MolNFT v1 · #70793 · protein
Crystal structure of the glycoside hydrolase, family 43 yxia protein from bacillus licheniformis. northeast structural genomics consortium target BIR14.
3LV4 · Glycoside hydrolase yxia: “Crystal structure of the glycoside hydrolase, family 43 yxia protein from bacillus licheniformis. northeast…”. X-ray diffraction, 1 ligand (CA), 10 pockets (best druggability 0.65). MolNFT v1 #70793 on…
- 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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