Research workbench
Crystal structure of a putative acetamidase (TM0119) from thermotoga maritima MSB8 at 2.50 a resolution
Analyse Crystal structure of a putative acetamidase (TM0119) from thermotoga maritima… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2F4L
- Type
- protein
- Length
- 1,100 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetamidase, putative
- UniProt
- Q9WXX3
- Ligands
- ZN, CL
- Pockets
- 14 · best druggability 0.58
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetamidase, putative | protein | 275 | 13% helix, 44% strand | Q9WXX3 |
| B | Acetamidase, putative | protein | 273 | 14% helix, 45% strand | Q9WXX3 |
| C | Acetamidase, putative | protein | 278 | 12% helix, 45% strand | Q9WXX3 |
| D | Acetamidase, putative | protein | 274 | 12% helix, 45% strand | Q9WXX3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.58 | 0.74 | 44 | empty |
| 2 | 292 | 0.55 | 0.76 | 33 | empty |
| 3 | 229 | 0.55 | 0.78 | 23 | empty |
| 4 | 167 | 0.48 | 0.77 | 26 | ZN |
| 5 | 167 | 0.47 | 0.76 | 23 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2419 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 2309 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 71 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 58 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 2F4L · Crystal structure of a putative acetamidase (tm0119) from thermotoga maritima msb8 at… · 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 Q9WXX3
- Elsewhere: RCSB PDB 2F4L · PDBe 2F4L · UniProt Q9WXX3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.