MolNFT v1 · #152052 · protein
Structure of alpha-L-rhamnosidase from dictyoglumus thermophilum
6I60 · Alpha-rhamnosidase: “Structure of alpha-L-rhamnosidase from dictyoglumus thermophilum”. X-ray diffraction, 1 ligand (AE3), 20 pockets (best druggability 0.73). MolNFT v1 #152052 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6I60
- Type
- protein
- Length
- 1,769 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-rhamnosidase
- UniProt
- B5YC64
- Ligands
- AE3
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-rhamnosidase | protein | 883 | 23% helix, 30% strand | B5YC64 |
| B | Alpha-rhamnosidase | protein | 886 | 23% helix, 31% strand | B5YC64 |
Ligands and binding sites
- AE3 · 2-(2-ethoxyethoxy)ethanol · ligand · 5 copies · chains A, B
- PGE · Triethylene glycol · additive · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1059 | 0.73 | 0.76 | 87 | PGE |
| 2 | 77 | 0.69 | 0.94 | 21 | empty |
| 3 | 573 | 0.69 | 0.78 | 61 | empty |
| 4 | 297 | 0.64 | 0.81 | 36 | empty |
| 5 | 367 | 0.60 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1492 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6I60 · Structure of alpha-L-rhamnosidase from Dictyoglumus thermophilum · 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 B5YC64
- Elsewhere: RCSB PDB 6I60 · PDBe 6I60 · UniProt B5YC64
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