Research workbench
Crystal structure of the glycoside hydrolase, family 43 yxia protein from bacillus licheniformis. northeast structural genomics consortium target BIR14.
Analyse Crystal structure of the glycoside hydrolase, family 43 yxia protein from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LV4
- Type
- protein
- Length
- 880 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase yxia
- UniProt
- Q65D31
- Ligands
- CA
- Pockets
- 10 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase yxia | protein | 441 | 6% helix, 46% strand | Q65D31 |
| B | Glycoside hydrolase yxia | protein | 439 | 6% helix, 46% strand | Q65D31 |
Ligands and binding sites
- CA · Calcium ion · metal · 5 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.65 | 0.85 | 29 | empty |
| 2 | 363 | 0.63 | 0.78 | 25 | empty |
| 3 | 353 | 0.62 | 0.78 | 23 | empty |
| 4 | 166 | 0.60 | 0.83 | 30 | empty |
| 5 | 81 | 0.45 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 152 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3LV4 · Crystal structure of the glycoside hydrolase, family 43 YxiA protein from Bacillus… · 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 Q65D31
- Elsewhere: RCSB PDB 3LV4 · PDBe 3LV4 · UniProt Q65D31
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