Research workbench
Asymmetric assembly of merkel cell polyomavirus large T-antigen origin binding domains at the viral origin
Analyse Asymmetric assembly of merkel cell polyomavirus large T-antigen origin binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QFQ
- Type
- protein + DNA
- Length
- 408 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large T antigen; DNA (26-mer)
- UniProt
- E2IPT4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Large T antigen | protein | 119 | 25% helix, 27% strand | E2IPT4 |
| B | Large T antigen | protein | 120 | 26% helix, 29% strand | E2IPT4 |
| E | Large T antigen | protein | 117 | 26% helix, 35% strand | E2IPT4 |
| W | DNA (26-mer) | dna | 26 | — | — |
| C | DNA (26-mer) | dna | 26 | — | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.55 | 0.75 | 25 | empty |
| 2 | 167 | 0.52 | 0.79 | 27 | empty |
| 3 | 92 | 0.46 | 0.80 | 17 | empty |
| 4 | 137 | 0.42 | 0.76 | 29 | empty |
| 5 | 52 | 0.39 | 0.81 | 17 | empty |
Interfaces
8 interfaces between chains.
- W–C · 1143 Ų buried · 99 hydrogen bonds · nucleic-nucleic
- E–W · 380 Ų buried · 13 hydrogen bonds · protein-nucleic
- E–C · 379 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–W · 375 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–C · 372 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3QFQ · Asymmetric Assembly of Merkel Cell Polyomavirus Large T-antigen Origin Binding Domains at… · the same entry in another collection · chain A against A, 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 E2IPT4
- Elsewhere: RCSB PDB 3QFQ · PDBe 3QFQ · UniProt E2IPT4
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