Research workbench
The amidase-2 domain of LYSGH15
Analyse The amidase-2 domain of LYSGH15 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OLS
- Type
- protein
- Length
- 740 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endolysin
- UniProt
- D6QY02
- Ligands
- ZN, MG, FE
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Endolysin | protein | 185 | 39% helix, 15% strand | D6QY02 |
Ligands and binding sites
- ZN · Zinc ion · metal · 17 copies · chains A, C, B, D
- MG · Magnesium ion · metal · chains D
- FE · Fe (III) ion · metal · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 553 | 0.70 | 0.80 | 61 | empty |
| 2 | 374 | 0.59 | 0.76 | 38 | ZN |
| 3 | 279 | 0.58 | 0.78 | 35 | ZN |
| 4 | 103 | 0.38 | 0.75 | 22 | empty |
| 5 | 72 | 0.31 | 0.74 | 18 | empty |
Interfaces
4 interfaces between chains.
- C–D · 676 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 325 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 134 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4OLS · The amidase-2 domain of LysGH15 · 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 D6QY02
- Elsewhere: RCSB PDB 4OLS · PDBe 4OLS · UniProt D6QY02
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