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
- 4NNU
- Type
- protein + DNA
- Length
- 473 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor a, mitochondrial; DNA1; DNA2
- UniProt
- Q00059
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor a, mitochondrial | protein | 193 | 71% helix, 1% strand | Q00059 |
| B | Transcription factor a, mitochondrial | protein | 192 | 72% helix, 1% strand | Q00059 |
| C, E | DNA1 | dna | 22 | — | — |
| D, F | DNA2 | dna | 22 | — | — |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.80 | 0.82 | 62 | empty |
| 2 | 824 | 0.79 | 0.82 | 58 | empty |
| 3 | 337 | 0.59 | 0.77 | 19 | empty |
| 4 | 253 | 0.58 | 0.79 | 18 | empty |
| 5 | 234 | 0.51 | 0.76 | 21 | empty |
Interfaces
15 interfaces between chains.
- A–C · 1419 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–E · 1397 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–F · 1254 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–D · 1211 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–F · 981 Ų buried · 91 hydrogen bonds · nucleic-nucleic
Compared structures
- 4NNU · Distinct structural features of TFAM drive mitochondrial DNA packaging versus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q00059 · AlphaFold monomer V2.0 prediction for transcription factor a, mitochondrial (Q00059) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 4NNU · PDBe 4NNU · UniProt Q00059
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