Research workbench
Crystal structure of AD37 fiber knob in complex with trivalent sialic acid inhibitor ME0385
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
- 4K6T
- Type
- protein
- Length
- 1,110 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fiber protein
- UniProt
- Q64823
- Ligands
- 1P0, SIA, ZN, MG, CA, CL
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Fiber protein | protein | 186 | 5% helix, 45% strand | Q64823 |
| C | Fiber protein | protein | 182 | 5% helix, 45% strand | Q64823 |
| E, G | Fiber protein | protein | 185 | 3% helix, 45% strand | Q64823 |
Ligands and binding sites
- 1P0 · 2,2',2''-[nitrilotris(methanediyl-1H-1,2,3-triazole-4,1-diyl)]triethanol · ligand
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 6 copies · chains A, B, C, E, F, G
- ZN · Zinc ion · metal · 14 copies · chains A, B, C, E, F, G
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, E, F
- CA · Calcium ion · metal · chains G
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, E, F
- ACT · Acetate ion · additive · 9 copies · chains A, B, E, F, G
- GOL · Glycerol · additive · 3 copies · chains E, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.71 | 0.83 | 42 | empty |
| 2 | 336 | 0.70 | 0.83 | 37 | empty |
| 3 | 345 | 0.54 | 0.74 | 45 | EDO, MG |
Interfaces
7 interfaces between chains.
- E–G · 1059 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1058 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1052 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1051 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1046 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4K6T · 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 4K6T · PDBe 4K6T · UniProt Q64823
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