Research workbench
Crystal structure of the SV40 large T-antigen origin bining domain bound to site I DNA
Analyse Crystal structure of the SV40 large T-antigen origin bining domain bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FGN
- Type
- protein + DNA
- Length
- 296 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large T antigen; Site I DNA
- EC
- 3.6.4.-
- UniProt
- P03070
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Large T antigen (EC 3.6.4.-) | protein | 126 | 31% helix, 29% strand | P03070 |
| B | Large T antigen (EC 3.6.4.-) | protein | 124 | 30% helix, 27% strand | P03070 |
| Z | Site I DNA | dna | 23 | — | — |
| Y | Site I DNA | dna | 23 | — | — |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 171 | 0.45 | 0.75 | 25 | empty |
| 2 | 60 | 0.40 | 0.80 | 16 | empty |
| 3 | 84 | 0.31 | 0.74 | 14 | empty |
| 4 | 63 | 0.28 | 0.74 | 13 | empty |
| 5 | 57 | 0.26 | 0.73 | 11 | empty |
Interfaces
6 interfaces between chains.
- Z–Y · 981 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- A–Y · 416 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–Y · 384 Ų buried · 18 hydrogen bonds · protein-nucleic
- A–Z · 351 Ų buried · 9 hydrogen bonds · protein-nucleic
- B–Z · 314 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4FGN · Crystal structure of the SV40 large T-antigen origin bining domain bound to Site I DNA · 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 P03070
- Elsewhere: RCSB PDB 4FGN · PDBe 4FGN · UniProt P03070
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