 HOH D 35 435 152 HOH HOH . DA 5 HOH D 36 436 156 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 N N1 UPG . . . V 2 -3.917 -6.586 40.659 1 41.46 ? N1 UPG 300 D 1 HETATM 2 C C2 UPG . . . V 2 -5.22 -7.054 40.453 1 40.5 ? C2 UPG 300 D 1 HETATM 3 N N3 UPG . . . V 2 -6.2 -6.761 41.322 1 41.4 ? N3 UPG 300 D 1 HETATM 4 C C4 UPG . . . V 2 -5.95 -6.005 42.41 1 43.38 ? C4 UPG 300 D 1 HETATM 5 C C5 UPG . . . V 2 -4.65 -5.516 42.658 1 42.11 ? C5 UPG 300 D 1 HETATM 6 C C6 UPG . . . V 2 -3.633 -5.827 41.754 1 41.97 ? C6 UPG 300 D 1 HETATM 7 O O2 UPG . . . V 2 -5.453 -7.77 39.462 1 40.06 ? O2 UPG 300 D 1 HETATM 8 O O4 UPG . . . V 2 -6.887 -5.753 43.205 1 44.22 ? O4 UPG 300 D 1 HETATM 9 C C1C UPG . . . V 2 -2.891 -6.982 39.669 1 43.19 ? C1C UPG 300 D 1 HETATM 10 C C2C UPG . . . V 2 -2.061 -5.818 39.127 1 43.99 ? C2C UPG 300 D 1 HETATM 11 O O2C UPG . . . V 2 -2.545 -5.371 37.844 1 45.98 ? O2C UPG 300 D 1 HETATM 12 C C3C UPG . . . V 2 -0.681 -6.431 39.038 1 43.54 ? C3C UPG 300 D 1 HETATM 13 C C4C UPG . . . V 2 -0.646 -7.349 40.225 1 43.1 ? C4C UPG 300 D 1 HETATM 14 O O4C UPG . . . V 2 -1.947 -7.92 40.24 1 43.12 ? O4C UPG 300 D 1 HETATM 15 O O3C UPG . . . V 2 -0.575 -7.238 37.851 1 43.28 ? O3C UPG 300 D 1 HETATM 16 C C5C UPG . . . V 2 -0.597 -6.501 41.475 1 45.2 ? C5C UPG 300 D 1 HETATM 17 O O5C UPG . . . V 2 0.693 -6.083 41.808 1 45.84 ? O5C UPG 300 D 1 HETATM 18 P PA UPG . . . V 2 1.211 -4.648 41.347 1 45.54 ? PA UPG 300 D 1 HETATM 19 O O1A UPG . . . V 2 1.685 -4.798 39.93 1 44.99 ? O1A UPG 300 D 1 HETATM 20 O O2A UPG . . . V 2 0.227 -3.533 41.546 1 48.47 ? O2A UPG 300 D 1 HETATM 21 O O3A UPG . . . V 2 2.441 -4.412 42.339 1 46.55 ? O3A UPG 300 D 1 HETATM 22 P PB UPG . . . V 2 2.242 -4.473 43.922 1 45.69 ? PB UPG 300 D 1 HETATM 23 O O1B UPG . . . V 2 0.832 -4.684 44.319 1 47.38 ? O1B UPG 300 D 1 HETATM 24 O O2B UPG . . . V 2 2.762 -3.186 44.471 1 49.1 ? O2B UPG 300 D 1 HETATM 25 O O3B UPG . . . V 2 3.183 -5.679 44.481 1 48.34 ? O3B UPG 300 D 1 HETATM 26 C C1' UPG . . . V 2 2.733 -7.001 44.77 1 47.45 ? C1' UPG 300 D 1 HETATM 27 C C2' UPG . . . V 2 2.988 -7.331 46.222 1 48.02 ? C2' UPG 300 D 1 HETATM 28 C C3' UPG . . . V 2 4.481 -7.347 46.579 1 49.54 ? C3' UPG 300 D 1 HETATM 29 C C4' UPG . . . V 2 5.29 -8.177 45.615 1 50.57 ? C4' UPG 300 D 1 HETATM 30 C C5' UPG . . . V 2 4.886 -7.935 44.165 1 50.28 ? C5' UPG 300 D 1 HETATM 31 C C6' UPG . . . V 2 5.474 -9.036 43.32 1 48.34 ? C6' UPG 300 D 1 HETATM 32 O O2' UPG . . . V 2 2.338 -6.353 47.003 1 49.39 ? O2' UPG 300 D 1 HETATM 33 O O3' UPG . . . V 2 4.73 -7.889 47.89 1 50.85 ? O3' UPG 300 D 1 HETATM 34 O O4' UPG . . . V 2 6.685 -7.859 45.82 1 51.61 ? O4' UPG 300 D 1 HETATM 35 O O5' UPG . . . V 2 3.451 -7.941 43.977 1 49.49 ? O5' UPG 300 D 1 HETATM 36 O O6' UPG . . . V 2 4.702 -9.109 42.131 1 50.54 ? O6' UPG 300 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 36 #