Research workbench
Crystal structure of tfam (mitochondrial transcription factor a) in complex with lsp
Analyse Crystal structure of tfam (mitochondrial transcription factor a) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LBX
- Type
- protein + DNA
- Length
- 467 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
- MG
- Pockets
- 7 · best druggability 0.77
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 | 190 | 76% helix, 1% strand | Q00059 |
| B | Transcription factor a, mitochondrial | protein | 189 | 78% helix, 1% strand | Q00059 |
| C, E | DNA (5'- D(P*TP*TP*AP*AP*CP*AP*GP*TP*CP*AP*CP*CP*CP*CP*CP*CP*AP*AP*CP*TP*AP*A) -3') | dna | 22 | — | — |
| D, F | DNA (5'- D(P*TP*TP*AP*GP*TP*TP*GP*GP*GP*GP*GP*GP*TP*GP*AP*CP*TP*GP*TP*TP*AP*A) -3') | dna | 22 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.77 | 0.82 | 66 | empty |
| 2 | 957 | 0.75 | 0.78 | 64 | empty |
| 3 | 196 | 0.54 | 0.79 | 19 | empty |
| 4 | 199 | 0.49 | 0.77 | 15 | MG |
| 5 | 127 | 0.39 | 0.75 | 19 | empty |
Interfaces
11 interfaces between chains.
- A–C · 1469 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–F · 1430 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–D · 1379 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–E · 1271 Ų buried · 9 hydrogen bonds · protein-nucleic
- E–F · 974 Ų buried · 91 hydrogen bonds · nucleic-nucleic
Compared structures
- 7LBX · Crystal structure of TFAM (mitochondrial transcription factor A) in complex with LSP · 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 0.96
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 7LBX · PDBe 7LBX · UniProt Q00059
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