MolNFT v1 · #168147 · protein + DNA
Cryo-EM structure of cst bound to telomeric single-stranded DNA
6W6W · Cst complex subunit CTC1: “Cryo-EM structure of cst bound to telomeric single-stranded DNA”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.76). MolNFT v1 #168147 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6W6W
- Type
- protein + DNA
- Length
- 1,392 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cst complex subunit CTC1; DNA (5'-D(P*TP*AP*GP*G)-3'); Cst complex subunit STN1; Cst…
- UniProt
- Q2NKJ3, Q9H668, Q86WV5
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.76
Structure
electron microscopy · 5 distinct chains · 15% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cst complex subunit CTC1 | protein | 905 | 10% helix, 30% strand | Q2NKJ3 |
| E | DNA (5'-D(P*TP*AP*GP*G)-3') | dna | 4 | — | — |
| B | Cst complex subunit CTC1 | protein | 43 | 0% helix, 2% strand | Q2NKJ3 |
| C | Cst complex subunit STN1 | protein | 323 | 29% helix, 19% strand | Q9H668 |
| D | Cst complex subunit TEN1 | protein | 117 | 18% helix, 35% strand | Q86WV5 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 419 | 0.76 | 0.85 | 42 | empty |
| 2 | 751 | 0.67 | 0.75 | 72 | empty |
| 3 | 254 | 0.67 | 0.83 | 26 | empty |
| 4 | 264 | 0.64 | 0.81 | 33 | empty |
| 5 | 113 | 0.64 | 0.88 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2216 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1165 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 751 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 485 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6W6W · Cryo-EM structure of CST bound to telomeric single-stranded DNA · the same entry in another collection · chain D against D, TM-score 1.00
- Q86WV5 · AlphaFold monomer V2.0 prediction for cst complex subunit TEN1 (Q86WV5) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q2NKJ3 · AlphaFold monomer V2.0 prediction for cst complex subunit CTC1 (Q2NKJ3) · a predicted model of the same protein · chain A against A, TM-score 0.95
- Q9H668 · AlphaFold monomer V2.0 prediction for cst complex subunit STN1 (Q9H668) · a predicted model of the same protein · chain C against A, TM-score 0.48
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 Q2NKJ3
- Every structure of UniProt Q9H668
- Every structure of UniProt Q86WV5
- Elsewhere: RCSB PDB 6W6W · PDBe 6W6W · UniProt Q2NKJ3 · UniProt Q9H668 · UniProt Q86WV5
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