MolNFT v1 · #22111 · protein
Co-crystal structure of SV40 large T antigen helicase domain and ADP
1SVL: “Co-crystal structure of SV40 large T antigen helicase domain and ADP”. X-ray diffraction, 3 ligands (ADP, ZN, MG), 12 pockets (best druggability 0.84). MolNFT v1 #22111 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SVL
- Type
- protein
- Length
- 1,087 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large T antigen
- UniProt
- P03070
- Ligands
- ADP, ZN, MG
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Large T antigen | protein | 363 | 55% helix, 7% strand | P03070 |
| B, C | Large T antigen | protein | 362 | 54% helix, 8% strand | P03070 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.84 | 0.87 | 93 | MG, ADP |
| 2 | 758 | 0.80 | 0.84 | 77 | MG, ADP |
| 3 | 630 | 0.72 | 0.80 | 78 | empty |
| 4 | 65 | 0.68 | 0.94 | 14 | empty |
| 5 | 53 | 0.66 | 0.95 | 14 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1600 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1519 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1SVL · Co-crystal structure of SV40 large T antigen helicase domain and ADP · 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 1SVL · PDBe 1SVL · UniProt P03070
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