MolNFT v1 · #97203 · protein
Crystal structure of AD37 fiber knob in complex with trivalent sialic acid inhibitor ME0408
4K6W · Fiber protein: “Crystal structure of AD37 fiber knob in complex with trivalent sialic acid inhibitor ME0408”. X-ray diffraction, 4 ligands (18D, 1P0, ZN), 1 pocket (best druggability 0.72). MolNFT v1 #97203 on GenesisL1: 3D…
- PDB
- 4K6W
- Type
- protein
- Length
- 552 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- Q64823
- Ligands
- 18D, 1P0, ZN, MG
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fiber protein | protein | 183 | 3% helix, 44% strand | Q64823 |
| B | Fiber protein | protein | 185 | 3% helix, 45% strand | Q64823 |
| C | Fiber protein | protein | 184 | 5% helix, 44% strand | Q64823 |
Ligands and binding sites
- 18D · 3,5-dideoxy-5-(propanoylamino)-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid · ligand · 3 copies · chains A, B, C
- 1P0 · 2,2',2''-[nitrilotris(methanediyl-1H-1,2,3-triazole-4,1-diyl)]triethanol · ligand
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 2 copies · chains A, C
- ACT · Acetate ion · additive · 5 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 375 | 0.72 | 0.83 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1043 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1038 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1030 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4K6W · 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 4K6W · PDBe 4K6W · UniProt Q64823
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.