MolNFT v1 · #27109 · protein
The crystal structure of human adenovirus 2 penton base in complex with an AD2 N-terminal fibre peptide
1X9T · Penton protein: “The crystal structure of human adenovirus 2 penton base in complex with an AD2 N-terminal fibre peptide”. X-ray diffraction, 1 ligand (C15), 6 pockets (best druggability 0.69). MolNFT v1 #27109 on GenesisL1: 3D…
- PDB
- 1X9T
- Type
- protein
- Length
- 450 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Penton protein; N-terminl peptide of fiber protein
- UniProt
- P03276
- Ligands
- C15
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Penton protein | protein | 440 | 14% helix, 35% strand | P03276 |
| B | N-terminl peptide of fiber protein | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- C15 · N-dodecyl-N,N-dimethyl-3-ammonio-1-propanesulfonate · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.96 | 17 | empty |
| 2 | 225 | 0.54 | 0.77 | 30 | empty |
| 3 | 92 | 0.43 | 0.78 | 17 | empty |
| 4 | 57 | 0.35 | 0.78 | 20 | empty |
| 5 | 62 | 0.34 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 435 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1X9T · The crystal structure of human adenovirus 2 penton base in complex with an ad2 N-terminal… · 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 P03276
- Elsewhere: RCSB PDB 1X9T · PDBe 1X9T · UniProt P03276
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