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Sequence, Chains, Asymmetric and Biological Units

Title DISTINCT STRUCTURAL FEATURES OF TFAM DRIVE MITOCHONDRIAL DNA VERSUS TRANSCRIPTIONAL ACTIVATION
Keywords HMG, DNA BENDING, TFB2M, MTRNAP, BRU SUBSTITUTION TO HSP1, T TRANSCRIPTION REGULATOR-DNA COMPLEX
Experiment X-ray diffraction
Number of Models  1

   Database       ID code    StatusCoordinate files
        Header     Asymmetric unit     Biological unit  
PDB   4NOD     released     available     available     Quaternary Structure Server  
Asymmetric unit from PDB
 Unit     Type     Name   Chain ID   Residues   Atoms   Hetatoms 
1  Protein   TRANSCRIPTION FACTOR A, MITOCHONDRIAL  A 190 1602 0
2  Protein   TRANSCRIPTION FACTOR A, MITOCHONDRIAL  B 190 1602 0
3  DNA    C 22 440 20
4  DNA    E 22 440 20
5  Other macromolecule   5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*T *CP*CP*AP*A)-3'  D 22 435 0
6  Other macromolecule   5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*T *CP*CP*AP*A)-3'  F 22 435 0
7  Protein   TRANSCRIPTION FACTOR A, MITOCHONDRIAL  G 190 1602 0
8  Protein   TRANSCRIPTION FACTOR A, MITOCHONDRIAL  H 190 1602 0
9  DNA    I 22 440 20
10  DNA    K 22 439 20
11  Other macromolecule   5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*T *CP*CP*AP*A)-3'  J 22 434 0
12  Other macromolecule   5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*T *CP*CP*AP*A)-3'  L 22 434 0
total       936 9905 80
Proteins
Unit 1 SER44 VAL45 LEU46 ALA47 SER48 CYS49 PRO50 LYS51 LYS52 PRO53 VAL54 SER55 SER56 TYR57 LEU58 ARG59 PHE60 SER61 LYS62 GLU63 GLN64 LEU65 PRO66 ILE67 PHE68 LYS69 ALA70 GLN71 ASN72 PRO73 ASP74 ALA75 LYS76 THR77 THR78 GLU79 LEU80 ILE81 ARG82 ARG83 ILE84 ALA85 GLN86 ARG87 TRP88 ARG89 GLU90 LEU91 PRO92 ASP93 SER94 LYS95 LYS96 LYS97 ILE98 TYR99 GLN100 ASP101 ALA102 TYR103 ARG104 ALA105 GLU106 TRP107 GLN108 VAL109 TYR110 LYS111 GLU112 GLU113 ILE114 SER115 ARG116 PHE117 LYS118 GLU119 GLN120 LEU121 THR122 PRO123 SER124 GLN125 ILE126 MET127 SER128 LEU129 GLU130 LYS131 GLU132 ILE133 MET134 ASP135 LYS136 HIS137 LEU138 LYS139 ARG140 LYS141 ALA142 MET143 THR144 LYS145 LYS146 LYS147 GLU148 LEU149 THR150 LEU151 LEU152 GLY153 LYS154 PRO155 LYS156 ARG157 PRO158 ARG159 SER160 ALA161 TYR162 ASN163 VAL164 TYR165 VAL166 ALA167 GLU168 ARG169 PHE170 GLN171 GLU172 ALA173 LYS174 GLY175 ASP176 SER177 PRO178 GLN179 GLU180 LYS181 LEU182 LYS183 THR184 VAL185 LYS186 GLU187 ASN188 TRP189 LYS190 ASN191 LEU192 SER193 ASP194 SER195 GLU196 LYS197 GLU198 LEU199 TYR200 ILE201 GLN202 HIS203 ALA204 LYS205 GLU206 ASP207 GLU208 THR209 ARG210 TYR211 HIS212 ASN213 GLU214 MET215 LYS216 SER217 TRP218 GLU219 GLU220 GLN221 MET222 ILE223 GLU224 VAL225 GLY226 ARG227 LYS228 ASP229 LEU230 LEU231 ARG232 ARG233
Unit 2 SER44 VAL45 LEU46 ALA47 SER48 CYS49 PRO50 LYS51 LYS52 PRO53 VAL54 SER55 SER56 TYR57 LEU58 ARG59 PHE60 SER61 LYS62 GLU63 GLN64 LEU65 PRO66 ILE67 PHE68 LYS69 ALA70 GLN71 ASN72 PRO73 ASP74 ALA75 LYS76 THR77 THR78 GLU79 LEU80 ILE81 ARG82 ARG83 ILE84 ALA85 GLN86 ARG87 TRP88 ARG89 GLU90 LEU91 PRO92 ASP93 SER94 LYS95 LYS96 LYS97 ILE98 TYR99 GLN100 ASP101 ALA102 TYR103 ARG104 ALA105 GLU106 TRP107 GLN108 VAL109 TYR110 LYS111 GLU112 GLU113 ILE114 SER115 ARG116 PHE117 LYS118 GLU119 GLN120 LEU121 THR122 PRO123 SER124 GLN125 ILE126 MET127 SER128 LEU129 GLU130 LYS131 GLU132 ILE133 MET134 ASP135 LYS136 HIS137 LEU138 LYS139 ARG140 LYS141 ALA142 MET143 THR144 LYS145 LYS146 LYS147 GLU148 LEU149 THR150 LEU151 LEU152 GLY153 LYS154 PRO155 LYS156 ARG157 PRO158 ARG159 SER160 ALA161 TYR162 ASN163 VAL164 TYR165 VAL166 ALA167 GLU168 ARG169 PHE170 GLN171 GLU172 ALA173 LYS174 GLY175 ASP176 SER177 PRO178 GLN179 GLU180 LYS181 LEU182 LYS183 THR184 VAL185 LYS186 GLU187 ASN188 TRP189 LYS190 ASN191 LEU192 SER193 ASP194 SER195 GLU196 LYS197 GLU198 LEU199 TYR200 ILE201 GLN202 HIS203 ALA204 LYS205 GLU206 ASP207 GLU208 THR209 ARG210 TYR211 HIS212 ASN213 GLU214 MET215 LYS216 SER217 TRP218 GLU219 GLU220 GLN221 MET222 ILE223 GLU224 VAL225 GLY226 ARG227 LYS228 ASP229 LEU230 LEU231 ARG232 ARG233
Unit 7 SER44 VAL45 LEU46 ALA47 SER48 CYS49 PRO50 LYS51 LYS52 PRO53 VAL54 SER55 SER56 TYR57 LEU58 ARG59 PHE60 SER61 LYS62 GLU63 GLN64 LEU65 PRO66 ILE67 PHE68 LYS69 ALA70 GLN71 ASN72 PRO73 ASP74 ALA75 LYS76 THR77 THR78 GLU79 LEU80 ILE81 ARG82 ARG83 ILE84 ALA85 GLN86 ARG87 TRP88 ARG89 GLU90 LEU91 PRO92 ASP93 SER94 LYS95 LYS96 LYS97 ILE98 TYR99 GLN100 ASP101 ALA102 TYR103 ARG104 ALA105 GLU106 TRP107 GLN108 VAL109 TYR110 LYS111 GLU112 GLU113 ILE114 SER115 ARG116 PHE117 LYS118 GLU119 GLN120 LEU121 THR122 PRO123 SER124 GLN125 ILE126 MET127 SER128 LEU129 GLU130 LYS131 GLU132 ILE133 MET134 ASP135 LYS136 HIS137 LEU138 LYS139 ARG140 LYS141 ALA142 MET143 THR144 LYS145 LYS146 LYS147 GLU148 LEU149 THR150 LEU151 LEU152 GLY153 LYS154 PRO155 LYS156 ARG157 PRO158 ARG159 SER160 ALA161 TYR162 ASN163 VAL164 TYR165 VAL166 ALA167 GLU168 ARG169 PHE170 GLN171 GLU172 ALA173 LYS174 GLY175 ASP176 SER177 PRO178 GLN179 GLU180 LYS181 LEU182 LYS183 THR184 VAL185 LYS186 GLU187 ASN188 TRP189 LYS190 ASN191 LEU192 SER193 ASP194 SER195 GLU196 LYS197 GLU198 LEU199 TYR200 ILE201 GLN202 HIS203 ALA204 LYS205 GLU206 ASP207 GLU208 THR209 ARG210 TYR211 HIS212 ASN213 GLU214 MET215 LYS216 SER217 TRP218 GLU219 GLU220 GLN221 MET222 ILE223 GLU224 VAL225 GLY226 ARG227 LYS228 ASP229 LEU230 LEU231 ARG232 ARG233
Unit 8 SER44 VAL45 LEU46 ALA47 SER48 CYS49 PRO50 LYS51 LYS52 PRO53 VAL54 SER55 SER56 TYR57 LEU58 ARG59 PHE60 SER61 LYS62 GLU63 GLN64 LEU65 PRO66 ILE67 PHE68 LYS69 ALA70 GLN71 ASN72 PRO73 ASP74 ALA75 LYS76 THR77 THR78 GLU79 LEU80 ILE81 ARG82 ARG83 ILE84 ALA85 GLN86 ARG87 TRP88 ARG89 GLU90 LEU91 PRO92 ASP93 SER94 LYS95 LYS96 LYS97 ILE98 TYR99 GLN100 ASP101 ALA102 TYR103 ARG104 ALA105 GLU106 TRP107 GLN108 VAL109 TYR110 LYS111 GLU112 GLU113 ILE114 SER115 ARG116 PHE117 LYS118 GLU119 GLN120 LEU121 THR122 PRO123 SER124 GLN125 ILE126 MET127 SER128 LEU129 GLU130 LYS131 GLU132 ILE133 MET134 ASP135 LYS136 HIS137 LEU138 LYS139 ARG140 LYS141 ALA142 MET143 THR144 LYS145 LYS146 LYS147 GLU148 LEU149 THR150 LEU151 LEU152 GLY153 LYS154 PRO155 LYS156 ARG157 PRO158 ARG159 SER160 ALA161 TYR162 ASN163 VAL164 TYR165 VAL166 ALA167 GLU168 ARG169 PHE170 GLN171 GLU172 ALA173 LYS174 GLY175 ASP176 SER177 PRO178 GLN179 GLU180 LYS181 LEU182 LYS183 THR184 VAL185 LYS186 GLU187 ASN188 TRP189 LYS190 ASN191 LEU192 SER193 ASP194 SER195 GLU196 LYS197 GLU198 LEU199 TYR200 ILE201 GLN202 HIS203 ALA204 LYS205 GLU206 ASP207 GLU208 THR209 ARG210 TYR211 HIS212 ASN213 GLU214 MET215 LYS216 SER217 TRP218 GLU219 GLU220 GLN221 MET222 ILE223 GLU224 VAL225 GLY226 ARG227 LYS228 ASP229 LEU230 LEU231 ARG232 ARG233
Nucleic acids
Unit 3 DT1 DT2 DG3 DG4 DG5 DG6 DT7 DA8 DT9 DG10 DG11 DG12 DG13 DC14 DT15 DT16 DG17 DG18 BRU19 DT20 DG21 DG22
Unit 4 DT1 DT2 DG3 DG4 DG5 DG6 DT7 DA8 DT9 DG10 DG11 DG12 DG13 DC14 DT15 DT16 DG17 DG18 BRU19 DT20 DG21 DG22
Unit 9 DT1 DT2 DG3 DG4 DG5 DG6 DT7 DA8 DT9 DG10 DG11 DG12 DG13 DC14 DT15 DT16 DG17 DG18 BRU19 DT20 DG21 DG22
Unit 10 DT1 DT2 DG3 DG4 DG5 DG6 DT7 DA8 DT9 DG10 DG11 DG12 DG13 DC14 DT15 DT16 DG17 DG18 BRU19 DT20 DG21 DG22
Other macromolecules
Unit 5 DC1 DC2 DA3 DA4 DC5 DC6 DA7 DA8 DG9 DC10 DC11 DC12 DC13 DA14 DT15 DA16 DC17 DC18 DC19 DC20 DA21 DA22
Unit 6 DC1 DC2 DA3 DA4 DC5 DC6 DA7 DA8 DG9 DC10 DC11 DC12 DC13 DA14 DT15 DA16 DC17 DC18 DC19 DC20 DA21 DA22
Unit 11 DC1 DC2 DA3 DA4 DC5 DC6 DA7 DA8 DG9 DC10 DC11 DC12 DC13 DA14 DT15 DA16 DC17 DC18 DC19 DC20 DA21 DA22
Unit 12 DC1 DC2 DA3 DA4 DC5 DC6 DA7 DA8 DG9 DC10 DC11 DC12 DC13 DA14 DT15 DA16 DC17 DC18 DC19 DC20 DA21 DA22
Chirality of ribose and phosphate atoms

Check the naming of phosphate and ribose substituents. Recommended for phosphate oxygens and for ribose hydrogens in NMR structures.

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