MolNFT v1 · #167573 · protein + DNA
Cryo-EM structure of HTLV-1 instasome
6VOY · DNA-binding protein 7D: “Cryo-EM structure of HTLV-1 instasome”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #167573 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6VOY
- Type
- protein + DNA
- Length
- 1,904 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-binding protein 7D; SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit…
- UniProt
- P39476, A0A1Y1CAW1, Q13362
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 43% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA-binding protein 7D | protein | 276 | 33% helix, 12% strand | P39476, A0A1Y1CAW1 |
| B, D | DNA-binding protein 7D | protein | 259 | 32% helix, 8% strand | P39476, A0A1Y1CAW1 |
| E, F | SERINE/THREONINE-protein phosphatase 2A 56 kda regulatory subunit gamma isoform | protein | 327 | 59% helix, 0% strand | Q13362 |
| I, L | DNA (5'- D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3') | dna | 47 | — | — |
| J, M | DNA (25-mer) | dna | 25 | — | — |
| K, N | DNA (5'- D(P*AP*CP*AP*CP*AP*CP*TP*TP*GP*AP*CP*TP*AP*GP*GP*GP*TP*G)-3') | dna | 18 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, K, C, I, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 745 | 0.86 | 0.89 | 84 | empty |
| 2 | 698 | 0.86 | 0.89 | 85 | empty |
| 3 | 685 | 0.83 | 0.87 | 80 | empty |
| 4 | 777 | 0.83 | 0.86 | 86 | empty |
| 5 | 584 | 0.83 | 0.87 | 53 | empty |
Interfaces
32 interfaces between chains.
- C–D · 1585 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1507 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1244 Ų buried · 21 hydrogen bonds · protein-protein
- B–F · 1239 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1232 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6VOY · Cryo-EM structure of HTLV-1 instasome · the same entry in another collection · chain N against N, 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 P39476
- Every structure of UniProt A0A1Y1CAW1
- Every structure of UniProt Q13362
- Elsewhere: RCSB PDB 6VOY · PDBe 6VOY · UniProt P39476 · UniProt A0A1Y1CAW1 · UniProt Q13362
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