Research workbench
Distinct structural features of tfam drive mitochondrial DNA packaging versus transcriptional activation
Analyse Distinct structural features of tfam drive mitochondrial DNA packaging versus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NOD
- Type
- protein + DNA
- Length
- 936 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor a, mitochondrial; 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*…
- UniProt
- Q00059
- Pockets
- 19 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, G, H | Transcription factor a, mitochondrial | protein | 190 | 74% helix, 1% strand | Q00059 |
| C, E, I, K | 5'-D(*TP*TP*GP*GP*GP*GP*TP*AP*TP*GP*GP*GP*GP*CP*TP*TP*GP*GP *(BRU)P*TP*GP*G)-3' | dna | 22 | — | — |
| D, F, J, L | 5'-D(*CP*CP*AP*AP*CP*CP*AP*AP*GP*CP*CP*CP*CP*AP*TP*AP*CP*CP *CP*CP*AP*A)-3' | dna | 22 | — | — |
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.76 | 0.79 | 69 | empty |
| 2 | 1192 | 0.76 | 0.79 | 70 | empty |
| 3 | 891 | 0.76 | 0.79 | 61 | empty |
| 4 | 618 | 0.75 | 0.82 | 55 | empty |
| 5 | 436 | 0.69 | 0.80 | 40 | empty |
Interfaces
27 interfaces between chains.
- H–K · 1251 Ų buried · 10 hydrogen bonds · protein-nucleic
- G–I · 1248 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 1244 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–C · 1224 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–H · 1208 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4NOD · Distinct structural features of TFAM drive mitochondrial DNA packaging versus… · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q00059
- Elsewhere: RCSB PDB 4NOD · PDBe 4NOD · UniProt Q00059
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