Research workbench
Crystal structure of AD37 fiber knob in complex with trivalent sialic acid inhibitor ME0408
Analyse Crystal structure of AD37 fiber knob in complex with trivalent sialic acid… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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