MolNFT v1 · #76520 · protein
Crystal structure of AD37 fiber knob in complex with trivalent sialic acid inhibitor
3QND · Fiber protein: “Crystal structure of AD37 fiber knob in complex with trivalent sialic acid inhibitor”. X-ray diffraction, 2 ligands (SIA, ZN), 3 pockets (best druggability 0.70). MolNFT v1 #76520 on GenesisL1: 3D structure, binding…
- PDB
- 3QND
- Type
- protein
- Length
- 1,104 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- Q64823
- Ligands
- SIA, ZN
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, G | Fiber protein | protein | 184 | 3% helix, 43% strand | Q64823 |
| B | Fiber protein | protein | 185 | 5% helix, 45% strand | Q64823 |
| C | Fiber protein | protein | 183 | 5% helix, 44% strand | Q64823 |
Ligands and binding sites
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, B, C, E, F, G
- ZN · Zinc ion · metal · 7 copies · chains A, B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 363 | 0.70 | 0.82 | 44 | empty |
| 2 | 376 | 0.69 | 0.81 | 47 | empty |
| 3 | 92 | 0.33 | 0.73 | 17 | empty |
Interfaces
9 interfaces between chains.
- F–G · 1081 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1074 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1072 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1070 Ų buried · 25 hydrogen bonds · protein-protein
- E–G · 1064 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3QND · crystal structure of Ad37 fiber knob in complex with trivalent sialic acid inhibitor · 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 Q64823
- Elsewhere: RCSB PDB 3QND · PDBe 3QND · UniProt Q64823
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