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Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from bacteroides thetaiotaomicron vpi-5482 at 1.60 a resolution
Analyse Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GZA
- Type
- protein
- Length
- 869 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative alpha-L-fucosidase
- UniProt
- Q8A169
- Ligands
- UNL, NA
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative alpha-L-fucosidase | protein | 438 | 28% helix, 28% strand | Q8A169 |
| B | Putative alpha-L-fucosidase | protein | 431 | 28% helix, 29% strand | Q8A169 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · chains B
- NA · Sodium ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 288 | 0.57 | 0.77 | 36 | EPE, EDO |
| 2 | 256 | 0.54 | 0.76 | 34 | UNL, EDO |
| 3 | 115 | 0.39 | 0.75 | 24 | empty |
| 4 | 94 | 0.35 | 0.75 | 23 | empty |
| 5 | 57 | 0.30 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1471 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 3GZA · Crystal structure of putative alpha-L-fucosidase (NP_812709.1) from BACTEROIDES… · 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 Q8A169
- Elsewhere: RCSB PDB 3GZA · PDBe 3GZA · UniProt Q8A169
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