MolNFT v1 · #86074 · protein
Structure of trigonal fimh lectin domain crystal soaked with an alpha- D-mannoside O-linked to propynyl pyridine at 2.4A resolution
4AVK: “Structure of trigonal fimh lectin domain crystal soaked with an alpha- D-mannoside O-linked to propynyl…”. X-ray diffraction, 3 ligands (FVQ, NI, SO4), 2 pockets (best druggability 0.51). MolNFT v1 #86074 on GenesisL1: 3D structure…
- PDB
- 4AVK
- Type
- protein
- Length
- 316 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimh
- UniProt
- A2IC68
- Ligands
- FVQ, NI, SO4
- Pockets
- 2 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Fimh | protein | 158 | 6% helix, 53% strand | A2IC68 |
Ligands and binding sites
- FVQ · 3-(pyridin-3-yl)prop-2-yn-1-yl alpha-D-mannopyranoside · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains B
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 | 111 | 0.51 | 0.82 | 30 | empty |
| 2 | 65 | 0.29 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 544 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4AVK · Structure of trigonal FimH lectin domain crystal soaked with an alpha- D-mannoside… · 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 A2IC68
- Elsewhere: RCSB PDB 4AVK · PDBe 4AVK · UniProt A2IC68
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