Research workbench
Crystal structure of tfam (mitochondrial transcription factor a) bridging two non-sequence specific DNA substrates
Analyse Crystal structure of tfam (mitochondrial transcription factor a) bridging two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LBW
- Type
- protein + DNA
- Length
- 471 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor a, mitochondrial; DNA (5'…
- UniProt
- Q00059
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 77% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor a, mitochondrial | protein | 193 | 76% helix, 1% strand | Q00059 |
| B | Transcription factor a, mitochondrial | protein | 190 | 77% helix, 1% strand | Q00059 |
| C, E | DNA (5'- D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G) -3') | dna | 22 | — | — |
| D, F | DNA (5'- D(P*TP*AP*GP*CP*CP*TP*TP*TP*CP*TP*AP*TP*TP*AP*GP*CP*TP*CP*TP*TP*AP*G) -3') | dna | 22 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.79 | 0.82 | 63 | PEG, EDO |
| 2 | 774 | 0.77 | 0.81 | 63 | empty |
| 3 | 349 | 0.58 | 0.77 | 25 | empty |
| 4 | 233 | 0.52 | 0.77 | 18 | empty |
| 5 | 82 | 0.46 | 0.82 | 19 | empty |
Interfaces
15 interfaces between chains.
- C–F · 959 Ų buried · 84 hydrogen bonds · nucleic-nucleic
- D–E · 954 Ų buried · 86 hydrogen bonds · nucleic-nucleic
- A–C · 876 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–F · 865 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–D · 826 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 7LBW · Crystal structure of TFAM (mitochondrial transcription factor A) bridging two… · 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 A against A, TM-score 0.97
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 7LBW · PDBe 7LBW · UniProt Q00059
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