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Sequence, Chains, Asymmetric and Biological Units

Title CRYSTAL STRUCTURE OF STAPHYLOCOCCUS AUREUS NUCLEOSIDE DIPHOS KINASE COMPLEXED WITH ADP
Keywords FERRIDOXIN FOLD, ALPHA-BETA PROTEIN FAMILY, NUCLEOSIDE DIPHO KINASES (NDKS) CATALYZE THE TRANSFER OF A GAMMA PHOSPHATE F NUCLEOSIDE TRIPHOSPHATES TO NUCLEOSIDE DIPHOSPHATE, NUCLEOT BINDING, MAGNESIUM, METAL BINDING, PHOSPHORYLATION, TRANSFE
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   3Q8U     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   NUCLEOSIDE DIPHOSPHATE KINASE  A 149 1165 0
2  Protein   NUCLEOSIDE DIPHOSPHATE KINASE  B 149 1158 0
3  Protein   NUCLEOSIDE DIPHOSPHATE KINASE  C 149 1158 0
4  Protein   NUCLEOSIDE DIPHOSPHATE KINASE  D 149 1161 0
5  Protein   NUCLEOSIDE DIPHOSPHATE KINASE  E 149 1158 0
6  Protein   NUCLEOSIDE DIPHOSPHATE KINASE  F 149 1158 0
7  Ligand   NUCLEOSIDE DIPHOSPHATE KINASE  A 2 0 28
8  Ligand   NUCLEOSIDE DIPHOSPHATE KINASE  B 2 0 28
9  Ligand   NUCLEOSIDE DIPHOSPHATE KINASE  C 1 0 27
10  Ligand   NUCLEOSIDE DIPHOSPHATE KINASE  D 2 0 28
11  Ligand   NUCLEOSIDE DIPHOSPHATE KINASE  E 2 0 28
12  Ligand   NUCLEOSIDE DIPHOSPHATE KINASE  F 2 0 28
13 Water     441 0 441
total       1346 6958 608
Proteins
Unit 1 MET1 GLU2 ARG3 THR4 PHE5 LEU6 MET7 ILE8 LYS9 PRO10 ASP11 ALA12 VAL13 GLN14 ARG15 ASN16 LEU17 ILE18 GLY19 GLU20 VAL21 ILE22 SER23 ARG24 ILE25 GLU26 ARG27 LYS28 GLY29 LEU30 LYS31 LEU32 VAL33 GLY34 GLY35 LYS36 LEU37 MET38 GLN39 VAL40 PRO41 MET42 GLU43 LEU44 ALA45 GLU46 THR47 HIS48 TYR49 GLY50 GLU51 HIS52 GLN53 GLY54 LYS55 PRO56 PHE57 TYR58 ASN59 ASP60 LEU61 ILE62 SER63 PHE64 ILE65 THR66 SER67 ALA68 PRO69 VAL70 PHE71 ALA72 MET73 VAL74 VAL75 GLU76 GLY77 GLU78 ASP79 ALA80 VAL81 ASN82 VAL83 SER84 ARG85 HIS86 ILE87 ILE88 GLY89 SER90 THR91 ASN92 PRO93 SER94 GLU95 ALA96 SER97 PRO98 GLY99 SER100 ILE101 ARG102 GLY103 ASP104 LEU105 GLY106 LEU107 THR108 VAL109 GLY110 ARG111 ASN112 ILE113 ILE114 HIS115 GLY116 SER117 ASP118 SER119 LEU120 GLU121 SER122 ALA123 GLU124 ARG125 GLU126 ILE127 ASN128 LEU129 TRP130 PHE131 ASN132 GLU133 ASN134 GLU135 ILE136 THR137 SER138 TYR139 ALA140 SER141 PRO142 ARG143 ASP144 ALA145 TRP146 LEU147 TYR148 GLU149
Unit 2 MET1 GLU2 ARG3 THR4 PHE5 LEU6 MET7 ILE8 LYS9 PRO10 ASP11 ALA12 VAL13 GLN14 ARG15 ASN16 LEU17 ILE18 GLY19 GLU20 VAL21 ILE22 SER23 ARG24 ILE25 GLU26 ARG27 LYS28 GLY29 LEU30 LYS31 LEU32 VAL33 GLY34 GLY35 LYS36 LEU37 MET38 GLN39 VAL40 PRO41 MET42 GLU43 LEU44 ALA45 GLU46 THR47 HIS48 TYR49 GLY50 GLU51 HIS52 GLN53 GLY54 LYS55 PRO56 PHE57 TYR58 ASN59 ASP60 LEU61 ILE62 SER63 PHE64 ILE65 THR66 SER67 ALA68 PRO69 VAL70 PHE71 ALA72 MET73 VAL74 VAL75 GLU76 GLY77 GLU78 ASP79 ALA80 VAL81 ASN82 VAL83 SER84 ARG85 HIS86 ILE87 ILE88 GLY89 SER90 THR91 ASN92 PRO93 SER94 GLU95 ALA96 SER97 PRO98 GLY99 SER100 ILE101 ARG102 GLY103 ASP104 LEU105 GLY106 LEU107 THR108 VAL109 GLY110 ARG111 ASN112 ILE113 ILE114 HIS115 GLY116 SER117 ASP118 SER119 LEU120 GLU121 SER122 ALA123 GLU124 ARG125 GLU126 ILE127 ASN128 LEU129 TRP130 PHE131 ASN132 GLU133 ASN134 GLU135 ILE136 THR137 SER138 TYR139 ALA140 SER141 PRO142 ARG143 ASP144 ALA145 TRP146 LEU147 TYR148 GLU149
Unit 3 MET1 GLU2 ARG3 THR4 PHE5 LEU6 MET7 ILE8 LYS9 PRO10 ASP11 ALA12 VAL13 GLN14 ARG15 ASN16 LEU17 ILE18 GLY19 GLU20 VAL21 ILE22 SER23 ARG24 ILE25 GLU26 ARG27 LYS28 GLY29 LEU30 LYS31 LEU32 VAL33 GLY34 GLY35 LYS36 LEU37 MET38 GLN39 VAL40 PRO41 MET42 GLU43 LEU44 ALA45 GLU46 THR47 HIS48 TYR49 GLY50 GLU51 HIS52 GLN53 GLY54 LYS55 PRO56 PHE57 TYR58 ASN59 ASP60 LEU61 ILE62 SER63 PHE64 ILE65 THR66 SER67 ALA68 PRO69 VAL70 PHE71 ALA72 MET73 VAL74 VAL75 GLU76 GLY77 GLU78 ASP79 ALA80 VAL81 ASN82 VAL83 SER84 ARG85 HIS86 ILE87 ILE88 GLY89 SER90 THR91 ASN92 PRO93 SER94 GLU95 ALA96 SER97 PRO98 GLY99 SER100 ILE101 ARG102 GLY103 ASP104 LEU105 GLY106 LEU107 THR108 VAL109 GLY110 ARG111 ASN112 ILE113 ILE114 HIS115 GLY116 SER117 ASP118 SER119 LEU120 GLU121 SER122 ALA123 GLU124 ARG125 GLU126 ILE127 ASN128 LEU129 TRP130 PHE131 ASN132 GLU133 ASN134 GLU135 ILE136 THR137 SER138 TYR139 ALA140 SER141 PRO142 ARG143 ASP144 ALA145 TRP146 LEU147 TYR148 GLU149
Unit 4 MET1 GLU2 ARG3 THR4 PHE5 LEU6 MET7 ILE8 LYS9 PRO10 ASP11 ALA12 VAL13 GLN14 ARG15 ASN16 LEU17 ILE18 GLY19 GLU20 VAL21 ILE22 SER23 ARG24 ILE25 GLU26 ARG27 LYS28 GLY29 LEU30 LYS31 LEU32 VAL33 GLY34 GLY35 LYS36 LEU37 MET38 GLN39 VAL40 PRO41 MET42 GLU43 LEU44 ALA45 GLU46 THR47 HIS48 TYR49 GLY50 GLU51 HIS52 GLN53 GLY54 LYS55 PRO56 PHE57 TYR58 ASN59 ASP60 LEU61 ILE62 SER63 PHE64 ILE65 THR66 SER67 ALA68 PRO69 VAL70 PHE71 ALA72 MET73 VAL74 VAL75 GLU76 GLY77 GLU78 ASP79 ALA80 VAL81 ASN82 VAL83 SER84 ARG85 HIS86 ILE87 ILE88 GLY89 SER90 THR91 ASN92 PRO93 SER94 GLU95 ALA96 SER97 PRO98 GLY99 SER100 ILE101 ARG102 GLY103 ASP104 LEU105 GLY106 LEU107 THR108 VAL109 GLY110 ARG111 ASN112 ILE113 ILE114 HIS115 GLY116 SER117 ASP118 SER119 LEU120 GLU121 SER122 ALA123 GLU124 ARG125 GLU126 ILE127 ASN128 LEU129 TRP130 PHE131 ASN132 GLU133 ASN134 GLU135 ILE136 THR137 SER138 TYR139 ALA140 SER141 PRO142 ARG143 ASP144 ALA145 TRP146 LEU147 TYR148 GLU149
Unit 5 MET1 GLU2 ARG3 THR4 PHE5 LEU6 MET7 ILE8 LYS9 PRO10 ASP11 ALA12 VAL13 GLN14 ARG15 ASN16 LEU17 ILE18 GLY19 GLU20 VAL21 ILE22 SER23 ARG24 ILE25 GLU26 ARG27 LYS28 GLY29 LEU30 LYS31 LEU32 VAL33 GLY34 GLY35 LYS36 LEU37 MET38 GLN39 VAL40 PRO41 MET42 GLU43 LEU44 ALA45 GLU46 THR47 HIS48 TYR49 GLY50 GLU51 HIS52 GLN53 GLY54 LYS55 PRO56 PHE57 TYR58 ASN59 ASP60 LEU61 ILE62 SER63 PHE64 ILE65 THR66 SER67 ALA68 PRO69 VAL70 PHE71 ALA72 MET73 VAL74 VAL75 GLU76 GLY77 GLU78 ASP79 ALA80 VAL81 ASN82 VAL83 SER84 ARG85 HIS86 ILE87 ILE88 GLY89 SER90 THR91 ASN92 PRO93 SER94 GLU95 ALA96 SER97 PRO98 GLY99 SER100 ILE101 ARG102 GLY103 ASP104 LEU105 GLY106 LEU107 THR108 VAL109 GLY110 ARG111 ASN112 ILE113 ILE114 HIS115 GLY116 SER117 ASP118 SER119 LEU120 GLU121 SER122 ALA123 GLU124 ARG125 GLU126 ILE127 ASN128 LEU129 TRP130 PHE131 ASN132 GLU133 ASN134 GLU135 ILE136 THR137 SER138 TYR139 ALA140 SER141 PRO142 ARG143 ASP144 ALA145 TRP146 LEU147 TYR148 GLU149
Unit 6 MET1 GLU2 ARG3 THR4 PHE5 LEU6 MET7 ILE8 LYS9 PRO10 ASP11 ALA12 VAL13 GLN14 ARG15 ASN16 LEU17 ILE18 GLY19 GLU20 VAL21 ILE22 SER23 ARG24 ILE25 GLU26 ARG27 LYS28 GLY29 LEU30 LYS31 LEU32 VAL33 GLY34 GLY35 LYS36 LEU37 MET38 GLN39 VAL40 PRO41 MET42 GLU43 LEU44 ALA45 GLU46 THR47 HIS48 TYR49 GLY50 GLU51 HIS52 GLN53 GLY54 LYS55 PRO56 PHE57 TYR58 ASN59 ASP60 LEU61 ILE62 SER63 PHE64 ILE65 THR66 SER67 ALA68 PRO69 VAL70 PHE71 ALA72 MET73 VAL74 VAL75 GLU76 GLY77 GLU78 ASP79 ALA80 VAL81 ASN82 VAL83 SER84 ARG85 HIS86 ILE87 ILE88 GLY89 SER90 THR91 ASN92 PRO93 SER94 GLU95 ALA96 SER97 PRO98 GLY99 SER100 ILE101 ARG102 GLY103 ASP104 LEU105 GLY106 LEU107 THR108 VAL109 GLY110 ARG111 ASN112 ILE113 ILE114 HIS115 GLY116 SER117 ASP118 SER119 LEU120 GLU121 SER122 ALA123 GLU124 ARG125 GLU126 ILE127 ASN128 LEU129 TRP130 PHE131 ASN132 GLU133 ASN134 GLU135 ILE136 THR137 SER138 TYR139 ALA140 SER141 PRO142 ARG143 ASP144 ALA145 TRP146 LEU147 TYR148 GLU149
Ligands
Unit 7 ADP158 MG159
Unit 8 ADP158 MG159
Unit 9 ADP158
Unit 10 ADP158 MG159
Unit 11 ADP158 MG159
Unit 12 ADP158 MG159
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Perl script:    PDBscan.pl  (15 Sep 2016)
Author:    Peter Slickers  (slickers@leibniz-fli.de),  IMB Jena,  Germany