Research workbench
Crystal structure of human mitochondrial transcription factor a, tfam or mttfa, bound to the light strand promoter lsp
Analyse Crystal structure of human mitochondrial transcription factor a, tfam or mttfa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TQ6
- Type
- protein + DNA
- Length
- 472 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor a, mitochondrial; DNA (5'…
- UniProt
- Q00059
- Ligands
- PO4
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor a, mitochondrial | protein | 194 | 76% helix, 1% strand | Q00059 |
| B | Transcription factor a, mitochondrial | protein | 190 | 76% helix, 1% strand | Q00059 |
| C, E | DNA (5'- D(*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*(BRU) P*AP*AP*C)-3') | dna | 22 | — | — |
| D, F | DNA (5'- D(*GP*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*A)- 3') | dna | 22 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains C, D
- 1PE · Pentaethylene glycol · additive · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 649 | 0.77 | 0.83 | 55 | empty |
| 2 | 718 | 0.76 | 0.81 | 59 | empty |
| 3 | 378 | 0.72 | 0.84 | 37 | empty |
| 4 | 233 | 0.58 | 0.80 | 22 | empty |
| 5 | 158 | 0.54 | 0.80 | 15 | empty |
Interfaces
15 interfaces between chains.
- A–C · 1597 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–E · 1511 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–D · 1384 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–F · 1367 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–F · 980 Ų buried · 90 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3TQ6 · Crystal structure of human mitochondrial transcription factor A, TFAM or mtTFA, bound to… · 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 0.99
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 3TQ6 · PDBe 3TQ6 · UniProt Q00059
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