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Crystal structure of a putative glycosyl hydrolase (BT3469) from bacteroides thetaiotaomicron vpi-5482 at 2.49 a resolution
Analyse Crystal structure of a putative glycosyl hydrolase (BT3469) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JQT
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative glycosyl hydrolase
- UniProt
- Q8A237
- Ligands
- NA
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 8% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Putative glycosyl hydrolase | protein | 431 | 8% helix, 41% strand | Q8A237 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.71 | 0.79 | 44 | empty |
| 2 | 522 | 0.64 | 0.76 | 36 | EDO |
| 3 | 54 | 0.39 | 0.81 | 20 | empty |
| 4 | 57 | 0.37 | 0.79 | 17 | EDO |
| 5 | 59 | 0.37 | 0.79 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 916 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4JQT · Crystal structure of a putative glycosyl hydrolase (BT3469) 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 Q8A237
- Elsewhere: RCSB PDB 4JQT · PDBe 4JQT · UniProt Q8A237
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