data_4GZ6 # _model_server_result.job_id hIVEkDDpjFzKrjoSCYyGGg _model_server_result.datetime_utc '2024-11-24 09:41:21' _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 4gz6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1501}' # _entry.id 4GZ6 # _exptl.entry_id 4GZ6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 623.419 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen 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 4GZ6 _cell.length_a 272.338 _cell.length_b 272.338 _cell.length_c 143.46 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4GZ6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 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 ? 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 dodecameric 12 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,Z 1 1 B,J,K,L,M,N,O,AA 2 1 C,P,Q,R,S,T,BA 3 1 D,U,V,W,X,Y,CA 4 1 D,U,V,W,X,Y,CA 5 2,3,4 A,B,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,Z,AA,BA 5 1,5,6 # 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' 1_554 x,y,z-1 1 0 0 0 1 0 0 0 1 0 0 -143.46 3 'crystal symmetry operation' 2_564 -y,x-y+1,z-1 -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -136.169 235.851626 -143.46 4 'crystal symmetry operation' 3_454 -x+y-1,-x,z-1 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -272.338 0 -143.46 5 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -136.169 235.851626 0 6 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -272.338 0 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 U N N # _chem_comp.formula 'C17 H27 N3 O16 P2 S' _chem_comp.formula_weight 623.419 _chem_comp.id 12V _chem_comp.mon_nstd_flag . _chem_comp.name '(2S,3R,4R,5S,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-thiopyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'URIDINE DIPHOSPHO-5-THIO-N-ACETYLGLUCOSAMINE' # 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 C1B N1 12V sing 1 n n C2 N1 12V sing 2 n n N1 C6 12V sing 3 n n O2 C2 12V doub 4 n n C2 N3 12V sing 5 n n N3 C4 12V sing 6 n n C4 O4 12V doub 7 n n C4 C5 12V sing 8 n n C6 C5 12V doub 9 n n C5 H5 12V sing 10 n n C6 H6 12V sing 11 n n O5B PA 12V sing 12 n n O1A PA 12V doub 13 n n PA O3A 12V sing 14 n n PA O2A 12V sing 15 n n O3A PB 12V sing 16 n n O1' PB 12V sing 17 n n PB O1B 12V doub 18 n n PB O2B 12V sing 19 n n S5' C1' 12V sing 20 n n C1' C2' 12V sing 21 n n C1' O1' 12V sing 22 n n C1' H1' 12V sing 23 n n C1B O4B 12V sing 24 n n C1B C2B 12V sing 25 n n C1B H1B 12V sing 26 n n C3' C2' 12V sing 27 n n C2' N2' 12V sing 28 n n C2' H2' 12V sing 29 n n N2' C7' 12V sing 30 n n N2' HN2' 12V sing 31 n n O2' C2B 12V sing 32 n n O2' HO2' 12V sing 33 n n O2A HO2A 12V sing 34 n n C3B C2B 12V sing 35 n n C2B H2B 12V sing 36 n n O2B HO2B 12V sing 37 n n C4' C3' 12V sing 38 n n C3' O3' 12V sing 39 n n C3' H3' 12V sing 40 n n O3' HO3' 12V sing 41 n n O3B C3B 12V sing 42 n n C3B C4B 12V sing 43 n n C3B H3B 12V sing 44 n n O3B HO3B 12V sing 45 n n C5' C4' 12V sing 46 n n O4' C4' 12V sing 47 n n C4' H4' 12V sing 48 n n O4' HO4' 12V sing 49 n n C4B O4B 12V sing 50 n n C4B C5B 12V sing 51 n n C4B H4B 12V sing 52 n n C6' C5' 12V sing 53 n n C5' S5' 12V sing 54 n n C5' H5' 12V sing 55 n n O5B C5B 12V sing 56 n n C5B H5B 12V sing 57 n n C5B H5BA 12V sing 58 n n O6' C6' 12V sing 59 n n C6' H6' 12V sing 60 n n C6' "H6'A" 12V sing 61 n n O6' HO6' 12V sing 62 n n O7' C7' 12V doub 63 n n C7' C8' 12V sing 64 n n C8' H8' 12V sing 65 n n C8' "H8'A" 12V sing 66 n n C8' "H8'B" 12V sing 67 n n N3 HN3 12V sing 68 n n # _atom_sites.entry_id 4GZ6 _atom_sites.fract_transf_matrix[1][1] 0.003672 _atom_sites.fract_transf_matrix[1][2] 0.00212 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00424 _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] 0.006971 _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 12V A 1 1501 1501 12V UD3 . F 3 SO4 A 1 1502 1601 SO4 SO4 . G 3 SO4 A 1 1503 1602 SO4 SO4 . H 3 SO4 A 1 1504 1603 SO4 SO4 . I 3 SO4 A 1 1505 1604 SO4 SO4 . J 2 12V B 1 1501 1501 12V UD3 . K 3 SO4 B 1 1502 1601 SO4 SO4 . L 3 SO4 B 1 1503 1602 SO4 SO4 . M 3 SO4 B 1 1504 1603 SO4 SO4 . N 3 SO4 B 1 1505 1604 SO4 SO4 . O 3 SO4 B 1 1506 1605 SO4 SO4 . P 2 12V C 1 1501 1501 12V UD3 . Q 3 SO4 C 1 1502 1601 SO4 SO4 . R 3 SO4 C 1 1503 1602 SO4 SO4 . S 3 SO4 C 1 1504 1603 SO4 SO4 . T 3 SO4 C 1 1505 1604 SO4 SO4 . U 2 12V D 1 1501 1501 12V UD3 . V 3 SO4 D 1 1502 1601 SO4 SO4 . W 3 SO4 D 1 1503 1602 SO4 SO4 . X 3 SO4 D 1 1504 1603 SO4 SO4 . Y 3 SO4 D 1 1505 1604 SO4 SO4 . Z 4 HOH A 1 1601 6 HOH HOH . Z 4 HOH A 2 1602 7 HOH HOH . Z 4 HOH A 3 1603 9 HOH HOH . Z 4 HOH A 4 1604 11 HOH HOH . Z 4 HOH A 5 1605 12 HOH HOH . Z 4 HOH A 6 1606 15 HOH HOH . Z 4 HOH A 7 1607 16 HOH HOH . Z 4 HOH A 8 1608 18 HOH HOH . Z 4 HOH A 9 1609 19 HOH HOH . Z 4 HOH A 10 1610 20 HOH HOH . Z 4 HOH A 11 1611 21 HOH HOH . Z 4 HOH A 12 1612 32 HOH HOH . Z 4 HOH A 13 1613 34 HOH HOH . Z 4 HOH A 14 1614 41 HOH HOH . Z 4 HOH A 15 1615 50 HOH HOH . Z 4 HOH A 16 1616 52 HOH HOH . AA 4 HOH B 1 1601 1 HOH HOH . AA 4 HOH B 2 1602 5 HOH HOH . AA 4 HOH B 3 1603 14 HOH HOH . AA 4 HOH B 4 1604 23 HOH HOH . AA 4 HOH B 5 1605 24 HOH HOH . AA 4 HOH B 6 1606 30 HOH HOH . AA 4 HOH B 7 1607 33 HOH HOH . AA 4 HOH B 8 1608 37 HOH HOH . AA 4 HOH B 9 1609 39 HOH HOH . AA 4 HOH B 10 1610 43 HOH HOH . AA 4 HOH B 11 1611 45 HOH HOH . AA 4 HOH B 12 1612 47 HOH HOH . AA 4 HOH B 13 1613 48 HOH HOH . BA 4 HOH C 1 1601 3 HOH HOH . BA 4 HOH C 2 1602 10 HOH HOH . BA 4 HOH C 3 1603 22 HOH HOH . BA 4 HOH C 4 1604 26 HOH HOH . BA 4 HOH C 5 1605 28 HOH HOH . BA 4 HOH C 6 1606 38 HOH HOH . BA 4 HOH C 7 1607 44 HOH HOH . CA 4 HOH D 1 1601 2 HOH HOH . CA 4 HOH D 2 1602 4 HOH HOH . CA 4 HOH D 3 1603 8 HOH HOH . CA 4 HOH D 4 1604 13 HOH HOH . CA 4 HOH D 5 1605 17 HOH HOH . CA 4 HOH D 6 1606 25 HOH HOH . CA 4 HOH D 7 1607 27 HOH HOH . CA 4 HOH D 8 1608 29 HOH HOH . CA 4 HOH D 9 1609 31 HOH HOH . CA 4 HOH D 10 1610 35 HOH HOH . CA 4 HOH D 11 1611 36 HOH HOH . CA 4 HOH D 12 1612 40 HOH HOH . CA 4 HOH D 13 1613 42 HOH HOH . CA 4 HOH D 14 1614 46 HOH HOH . CA 4 HOH D 15 1615 49 HOH HOH . CA 4 HOH D 16 1616 51 HOH HOH . CA 4 HOH D 17 1617 53 HOH HOH . CA 4 HOH D 18 1618 54 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 12V . . . J 2 -96.697 27.511 -25.991 1 57.88 ? N1 12V 1501 B 1 HETATM 2 C C2 12V . . . J 2 -95.969 28.725 -26.232 1 58.46 ? C2 12V 1501 B 1 HETATM 3 O O2 12V . . . J 2 -96.521 29.674 -26.761 1 59.25 ? O2 12V 1501 B 1 HETATM 4 N N3 12V . . . J 2 -94.611 28.792 -25.848 1 58.28 ? N3 12V 1501 B 1 HETATM 5 C C4 12V . . . J 2 -94.096 27.719 -25.283 1 58.7 ? C4 12V 1501 B 1 HETATM 6 O O4 12V . . . J 2 -92.788 27.774 -24.909 1 58.94 ? O4 12V 1501 B 1 HETATM 7 C C5 12V . . . J 2 -94.771 26.489 -25.016 1 58.98 ? C5 12V 1501 B 1 HETATM 8 C C6 12V . . . J 2 -96.095 26.435 -25.395 1 58.52 ? C6 12V 1501 B 1 HETATM 9 P PA 12V . . . J 2 -101.798 23.623 -23.344 1 63.4 ? PA 12V 1501 B 1 HETATM 10 P PB 12V . . . J 2 -102.27 21.233 -24.877 1 56.56 ? PB 12V 1501 B 1 HETATM 11 C C1' 12V . . . J 2 -104.92 21.929 -24.823 1 41.5 ? C1' 12V 1501 B 1 HETATM 12 O O1' 12V . . . J 2 -103.88 21.722 -25.59 1 42.24 ? O1' 12V 1501 B 1 HETATM 13 O O1A 12V . . . J 2 -103.207 23.889 -22.975 1 62.94 ? O1A 12V 1501 B 1 HETATM 14 C C1B 12V . . . J 2 -98.139 27.413 -26.386 1 57.26 ? C1B 12V 1501 B 1 HETATM 15 O O1B 12V . . . J 2 -102.49 20.699 -23.489 1 56.26 ? O1B 12V 1501 B 1 HETATM 16 C C2' 12V . . . J 2 -105.884 20.706 -24.644 1 74.58 ? C2' 12V 1501 B 1 HETATM 17 N N2' 12V . . . J 2 -105.241 19.599 -23.98 1 74.06 ? N2' 12V 1501 B 1 HETATM 18 O O2' 12V . . . J 2 -98.27 26.529 -28.648 1 58.03 ? O2' 12V 1501 B 1 HETATM 19 O O2A 12V . . . J 2 -100.598 23.425 -22.449 1 63.53 ? O2A 12V 1501 B 1 HETATM 20 C C2B 12V . . . J 2 -98.44 26.206 -27.303 1 57.51 ? C2B 12V 1501 B 1 HETATM 21 O O2B 12V . . . J 2 -101.67 20.513 -26.021 1 56.67 ? O2B 12V 1501 B 1 HETATM 22 C C3' 12V . . . J 2 -106.497 20.247 -26.006 1 67.66 ? C3' 12V 1501 B 1 HETATM 23 O O3' 12V . . . J 2 -107.417 19.227 -25.726 1 69.29 ? O3' 12V 1501 B 1 HETATM 24 O O3A 12V . . . J 2 -101.637 22.626 -24.568 1 58.84 ? O3A 12V 1501 B 1 HETATM 25 C C3B 12V . . . J 2 -99.935 25.956 -26.989 1 57.42 ? C3B 12V 1501 B 1 HETATM 26 O O3B 12V . . . J 2 -100.629 26.825 -27.818 1 57.56 ? O3B 12V 1501 B 1 HETATM 27 C C4' 12V . . . J 2 -107.339 21.311 -26.747 1 65.58 ? C4' 12V 1501 B 1 HETATM 28 O O4' 12V . . . J 2 -107.827 20.676 -27.9 1 64.19 ? O4' 12V 1501 B 1 HETATM 29 C C4B 12V . . . J 2 -100.068 26.432 -25.53 1 57.39 ? C4B 12V 1501 B 1 HETATM 30 O O4B 12V . . . J 2 -98.948 27.284 -25.277 1 57.21 ? O4B 12V 1501 B 1 HETATM 31 C C5' 12V . . . J 2 -106.509 22.512 -27.173 1 65.32 ? C5' 12V 1501 B 1 HETATM 32 S S5' 12V . . . J 2 -105.931 23.299 -25.664 1 70.9 ? S5' 12V 1501 B 1 HETATM 33 C C5B 12V . . . J 2 -100.032 25.26 -24.527 1 57.68 ? C5B 12V 1501 B 1 HETATM 34 O O5B 12V . . . J 2 -101.324 25.081 -24.148 1 58.12 ? O5B 12V 1501 B 1 HETATM 35 C C6' 12V . . . J 2 -107.327 23.686 -27.643 1 64.43 ? C6' 12V 1501 B 1 HETATM 36 O O6' 12V . . . J 2 -108.321 23.987 -26.701 1 64.39 ? O6' 12V 1501 B 1 HETATM 37 C C7' 12V . . . J 2 -105.446 19.368 -22.639 1 73.56 ? C7' 12V 1501 B 1 HETATM 38 O O7' 12V . . . J 2 -106.183 20.084 -21.949 1 73.49 ? O7' 12V 1501 B 1 HETATM 39 C C8' 12V . . . J 2 -104.733 18.196 -22.031 1 73.3 ? C8' 12V 1501 B 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #