MolNFT v1 · #151054 · protein + DNA
Tfam bound to site-X
6HC3 · Transcription factor a, mitochondrial: “Tfam bound to site-X”. X-ray diffraction, 18 pockets (best druggability 0.78). MolNFT v1 #151054 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6HC3
- Type
- protein + DNA
- Length
- 943 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription factor a, mitochondrial; DNA/RNA (5'…
- UniProt
- Q00059
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Transcription factor a, mitochondrial | protein | 192 | 76% helix, 0% strand | Q00059 |
| B, E, H, K | DNA/RNA (5'- D(*TP*AP*AP*CP*AP*AP*AP*AP*AP*AP*TP*TP*TP*CP*CP*AP*CP*CP*AP*AP*AP*C)- 3') | dna | 22 | — | — |
| C, F, I, L | DNA (5'- D(*TP*TP*TP*GP*GP*TP*GP*GP*AP*AP*AP*TP*TP*TP*TP*TP*TP*GP*TP*TP*AP*G)- 3') | dna | 22 | — | — |
| J | Transcription factor a, mitochondrial | protein | 191 | 76% helix, 0% strand | Q00059 |
Ligands and binding sites
- TLA · L(+)-tartaric acid · additive · 5 copies · chains A, D, G
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, D, G, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 689 | 0.78 | 0.84 | 70 | empty |
| 2 | 728 | 0.76 | 0.82 | 62 | 1PE |
| 3 | 938 | 0.74 | 0.77 | 73 | empty |
| 4 | 604 | 0.74 | 0.81 | 60 | empty |
| 5 | 216 | 0.57 | 0.80 | 19 | empty |
Interfaces
28 interfaces between chains.
- G–H · 1458 Ų buried · 20 hydrogen bonds · protein-nucleic
- J–K · 1411 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–E · 1405 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–B · 1390 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–F · 1353 Ų buried · 23 hydrogen bonds · protein-nucleic
Compared structures
- 6HC3 · TFAM bound to Site-X · 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 6HC3 · PDBe 6HC3 · UniProt Q00059
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