Research workbench
Cryo-EM structures of human fucosidase FUCA1 reveal insight into substate recognition and catalysis.
Analyse Cryo-EM structures of human fucosidase FUCA1 reveal insight into substate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PM4
- Type
- protein
- Length
- 1,724 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tissue alpha-L-fucosidase
- EC
- 3.2.1.51
- UniProt
- P04066
- Ligands
- DFU, NAG
- Pockets
- 16 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 30% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Tissue alpha-L-fucosidase (EC 3.2.1.51) | protein | 431 | 30% helix, 21% strand | P04066 |
Ligands and binding sites
- DFU · (2S,3R,4S,5R)-2-methylpiperidine-3,4,5-triol · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.80 | 0.88 | 58 | empty |
| 2 | 364 | 0.78 | 0.88 | 57 | empty |
| 3 | 573 | 0.65 | 0.76 | 50 | empty |
| 4 | 159 | 0.65 | 0.86 | 24 | empty |
| 5 | 154 | 0.64 | 0.85 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1261 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 1261 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 946 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 943 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 159 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7PM4 · Cryo-EM structures of human fucosidase FucA1 reveal insight into substate recognition and… · the same entry in another collection · chain D against D, TM-score 1.00
- P04066 · AlphaFold monomer V2.0 prediction for tissue alpha-L-fucosidase (P04066) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P04066
- Elsewhere: RCSB PDB 7PM4 · PDBe 7PM4 · UniProt P04066
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