MolNFT v1 · #149564 · protein
Crystal structure of human adenovirus 52 short fiber knob in complex with alpha-(2,8)-trisialic acid (DP3)
6G47 · Fiber-1: “Crystal structure of human adenovirus 52 short fiber knob in complex with alpha-(2,8)-trisialic acid (DP3)”. X-ray diffraction, 1 ligand (SIA), 2 pockets (best druggability 0.80). MolNFT v1 #149564 on GenesisL1: 3D…
- PDB
- 6G47
- Type
- protein
- Length
- 496 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber-1
- UniProt
- A0MK70
- Ligands
- SIA
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber-1 | protein | 171 | 10% helix, 43% strand | A0MK70 |
| B | Fiber-1 | protein | 160 | 9% helix, 46% strand | A0MK70 |
| C | Fiber-1 | protein | 165 | 8% helix, 45% strand | A0MK70 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains C, A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B, C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 2 copies · chains B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.80 | 0.97 | 30 | MPD |
| 2 | 72 | 0.29 | 0.73 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1056 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1038 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 994 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6G47 · Crystal Structure of Human Adenovirus 52 Short Fiber Knob in Complex with… · 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 A0MK70
- Elsewhere: RCSB PDB 6G47 · PDBe 6G47 · UniProt A0MK70
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.