Research workbench
Tfam in complex with site-Y
Analyse Tfam in complex with site-Y in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HB4
- Type
- protein + DNA
- Length
- 953 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor a, mitochondrial; DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*A…
- UniProt
- Q00059
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription factor a, mitochondrial | protein | 197 | 74% helix, 1% strand | Q00059 |
| B, E, H, K | DNA (5'*CP*TP*GP*TP*GP*CP*AP*GP*AP*CP*AP*TP*TP*CP*AP*AP*TP*TP*GP*TP*TP*A) -3') | dna | 22 | — | — |
| C, F, I, L | DNA (5'- D(*TP*AP*AP*CP*AP*AP*TP*TP*GP*AP*AP*TP*GP*TP*CP*TP*GP*CP*AP*CP*AP*G)- 3') | dna | 22 | — | — |
| D | Transcription factor a, mitochondrial | protein | 194 | 75% helix, 1% strand | Q00059 |
| G, J | Transcription factor a, mitochondrial | protein | 193 | 76% helix, 0% strand | Q00059 |
Ligands and binding sites
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, D, E, F, G
- GOL · Glycerol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.80 | 0.83 | 73 | 1PE |
| 2 | 1114 | 0.80 | 0.81 | 80 | empty |
| 3 | 898 | 0.80 | 0.82 | 65 | GOL |
| 4 | 943 | 0.79 | 0.81 | 60 | empty |
| 5 | 183 | 0.56 | 0.80 | 21 | empty |
Interfaces
32 interfaces between chains.
- D–E · 1556 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 1476 Ų buried · 19 hydrogen bonds · protein-nucleic
- J–K · 1475 Ų buried · 12 hydrogen bonds · protein-nucleic
- G–H · 1475 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–F · 1213 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 6HB4 · TFAM in Complex with Site-Y · 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 6HB4 · PDBe 6HB4 · UniProt Q00059
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.