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Crystal structure of SV40 large T antigen origin binding domain with DNA
Analyse Crystal structure of SV40 large T antigen origin binding domain with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2NTC
- Type
- protein + DNA
- Length
- 295 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 21-nt pen element of the SV40 DNA origin; Large T antigen
- UniProt
- P03070
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| W | 21-nt pen element of the SV40 DNA origin | dna | 21 | — | — |
| C | 21-nt pen element of the SV40 DNA origin | dna | 21 | — | — |
| A | Large T antigen | protein | 127 | 28% helix, 32% strand | P03070 |
| B | Large T antigen | protein | 126 | 29% helix, 31% strand | P03070 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.41 | 0.78 | 21 | empty |
| 2 | 76 | 0.37 | 0.78 | 16 | empty |
| 3 | 85 | 0.34 | 0.75 | 17 | empty |
| 4 | 64 | 0.30 | 0.74 | 12 | empty |
Interfaces
6 interfaces between chains.
- W–C · 938 Ų buried · 105 hydrogen bonds · nucleic-nucleic
- W–B · 425 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–A · 422 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–B · 389 Ų buried · 10 hydrogen bonds · protein-nucleic
- W–A · 363 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 2NTC · Crystal Structure of sv40 large T antigen origin binding domain with DNA · the same entry in another collection · chain W against W, 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 2NTC · PDBe 2NTC · UniProt P03070
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