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A crystal structure of SV40 large T antigen
Analyse A crystal structure of SV40 large T antigen in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GDF
- Type
- protein + DNA
- Length
- 2,116 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large T antigen; DNA (32-mer)
- UniProt
- Q9DH70
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | Large T antigen | protein | 497 | 45% helix, 14% strand | Q9DH70 |
| C, G | DNA (32-mer) | dna | 32 | — | — |
| D, H | DNA (32-mer) | dna | 32 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, E, F
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 | 716 | 0.82 | 0.86 | 71 | empty |
| 2 | 808 | 0.81 | 0.84 | 72 | empty |
| 3 | 707 | 0.80 | 0.84 | 71 | empty |
| 4 | 636 | 0.79 | 0.84 | 67 | empty |
| 5 | 766 | 0.77 | 0.81 | 71 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1803 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1798 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1401 Ų buried · 107 hydrogen bonds · nucleic-nucleic
- G–H · 1397 Ų buried · 107 hydrogen bonds · nucleic-nucleic
- A–D · 886 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 4GDF · A Crystal Structure of SV40 Large T Antigen · 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 Q9DH70
- Elsewhere: RCSB PDB 4GDF · PDBe 4GDF · UniProt Q9DH70
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