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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM RICE
Keywords NUCLEOSIDE DIPHOSPHATE KINASE, RICE, TRANSFERASE
Experiment X-ray diffraction
Number of Models  1


   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  

PDB   1PKU     released     available     available     Quaternary Structure Server  


Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  A 149 1196 0
2  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  B 149 1196 0
3  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  C 149 1196 0
4  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  D 149 1196 0
5  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  E 149 1196 0
6  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  F 149 1196 0
7  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  G 149 1196 0
8  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  H 149 1196 0
9  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  I 149 1196 0
10  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  J 149 1196 0
11  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  K 149 1196 0
12  Protein   NUCLEOSIDE DIPHOSPHATE KINASE I  L 149 1196 0
13 Water     226 0 226
total       2014 14352 226

Proteins
Unit 1 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 2 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 3 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 4 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 5 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 6 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 7 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 8 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 9 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 10 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 11 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151
Unit 12 ARG3 MET4 GLU5 GLN6 SER7 PHE8 ILE9 MET10 ILE11 LYS12 PRO13 ASP14 GLY15 VAL16 GLN17 ARG18 GLY19 LEU20 ILE21 GLY22 ASP23 ILE24 ILE25 SER26 ARG27 PHE28 GLU29 LYS30 LYS31 GLY32 PHE33 TYR34 LEU35 ARG36 GLY37 MET38 LYS39 PHE40 MET41 ASN42 VAL43 GLU44 ARG45 SER46 PHE47 ALA48 GLN49 GLN50 HIS51 TYR52 ALA53 ASP54 LEU55 SER56 ASP57 LYS58 PRO59 PHE60 PHE61 PRO62 GLY63 LEU64 VAL65 GLU66 TYR67 ILE68 ILE69 SER70 GLY71 PRO72 VAL73 VAL74 ALA75 MET76 VAL77 TRP78 GLU79 GLY80 LYS81 ASP82 VAL83 VAL84 ALA85 THR86 GLY87 ARG88 ARG89 ILE90 ILE91 GLY92 ALA93 THR94 ARG95 PRO96 TRP97 GLU98 ALA99 ALA100 PRO101 GLY102 THR103 ILE104 ARG105 ALA106 ASP107 TYR108 ALA109 VAL110 GLU111 VAL112 GLY113 ARG114 ASN115 VAL116 ILE117 HIS118 GLY119 SER120 ASP121 SER122 VAL123 ASP124 ASN125 GLY126 LYS127 LYS128 GLU129 ILE130 ALA131 LEU132 TRP133 PHE134 PRO135 GLU136 GLY137 LEU138 ALA139 GLU140 TRP141 ARG142 SER143 ASN144 LEU145 HIS146 PRO147 TRP148 ILE149 TYR150 GLU151

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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany