0.014286 0.008248 0.000000 0.000000 0.016496 0.000000 0.000000 0.000000 0.006589 0.00000 0.00000 0.00000 Meyer, P. Janin, J. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 18 90.00 90.00 120.00 70.000 70.000 151.770 C10 H15 N5 O10 P2 427.201 n ADENOSINE-5'-DIPHOSPHATE non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking Mg 2 24.305 MAGNESIUM ION non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking O4 P -3 94.971 PHOSPHATE ION non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Biochemistry BICHAW 0033 0006-2960 38 4701 4711 10.1021/bi9827565 10200157 Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase. 1999 US Biochemistry BICHAW 0033 0006-2960 34 11062 Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium 1995 US Biochemistry BICHAW 0033 0006-2960 33 459 Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase 1994 10.2210/pdb1b4s/pdb pdb_00001b4s 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 IMAGE PLATE 1998-07 MARRESEARCH M x-ray 1 1.375 1.0 D41A LURE 1.375 SYNCHROTRON LURE BEAMLINE D41A 16735.242 NUCLEOSIDE DIPHOSPHATE KINASE 2.7.4.6 H122G 3 man polymer 94.971 PHOSPHATE ION 3 syn non-polymer 24.305 MAGNESIUM ION 3 syn non-polymer 427.201 ADENOSINE-5'-DIPHOSPHATE 3 syn non-polymer 18.015 water 108 nat water NDPK no no MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIGGSDSVESANREIALWFKPEELLTEVKPNPNLYE A,B,C polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Dictyostelium Escherichia sample 44689 Dictyostelium discoideum 562 Escherichia coli 1 2.14 42.44 7.5 pH 7.5 database_2 pdbx_database_status pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site pdbx_initial_refinement_model repository Initial release Version format compliance Version format compliance Database references Derived calculations Other Refinement description 1 0 1999-06-15 1 1 2008-03-24 1 2 2011-07-13 1 3 2021-11-03 1 4 2023-08-02 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.value _struct_conn.pdbx_dist_value _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1998-12-28 REL PO4 PHOSPHATE ION MG MAGNESIUM ION ADP ADENOSINE-5'-DIPHOSPHATE HOH water 1KDN PDB experimental model PO4 161 2 PO4 PO4 161 A MG 162 3 MG MG 162 A ADP 160 4 ADP ADP 160 A PO4 161 2 PO4 PO4 161 B MG 162 3 MG MG 162 B ADP 160 4 ADP ADP 160 B PO4 161 2 PO4 PO4 161 C MG 162 3 MG MG 162 C ADP 160 4 ADP ADP 160 C HOH 1 5 HOH HOH 163 A HOH 5 5 HOH HOH 164 A HOH 6 5 HOH HOH 165 A HOH 7 5 HOH HOH 166 A HOH 10 5 HOH HOH 167 A HOH 12 5 HOH HOH 168 A HOH 19 5 HOH HOH 169 A HOH 23 5 HOH HOH 170 A HOH 24 5 HOH HOH 171 A HOH 29 5 HOH HOH 172 A HOH 31 5 HOH HOH 173 A HOH 33 5 HOH HOH 174 A HOH 37 5 HOH HOH 175 A HOH 39 5 HOH HOH 176 A HOH 45 5 HOH HOH 177 A HOH 48 5 HOH HOH 178 A HOH 49 5 HOH HOH 179 A HOH 50 5 HOH HOH 180 A HOH 51 5 HOH HOH 181 A HOH 66 5 HOH HOH 182 A HOH 67 5 HOH HOH 183 A HOH 68 5 HOH HOH 184 A HOH 70 5 HOH HOH 185 A HOH 71 5 HOH HOH 186 A HOH 75 5 HOH HOH 187 A HOH 78 5 HOH HOH 188 A HOH 81 5 HOH HOH 189 A HOH 86 5 HOH HOH 190 A HOH 87 5 HOH HOH 191 A HOH 90 5 HOH HOH 192 A HOH 94 5 HOH HOH 193 A HOH 96 5 HOH HOH 194 A HOH 100 5 HOH HOH 195 A HOH 101 5 HOH HOH 196 A HOH 105 5 HOH HOH 197 A HOH 3 5 HOH HOH 163 B HOH 4 5 HOH HOH 164 B HOH 8 5 HOH HOH 165 B HOH 13 5 HOH HOH 166 B HOH 16 5 HOH HOH 167 B HOH 17 5 HOH HOH 168 B HOH 18 5 HOH HOH 169 B HOH 21 5 HOH HOH 170 B HOH 25 5 HOH HOH 171 B HOH 30 5 HOH HOH 172 B HOH 34 5 HOH HOH 173 B HOH 35 5 HOH HOH 174 B HOH 40 5 HOH HOH 175 B HOH 41 5 HOH HOH 176 B HOH 43 5 HOH HOH 177 B HOH 44 5 HOH HOH 178 B HOH 46 5 HOH HOH 179 B HOH 47 5 HOH HOH 180 B HOH 52 5 HOH HOH 181 B HOH 62 5 HOH HOH 182 B HOH 63 5 HOH HOH 183 B HOH 65 5 HOH HOH 184 B HOH 69 5 HOH HOH 185 B HOH 73 5 HOH HOH 186 B HOH 77 5 HOH HOH 187 B HOH 80 5 HOH HOH 188 B HOH 84 5 HOH HOH 189 B HOH 85 5 HOH HOH 190 B HOH 88 5 HOH HOH 191 B HOH 89 5 HOH HOH 192 B HOH 91 5 HOH HOH 193 B HOH 97 5 HOH HOH 194 B HOH 99 5 HOH HOH 195 B HOH 103 5 HOH HOH 196 B HOH 104 5 HOH HOH 197 B HOH 107 5 HOH HOH 198 B HOH 110 5 HOH HOH 199 B HOH 114 5 HOH HOH 200 B HOH 116 5 HOH HOH 201 B HOH 119 5 HOH HOH 202 B HOH 102 5 HOH HOH 203 B HOH 108 5 HOH HOH 204 B HOH 111 5 HOH HOH 205 B HOH 2 5 HOH HOH 163 C HOH 9 5 HOH HOH 164 C HOH 11 5 HOH HOH 165 C HOH 20 5 HOH HOH 166 C HOH 22 5 HOH HOH 167 C HOH 27 5 HOH HOH 168 C HOH 28 5 HOH HOH 169 C HOH 32 5 HOH HOH 170 C HOH 36 5 HOH HOH 171 C HOH 38 5 HOH HOH 172 C HOH 53 5 HOH HOH 173 C HOH 60 5 HOH HOH 174 C HOH 61 5 HOH HOH 175 C HOH 64 5 HOH HOH 176 C HOH 72 5 HOH HOH 177 C HOH 74 5 HOH HOH 178 C HOH 76 5 HOH HOH 179 C HOH 79 5 HOH HOH 180 C HOH 82 5 HOH HOH 181 C HOH 83 5 HOH HOH 182 C HOH 92 5 HOH HOH 183 C HOH 93 5 HOH HOH 184 C HOH 95 5 HOH HOH 185 C HOH 98 5 HOH HOH 186 C HOH 106 5 HOH HOH 187 C HOH 109 5 HOH HOH 188 C HOH 113 5 HOH HOH 189 C HOH 115 5 HOH HOH 190 C HOH 117 5 HOH HOH 191 C HOH 121 5 HOH HOH 192 C n 1 1 A n 2 2 A n 3 3 A n 4 4 A n 5 5 A VAL 6 n 6 VAL 6 A ASN 7 n 7 ASN 7 A LYS 8 n 8 LYS 8 A GLU 9 n 9 GLU 9 A ARG 10 n 10 ARG 10 A THR 11 n 11 THR 11 A PHE 12 n 12 PHE 12 A LEU 13 n 13 LEU 13 A ALA 14 n 14 ALA 14 A VAL 15 n 15 VAL 15 A LYS 16 n 16 LYS 16 A PRO 17 n 17 PRO 17 A ASP 18 n 18 ASP 18 A GLY 19 n 19 GLY 19 A VAL 20 n 20 VAL 20 A ALA 21 n 21 ALA 21 A ARG 22 n 22 ARG 22 A GLY 23 n 23 GLY 23 A LEU 24 n 24 LEU 24 A VAL 25 n 25 VAL 25 A GLY 26 n 26 GLY 26 A GLU 27 n 27 GLU 27 A ILE 28 n 28 ILE 28 A ILE 29 n 29 ILE 29 A ALA 30 n 30 ALA 30 A ARG 31 n 31 ARG 31 A TYR 32 n 32 TYR 32 A GLU 33 n 33 GLU 33 A LYS 34 n 34 LYS 34 A LYS 35 n 35 LYS 35 A GLY 36 n 36 GLY 36 A PHE 37 n 37 PHE 37 A VAL 38 n 38 VAL 38 A LEU 39 n 39 LEU 39 A VAL 40 n 40 VAL 40 A GLY 41 n 41 GLY 41 A LEU 42 n 42 LEU 42 A LYS 43 n 43 LYS 43 A GLN 44 n 44 GLN 44 A LEU 45 n 45 LEU 45 A VAL 46 n 46 VAL 46 A PRO 47 n 47 PRO 47 A THR 48 n 48 THR 48 A LYS 49 n 49 LYS 49 A ASP 50 n 50 ASP 50 A LEU 51 n 51 LEU 51 A ALA 52 n 52 ALA 52 A GLU 53 n 53 GLU 53 A SER 54 n 54 SER 54 A HIS 55 n 55 HIS 55 A TYR 56 n 56 TYR 56 A ALA 57 n 57 ALA 57 A GLU 58 n 58 GLU 58 A HIS 59 n 59 HIS 59 A LYS 60 n 60 LYS 60 A GLU 61 n 61 GLU 61 A ARG 62 n 62 ARG 62 A PRO 63 n 63 PRO 63 A PHE 64 n 64 PHE 64 A PHE 65 n 65 PHE 65 A GLY 66 n 66 GLY 66 A GLY 67 n 67 GLY 67 A LEU 68 n 68 LEU 68 A VAL 69 n 69 VAL 69 A SER 70 n 70 SER 70 A PHE 71 n 71 PHE 71 A ILE 72 n 72 ILE 72 A THR 73 n 73 THR 73 A SER 74 n 74 SER 74 A GLY 75 n 75 GLY 75 A PRO 76 n 76 PRO 76 A VAL 77 n 77 VAL 77 A VAL 78 n 78 VAL 78 A ALA 79 n 79 ALA 79 A MET 80 n 80 MET 80 A VAL 81 n 81 VAL 81 A PHE 82 n 82 PHE 82 A GLU 83 n 83 GLU 83 A GLY 84 n 84 GLY 84 A LYS 85 n 85 LYS 85 A GLY 86 n 86 GLY 86 A VAL 87 n 87 VAL 87 A VAL 88 n 88 VAL 88 A ALA 89 n 89 ALA 89 A SER 90 n 90 SER 90 A ALA 91 n 91 ALA 91 A ARG 92 n 92 ARG 92 A LEU 93 n 93 LEU 93 A MET 94 n 94 MET 94 A ILE 95 n 95 ILE 95 A GLY 96 n 96 GLY 96 A VAL 97 n 97 VAL 97 A THR 98 n 98 THR 98 A ASN 99 n 99 ASN 99 A PRO 100 n 100 PRO 100 A LEU 101 n 101 LEU 101 A ALA 102 n 102 ALA 102 A SER 103 n 103 SER 103 A ALA 104 n 104 ALA 104 A PRO 105 n 105 PRO 105 A GLY 106 n 106 GLY 106 A SER 107 n 107 SER 107 A ILE 108 n 108 ILE 108 A ARG 109 n 109 ARG 109 A GLY 110 n 110 GLY 110 A ASP 111 n 111 ASP 111 A PHE 112 n 112 PHE 112 A GLY 113 n 113 GLY 113 A VAL 114 n 114 VAL 114 A ASP 115 n 115 ASP 115 A VAL 116 n 116 VAL 116 A GLY 117 n 117 GLY 117 A ARG 118 n 118 ARG 118 A ASN 119 n 119 ASN 119 A ILE 120 n 120 ILE 120 A ILE 121 n 121 ILE 121 A GLY 122 n 122 GLY 122 A GLY 123 n 123 GLY 123 A SER 124 n 124 SER 124 A ASP 125 n 125 ASP 125 A SER 126 n 126 SER 126 A VAL 127 n 127 VAL 127 A GLU 128 n 128 GLU 128 A SER 129 n 129 SER 129 A ALA 130 n 130 ALA 130 A ASN 131 n 131 ASN 131 A ARG 132 n 132 ARG 132 A GLU 133 n 133 GLU 133 A ILE 134 n 134 ILE 134 A ALA 135 n 135 ALA 135 A LEU 136 n 136 LEU 136 A TRP 137 n 137 TRP 137 A PHE 138 n 138 PHE 138 A LYS 139 n 139 LYS 139 A PRO 140 n 140 PRO 140 A GLU 141 n 141 GLU 141 A GLU 142 n 142 GLU 142 A LEU 143 n 143 LEU 143 A LEU 144 n 144 LEU 144 A THR 145 n 145 THR 145 A GLU 146 n 146 GLU 146 A VAL 147 n 147 VAL 147 A LYS 148 n 148 LYS 148 A PRO 149 n 149 PRO 149 A ASN 150 n 150 ASN 150 A PRO 151 n 151 PRO 151 A ASN 152 n 152 ASN 152 A LEU 153 n 153 LEU 153 A TYR 154 n 154 TYR 154 A GLU 155 n 155 GLU 155 A n 1 1 B n 2 2 B n 3 3 B n 4 4 B n 5 5 B VAL 6 n 6 VAL 6 B ASN 7 n 7 ASN 7 B LYS 8 n 8 LYS 8 B GLU 9 n 9 GLU 9 B ARG 10 n 10 ARG 10 B THR 11 n 11 THR 11 B PHE 12 n 12 PHE 12 B LEU 13 n 13 LEU 13 B ALA 14 n 14 ALA 14 B VAL 15 n 15 VAL 15 B LYS 16 n 16 LYS 16 B PRO 17 n 17 PRO 17 B ASP 18 n 18 ASP 18 B GLY 19 n 19 GLY 19 B VAL 20 n 20 VAL 20 B ALA 21 n 21 ALA 21 B ARG 22 n 22 ARG 22 B GLY 23 n 23 GLY 23 B LEU 24 n 24 LEU 24 B VAL 25 n 25 VAL 25 B GLY 26 n 26 GLY 26 B GLU 27 n 27 GLU 27 B ILE 28 n 28 ILE 28 B ILE 29 n 29 ILE 29 B ALA 30 n 30 ALA 30 B ARG 31 n 31 ARG 31 B TYR 32 n 32 TYR 32 B GLU 33 n 33 GLU 33 B LYS 34 n 34 LYS 34 B LYS 35 n 35 LYS 35 B GLY 36 n 36 GLY 36 B PHE 37 n 37 PHE 37 B VAL 38 n 38 VAL 38 B LEU 39 n 39 LEU 39 B VAL 40 n 40 VAL 40 B GLY 41 n 41 GLY 41 B LEU 42 n 42 LEU 42 B LYS 43 n 43 LYS 43 B GLN 44 n 44 GLN 44 B LEU 45 n 45 LEU 45 B VAL 46 n 46 VAL 46 B PRO 47 n 47 PRO 47 B THR 48 n 48 THR 48 B LYS 49 n 49 LYS 49 B ASP 50 n 50 ASP 50 B LEU 51 n 51 LEU 51 B ALA 52 n 52 ALA 52 B GLU 53 n 53 GLU 53 B SER 54 n 54 SER 54 B HIS 55 n 55 HIS 55 B TYR 56 n 56 TYR 56 B ALA 57 n 57 ALA 57 B GLU 58 n 58 GLU 58 B HIS 59 n 59 HIS 59 B LYS 60 n 60 LYS 60 B GLU 61 n 61 GLU 61 B ARG 62 n 62 ARG 62 B PRO 63 n 63 PRO 63 B PHE 64 n 64 PHE 64 B PHE 65 n 65 PHE 65 B GLY 66 n 66 GLY 66 B GLY 67 n 67 GLY 67 B LEU 68 n 68 LEU 68 B VAL 69 n 69 VAL 69 B SER 70 n 70 SER 70 B PHE 71 n 71 PHE 71 B ILE 72 n 72 ILE 72 B THR 73 n 73 THR 73 B SER 74 n 74 SER 74 B GLY 75 n 75 GLY 75 B PRO 76 n 76 PRO 76 B VAL 77 n 77 VAL 77 B VAL 78 n 78 VAL 78 B ALA 79 n 79 ALA 79 B MET 80 n 80 MET 80 B VAL 81 n 81 VAL 81 B PHE 82 n 82 PHE 82 B GLU 83 n 83 GLU 83 B GLY 84 n 84 GLY 84 B LYS 85 n 85 LYS 85 B GLY 86 n 86 GLY 86 B VAL 87 n 87 VAL 87 B VAL 88 n 88 VAL 88 B ALA 89 n 89 ALA 89 B SER 90 n 90 SER 90 B ALA 91 n 91 ALA 91 B ARG 92 n 92 ARG 92 B LEU 93 n 93 LEU 93 B MET 94 n 94 MET 94 B ILE 95 n 95 ILE 95 B GLY 96 n 96 GLY 96 B VAL 97 n 97 VAL 97 B THR 98 n 98 THR 98 B ASN 99 n 99 ASN 99 B PRO 100 n 100 PRO 100 B LEU 101 n 101 LEU 101 B ALA 102 n 102 ALA 102 B SER 103 n 103 SER 103 B ALA 104 n 104 ALA 104 B PRO 105 n 105 PRO 105 B GLY 106 n 106 GLY 106 B SER 107 n 107 SER 107 B ILE 108 n 108 ILE 108 B ARG 109 n 109 ARG 109 B GLY 110 n 110 GLY 110 B ASP 111 n 111 ASP 111 B PHE 112 n 112 PHE 112 B GLY 113 n 113 GLY 113 B VAL 114 n 114 VAL 114 B ASP 115 n 115 ASP 115 B VAL 116 n 116 VAL 116 B GLY 117 n 117 GLY 117 B ARG 118 n 118 ARG 118 B ASN 119 n 119 ASN 119 B ILE 120 n 120 ILE 120 B ILE 121 n 121 ILE 121 B GLY 122 n 122 GLY 122 B GLY 123 n 123 GLY 123 B SER 124 n 124 SER 124 B ASP 125 n 125 ASP 125 B SER 126 n 126 SER 126 B VAL 127 n 127 VAL 127 B GLU 128 n 128 GLU 128 B SER 129 n 129 SER 129 B ALA 130 n 130 ALA 130 B ASN 131 n 131 ASN 131 B ARG 132 n 132 ARG 132 B GLU 133 n 133 GLU 133 B ILE 134 n 134 ILE 134 B ALA 135 n 135 ALA 135 B LEU 136 n 136 LEU 136 B TRP 137 n 137 TRP 137 B PHE 138 n 138 PHE 138 B LYS 139 n 139 LYS 139 B PRO 140 n 140 PRO 140 B GLU 141 n 141 GLU 141 B GLU 142 n 142 GLU 142 B LEU 143 n 143 LEU 143 B LEU 144 n 144 LEU 144 B THR 145 n 145 THR 145 B GLU 146 n 146 GLU 146 B VAL 147 n 147 VAL 147 B LYS 148 n 148 LYS 148 B PRO 149 n 149 PRO 149 B ASN 150 n 150 ASN 150 B PRO 151 n 151 PRO 151 B ASN 152 n 152 ASN 152 B LEU 153 n 153 LEU 153 B TYR 154 n 154 TYR 154 B GLU 155 n 155 GLU 155 B n 1 1 C n 2 2 C n 3 3 C n 4 4 C n 5 5 C VAL 6 n 6 VAL 6 C ASN 7 n 7 ASN 7 C LYS 8 n 8 LYS 8 C GLU 9 n 9 GLU 9 C ARG 10 n 10 ARG 10 C THR 11 n 11 THR 11 C PHE 12 n 12 PHE 12 C LEU 13 n 13 LEU 13 C ALA 14 n 14 ALA 14 C VAL 15 n 15 VAL 15 C LYS 16 n 16 LYS 16 C PRO 17 n 17 PRO 17 C ASP 18 n 18 ASP 18 C GLY 19 n 19 GLY 19 C VAL 20 n 20 VAL 20 C ALA 21 n 21 ALA 21 C ARG 22 n 22 ARG 22 C GLY 23 n 23 GLY 23 C LEU 24 n 24 LEU 24 C VAL 25 n 25 VAL 25 C GLY 26 n 26 GLY 26 C GLU 27 n 27 GLU 27 C ILE 28 n 28 ILE 28 C ILE 29 n 29 ILE 29 C ALA 30 n 30 ALA 30 C ARG 31 n 31 ARG 31 C TYR 32 n 32 TYR 32 C GLU 33 n 33 GLU 33 C LYS 34 n 34 LYS 34 C LYS 35 n 35 LYS 35 C GLY 36 n 36 GLY 36 C PHE 37 n 37 PHE 37 C VAL 38 n 38 VAL 38 C LEU 39 n 39 LEU 39 C VAL 40 n 40 VAL 40 C GLY 41 n 41 GLY 41 C LEU 42 n 42 LEU 42 C LYS 43 n 43 LYS 43 C GLN 44 n 44 GLN 44 C LEU 45 n 45 LEU 45 C VAL 46 n 46 VAL 46 C PRO 47 n 47 PRO 47 C THR 48 n 48 THR 48 C LYS 49 n 49 LYS 49 C ASP 50 n 50 ASP 50 C LEU 51 n 51 LEU 51 C ALA 52 n 52 ALA 52 C GLU 53 n 53 GLU 53 C SER 54 n 54 SER 54 C HIS 55 n 55 HIS 55 C TYR 56 n 56 TYR 56 C ALA 57 n 57 ALA 57 C GLU 58 n 58 GLU 58 C HIS 59 n 59 HIS 59 C LYS 60 n 60 LYS 60 C GLU 61 n 61 GLU 61 C ARG 62 n 62 ARG 62 C PRO 63 n 63 PRO 63 C PHE 64 n 64 PHE 64 C PHE 65 n 65 PHE 65 C GLY 66 n 66 GLY 66 C GLY 67 n 67 GLY 67 C LEU 68 n 68 LEU 68 C VAL 69 n 69 VAL 69 C SER 70 n 70 SER 70 C PHE 71 n 71 PHE 71 C ILE 72 n 72 ILE 72 C THR 73 n 73 THR 73 C SER 74 n 74 SER 74 C GLY 75 n 75 GLY 75 C PRO 76 n 76 PRO 76 C VAL 77 n 77 VAL 77 C VAL 78 n 78 VAL 78 C ALA 79 n 79 ALA 79 C MET 80 n 80 MET 80 C VAL 81 n 81 VAL 81 C PHE 82 n 82 PHE 82 C GLU 83 n 83 GLU 83 C GLY 84 n 84 GLY 84 C LYS 85 n 85 LYS 85 C GLY 86 n 86 GLY 86 C VAL 87 n 87 VAL 87 C VAL 88 n 88 VAL 88 C ALA 89 n 89 ALA 89 C SER 90 n 90 SER 90 C ALA 91 n 91 ALA 91 C ARG 92 n 92 ARG 92 C LEU 93 n 93 LEU 93 C MET 94 n 94 MET 94 C ILE 95 n 95 ILE 95 C GLY 96 n 96 GLY 96 C VAL 97 n 97 VAL 97 C THR 98 n 98 THR 98 C ASN 99 n 99 ASN 99 C PRO 100 n 100 PRO 100 C LEU 101 n 101 LEU 101 C ALA 102 n 102 ALA 102 C SER 103 n 103 SER 103 C ALA 104 n 104 ALA 104 C PRO 105 n 105 PRO 105 C GLY 106 n 106 GLY 106 C SER 107 n 107 SER 107 C ILE 108 n 108 ILE 108 C ARG 109 n 109 ARG 109 C GLY 110 n 110 GLY 110 C ASP 111 n 111 ASP 111 C PHE 112 n 112 PHE 112 C GLY 113 n 113 GLY 113 C VAL 114 n 114 VAL 114 C ASP 115 n 115 ASP 115 C VAL 116 n 116 VAL 116 C GLY 117 n 117 GLY 117 C ARG 118 n 118 ARG 118 C ASN 119 n 119 ASN 119 C ILE 120 n 120 ILE 120 C ILE 121 n 121 ILE 121 C GLY 122 n 122 GLY 122 C GLY 123 n 123 GLY 123 C SER 124 n 124 SER 124 C ASP 125 n 125 ASP 125 C SER 126 n 126 SER 126 C VAL 127 n 127 VAL 127 C GLU 128 n 128 GLU 128 C SER 129 n 129 SER 129 C ALA 130 n 130 ALA 130 C ASN 131 n 131 ASN 131 C ARG 132 n 132 ARG 132 C GLU 133 n 133 GLU 133 C ILE 134 n 134 ILE 134 C ALA 135 n 135 ALA 135 C LEU 136 n 136 LEU 136 C TRP 137 n 137 TRP 137 C PHE 138 n 138 PHE 138 C LYS 139 n 139 LYS 139 C PRO 140 n 140 PRO 140 C GLU 141 n 141 GLU 141 C GLU 142 n 142 GLU 142 C LEU 143 n 143 LEU 143 C LEU 144 n 144 LEU 144 C THR 145 n 145 THR 145 C GLU 146 n 146 GLU 146 C VAL 147 n 147 VAL 147 C LYS 148 n 148 LYS 148 C PRO 149 n 149 PRO 149 C ASN 150 n 150 ASN 150 C PRO 151 n 151 PRO 151 C ASN 152 n 152 ASN 152 C LEU 153 n 153 LEU 153 C TYR 154 n 154 TYR 154 C GLU 155 n 155 GLU 155 C author_defined_assembly 6 hexameric A ADP 160 F O1B ADP 1_555 A MG 162 E MG MG 1_555 A ADP 160 F O1A ADP 1_555 65.0 A ADP 160 F O1B ADP 1_555 A MG 162 E MG MG 1_555 A PO4 161 D O1 PO4 1_555 80.2 A ADP 160 F O1A ADP 1_555 A MG 162 E MG MG 1_555 A PO4 161 D O1 PO4 1_555 78.7 B ADP 160 I O1B ADP 1_555 B MG 162 H MG MG 1_555 B ADP 160 I O1A ADP 1_555 73.8 B ADP 160 I O1B ADP 1_555 B MG 162 H MG MG 1_555 B PO4 161 G O2 PO4 1_555 79.5 B ADP 160 I O1A ADP 1_555 B MG 162 H MG MG 1_555 B PO4 161 G O2 PO4 1_555 86.4 B ADP 160 I O1B ADP 1_555 B MG 162 H MG MG 1_555 B HOH 203 N O HOH 1_555 99.0 B ADP 160 I O1A ADP 1_555 B MG 162 H MG MG 1_555 B HOH 203 N O HOH 1_555 172.3 B PO4 161 G O2 PO4 1_555 B MG 162 H MG MG 1_555 B HOH 203 N O HOH 1_555 89.4 B ADP 160 I O1B ADP 1_555 B MG 162 H MG MG 1_555 B HOH 204 N O HOH 1_555 89.1 B ADP 160 I O1A ADP 1_555 B MG 162 H MG MG 1_555 B HOH 204 N O HOH 1_555 80.4 B PO4 161 G O2 PO4 1_555 B MG 162 H MG MG 1_555 B HOH 204 N O HOH 1_555 164.6 B HOH 203 N O HOH 1_555 B MG 162 H MG MG 1_555 B HOH 204 N O HOH 1_555 102.7 B ADP 160 I O1B ADP 1_555 B MG 162 H MG MG 1_555 B HOH 205 N O HOH 1_555 148.5 B ADP 160 I O1A ADP 1_555 B MG 162 H MG MG 1_555 B HOH 205 N O HOH 1_555 76.9 B PO4 161 G O2 PO4 1_555 B MG 162 H MG MG 1_555 B HOH 205 N O HOH 1_555 87.4 B HOH 203 N O HOH 1_555 B MG 162 H MG MG 1_555 B HOH 205 N O HOH 1_555 109.4 B HOH 204 N O HOH 1_555 B MG 162 H MG MG 1_555 B HOH 205 N O HOH 1_555 97.3 C ADP 160 L O1A ADP 1_555 C MG 162 K MG MG 1_555 C ADP 160 L O1B ADP 1_555 73.3 C ADP 160 L O1A ADP 1_555 C MG 162 K MG MG 1_555 C PO4 161 J O1 PO4 1_555 92.5 C ADP 160 L O1B ADP 1_555 C MG 162 K MG MG 1_555 C PO4 161 J O1 PO4 1_555 79.2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -0.5000000000 -0.8660254038 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 6_765 -x+2,-x+y+1,-z+1/3 crystal symmetry operation 105.0000000000 60.6217782649 50.5900000000 A O GLY 122 A O GLY 122 A N ALA 14 A N ALA 14 A O THR 11 A O THR 11 A N PHE 82 A N PHE 82 A O VAL 77 A O VAL 77 A N LEU 45 A N LEU 45 B O GLY 122 B O GLY 122 B N ALA 14 B N ALA 14 B O THR 11 B O THR 11 B N PHE 82 B N PHE 82 B O VAL 77 B O VAL 77 B N LEU 45 B N LEU 45 C O GLY 122 C O GLY 122 C N ALA 14 C N ALA 14 C O THR 11 C O THR 11 C N PHE 82 C N PHE 82 C O VAL 77 C O VAL 77 C N LEU 45 C N LEU 45 1 A MET 1 A MET 1 1 Y 1 A SER 2 A SER 2 1 Y 1 A THR 3 A THR 3 1 Y 1 A ASN 4 A ASN 4 1 Y 1 A LYS 5 A LYS 5 1 Y 1 B MET 1 B MET 1 1 Y 1 B SER 2 B SER 2 1 Y 1 B THR 3 B THR 3 1 Y 1 B ASN 4 B ASN 4 1 Y 1 B LYS 5 B LYS 5 1 Y 1 C MET 1 C MET 1 1 Y 1 C SER 2 C SER 2 1 Y 1 C THR 3 C THR 3 1 Y 1 C ASN 4 C ASN 4 1 Y 1 C LYS 5 C LYS 5 1 Y 1 9.39 1.50 119.30 128.69 C C C C N CA GLY PRO PRO 75 76 76 Y 1 A VAL 114 -138.28 -35.36 1 A ASN 119 -92.20 33.56 1 A ILE 120 55.83 -42.44 1 B LYS 43 -172.33 144.57 1 B VAL 114 -140.43 -34.18 1 B ASN 119 -96.22 37.60 1 B ILE 120 53.93 -47.28 1 C ASN 7 -63.68 57.23 1 C TYR 56 -99.17 33.56 1 C VAL 114 -137.83 -43.27 1 C ARG 118 -118.85 59.45 1 C ASN 119 -94.99 34.92 1 C ILE 120 56.08 -48.71 22.0 MUTANT HAS LOST NDPK ACTIVITY, BUT EFFICIENTLY PHOSPHORYLATES IMIDAZOLE AND OTHER PHOSPHATE ACCEPTOR MOLECULES (AMINES AND ALCOHOLS). THE PROTEIN WAS CRYSTALLIZED WITH ATP, BUT THE NUCLEOTIDE IS SEEN TO BE HYDROLYZED TO ADP+PO4 IN THE CRYSTAL. 0.3050000 0.2030000 0.2030000 2.5 8 14555 99.9 RANDOM 1 2.0 MOLECULAR REPLACEMENT 1KDN 2.5 8 108 3633 3 99 3423 0.012 1.9 2.0 2.5 8.0 1B4S 14555 3.0 0.0830000 1 9.8 99.9 model building X-PLOR refinement X-PLOR data reduction DENZO data scaling SCALEPACK phasing X-PLOR STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE H122G MUTANT 1 N N 1 N N 1 N N 2 N N 3 N N 4 N N 2 N N 3 N N 4 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N A PRO 17 A PRO 17 HELX_P A ALA 21 A ALA 21 1 A0 5 A VAL 25 A VAL 25 HELX_P A LYS 35 A LYS 35 1 A1 11 A LYS 49 A LYS 49 HELX_P A HIS 55 A HIS 55 1 A2 7 A ALA 57 A ALA 57 HELX_P A HIS 59 A HIS 59 5 A3 3 A PHE 65 A PHE 65 HELX_P A PHE 71 A PHE 71 1 A5 7 A VAL 87 A VAL 87 HELX_P A ILE 95 A ILE 95 1 A6 9 A PRO 100 A PRO 100 HELX_P A ALA 102 A ALA 102 5 A7 3 A ILE 108 A ILE 108 HELX_P A PHE 112 A PHE 112 1 A8 5 A VAL 127 A VAL 127 HELX_P A TRP 137 A TRP 137 1 A9 11 A PRO 140 A PRO 140 HELX_P A GLU 142 A GLU 142 5 A10 3 B PRO 17 B PRO 17 HELX_P B ALA 21 B ALA 21 1 B0 5 B VAL 25 B VAL 25 HELX_P B LYS 34 B LYS 34 1 B1 10 B LYS 49 B LYS 49 HELX_P B HIS 55 B HIS 55 1 B2 7 B ALA 57 B ALA 57 HELX_P B HIS 59 B HIS 59 5 B3 3 B PHE 65 B PHE 65 HELX_P B ILE 72 B ILE 72 1 B4 8 B VAL 87 B VAL 87 HELX_P B ILE 95 B ILE 95 1 B5 9 B ILE 108 B ILE 108 HELX_P B PHE 112 B PHE 112 1 B6 5 B VAL 127 B VAL 127 HELX_P B TRP 137 B TRP 137 1 B7 11 B PRO 140 B PRO 140 HELX_P B GLU 142 B GLU 142 5 B8 3 C PRO 17 C PRO 17 HELX_P C ALA 21 C ALA 21 1 C0 5 C VAL 25 C VAL 25 HELX_P C LYS 35 C LYS 35 1 C1 11 C LYS 49 C LYS 49 HELX_P C HIS 55 C HIS 55 1 C2 7 C ALA 57 C ALA 57 HELX_P C HIS 59 C HIS 59 5 C3 3 C PHE 65 C PHE 65 HELX_P C ILE 72 C ILE 72 1 C4 8 C VAL 87 C VAL 87 HELX_P C ILE 95 C ILE 95 1 C5 9 C PRO 100 C PRO 100 HELX_P C ALA 102 C ALA 102 5 C6 3 C ILE 108 C ILE 108 HELX_P C PHE 112 C PHE 112 1 C7 5 C VAL 127 C VAL 127 HELX_P C TRP 137 C TRP 137 1 C8 11 C PRO 140 C PRO 140 HELX_P C GLU 142 C GLU 142 5 C9 3 metalc 2.556 A ADP 160 F O1B ADP 1_555 A MG 162 E MG MG 1_555 metalc 2.525 A ADP 160 F O1A ADP 1_555 A MG 162 E MG MG 1_555 metalc 2.236 A PO4 161 D O1 PO4 1_555 A MG 162 E MG MG 1_555 metalc 2.217 B ADP 160 I O1B ADP 1_555 B MG 162 H MG MG 1_555 metalc 2.274 B ADP 160 I O1A ADP 1_555 B MG 162 H MG MG 1_555 metalc 2.044 B PO4 161 G O2 PO4 1_555 B MG 162 H MG MG 1_555 metalc 2.113 B MG 162 H MG MG 1_555 B HOH 203 N O HOH 1_555 metalc 2.070 B MG 162 H MG MG 1_555 B HOH 204 N O HOH 1_555 metalc 1.845 B MG 162 H MG MG 1_555 B HOH 205 N O HOH 1_555 metalc 2.145 C ADP 160 L O1A ADP 1_555 C MG 162 K MG MG 1_555 metalc 2.558 C ADP 160 L O1B ADP 1_555 C MG 162 K MG MG 1_555 metalc 2.401 C PO4 161 J O1 PO4 1_555 C MG 162 K MG MG 1_555 PHOSPHOTRANSFERASE TRANSFERASE, KINASE, ATP-BINDING, PHOSPHOTRANSFERASE NDKC_DICDI UNP 1 1 P22887 MSTNKVNKERTFLAVKPDGVARGLVGEIIARYEKKGFVLVGLKQLVPTKDLAESHYAEHKERPFFGGLVSFITSGPVVAM VFEGKGVVASARLMIGVTNPLASAPGSIRGDFGVDVGRNIIHGSDSVESANREIALWFKPEELLTEVKPNPNLYE 1 155 1B4S 1 155 P22887 A 1 1 155 1 155 1B4S 1 155 P22887 B 1 1 155 1 155 1B4S 1 155 P22887 C 1 1 155 1 HIS engineered mutation GLY 122 1B4S A P22887 UNP 122 122 2 HIS engineered mutation GLY 122 1B4S B P22887 UNP 122 122 3 HIS engineered mutation GLY 122 1B4S C P22887 UNP 122 122 4 4 4 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A ILE 121 A ILE 121 A GLY 123 A GLY 123 A ARG 10 A ARG 10 A VAL 15 A VAL 15 A PRO 76 A PRO 76 A GLU 83 A GLU 83 A VAL 38 A VAL 38 A VAL 46 A VAL 46 B ILE 121 B ILE 121 B GLY 123 B GLY 123 B ARG 10 B ARG 10 B VAL 15 B VAL 15 B PRO 76 B PRO 76 B GLU 83 B GLU 83 B VAL 38 B VAL 38 B VAL 46 B VAL 46 C ILE 121 C ILE 121 C GLY 123 C GLY 123 C ARG 10 C ARG 10 C VAL 15 C VAL 15 C VAL 77 C VAL 77 C GLU 83 C GLU 83 C VAL 38 C VAL 38 C LEU 45 C LEU 45 BINDING SITE FOR RESIDUE PO4 A 161 A PO4 161 Software 9 BINDING SITE FOR RESIDUE MG A 162 A MG 162 Software 2 BINDING SITE FOR RESIDUE PO4 B 161 B PO4 161 Software 11 BINDING SITE FOR RESIDUE MG B 162 B MG 162 Software 5 BINDING SITE FOR RESIDUE PO4 C 161 C PO4 161 Software 8 BINDING SITE FOR RESIDUE MG C 162 C MG 162 Software 2 BINDING SITE FOR RESIDUE ADP A 160 A ADP 160 Software 12 BINDING SITE FOR RESIDUE ADP B 160 B ADP 160 Software 15 BINDING SITE FOR RESIDUE ADP C 160 C ADP 160 Software 13 A LYS 16 A LYS 16 9 1_555 A HIS 55 A HIS 55 9 1_555 A TYR 56 A TYR 56 9 1_555 A ARG 92 A ARG 92 9 1_555 A ARG 109 A ARG 109 9 1_555 A GLY 122 A GLY 122 9 1_555 A GLY 123 A GLY 123 9 1_555 A ADP 160 F ADP 9 1_555 A MG 162 E MG 9 1_555 A ADP 160 F ADP 2 1_555 A PO4 161 D PO4 2 1_555 B LYS 16 B LYS 16 11 1_555 B HIS 55 B HIS 55 11 1_555 B TYR 56 B TYR 56 11 1_555 B ARG 92 B ARG 92 11 1_555 B GLY 122 B GLY 122 11 1_555 B GLY 123 B GLY 123 11 1_555 B ADP 160 I ADP 11 1_555 B MG 162 H MG 11 1_555 B HOH 182 N HOH 11 1_555 B HOH 203 N HOH 11 1_555 B HOH 205 N HOH 11 1_555 B ADP 160 I ADP 5 1_555 B PO4 161 G PO4 5 1_555 B HOH 203 N HOH 5 1_555 B HOH 204 N HOH 5 1_555 B HOH 205 N HOH 5 1_555 C LYS 16 C LYS 16 8 1_555 C HIS 55 C HIS 55 8 1_555 C TYR 56 C TYR 56 8 1_555 C ARG 92 C ARG 92 8 1_555 C GLY 122 C GLY 122 8 1_555 C GLY 123 C GLY 123 8 1_555 C ADP 160 L ADP 8 1_555 C MG 162 K MG 8 1_555 C ADP 160 L ADP 2 1_555 C PO4 161 J PO4 2 1_555 A LYS 16 A LYS 16 12 1_555 A TYR 56 A TYR 56 12 1_555 A HIS 59 A HIS 59 12 1_555 A PHE 64 A PHE 64 12 1_555 A LEU 68 A LEU 68 12 1_555 A ARG 92 A ARG 92 12 1_555 A THR 98 A THR 98 12 1_555 A ARG 109 A ARG 109 12 1_555 A VAL 116 A VAL 116 12 1_555 A ASN 119 A ASN 119 12 1_555 A PO4 161 D PO4 12 1_555 A MG 162 E MG 12 1_555 B LYS 16 B LYS 16 15 1_555 B TYR 56 B TYR 56 15 1_555 B HIS 59 B HIS 59 15 1_555 B PHE 64 B PHE 64 15 1_555 B LEU 68 B LEU 68 15 1_555 B ARG 92 B ARG 92 15 1_555 B THR 98 B THR 98 15 1_555 B ARG 109 B ARG 109 15 1_555 B VAL 116 B VAL 116 15 1_555 B ASN 119 B ASN 119 15 1_555 B PO4 161 G PO4 15 1_555 B MG 162 H MG 15 1_555 B HOH 175 N HOH 15 1_555 B HOH 204 N HOH 15 1_555 B HOH 205 N HOH 15 1_555 C LYS 16 C LYS 16 13 1_555 C TYR 56 C TYR 56 13 1_555 C HIS 59 C HIS 59 13 1_555 C ARG 62 C ARG 62 13 1_555 C PHE 64 C PHE 64 13 1_555 C LEU 68 C LEU 68 13 1_555 C ARG 92 C ARG 92 13 1_555 C THR 98 C THR 98 13 1_555 C ARG 109 C ARG 109 13 1_555 C VAL 116 C VAL 116 13 1_555 C ASN 119 C ASN 119 13 1_555 C PO4 161 J PO4 13 1_555 C MG 162 K MG 13 1_555 152 P 31 2 1