MolNFT v1 · #86059 · protein
Structure of a triclinic crystal of the fimh lectin domain in complex with a propynyl biphenyl alpha-D-mannoside, at 1.4 a resolution
4AV5: “Structure of a triclinic crystal of the fimh lectin domain in complex with a propynyl biphenyl…”. X-ray diffraction, 2 ligands (FYZ, SO4), 4 pockets (best druggability 0.72). MolNFT v1 #86059 on GenesisL1: 3D structure, binding…
- PDB
- 4AV5
- Type
- protein
- Length
- 632 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fimh
- UniProt
- A2IC68
- Ligands
- FYZ, SO4
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Fimh | protein | 158 | 6% helix, 51% strand | A2IC68 |
Ligands and binding sites
- FYZ · (2R,3S,4S,5S,6S)-2-(hydroxymethyl)-6-[3-(4-phenylphenyl)prop-2-ynoxy]oxane-3,4,5-triol · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 517 | 0.72 | 0.81 | 69 | empty |
| 2 | 254 | 0.67 | 0.84 | 35 | empty |
| 3 | 379 | 0.61 | 0.77 | 41 | empty |
| 4 | 66 | 0.31 | 0.75 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 595 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 428 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 379 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 364 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 223 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4AV5 · Structure of a triclinic crystal of the FimH lectin domain in complex with a propynyl… · 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 4AV5 · PDBe 4AV5 · UniProt A2IC68
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